CosMx data `render_images` after cropping via `query.bounding_box`

[nilseling]

Hi @LucaMarconato

great work on spatialdata! I started playing around with this and noticed and error when cropping an image from the CosMx dataset:

import spatialdata as sd
import spatialdata_plot

data = sd.read_zarr("data.zarr")

cur_img = data.filter_by_coordinate_system("10")

cropped_img = cur_img.query.bounding_box(
    axes=["x", "y"],
    min_coordinate=[1000,1500],
    max_coordinate=[1500,2000],
    target_coordinate_system="10"
)

cropped_img.pl.render_images().pl.show()

returns

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
Cell In[119], line 1
----> 1 cropped_img.pl.render_images().pl.show(coordinate_systems="10")

File ~/opt/anaconda3/envs/spatialdata-env/lib/python3.9/site-packages/spatialdata_plot/pl/basic.py:645, in PlotAccessor.show(self, coordinate_systems, legend_fontsize, legend_fontweight, legend_loc, legend_fontoutline, na_in_legend, colorbar, wspace, hspace, ncols, frameon, figsize, dpi, fig, title, share_extent, pad_extent, ax, return_ax, save)
    643 if members["has_labels"].values[0]:
    644     for key in sdata.labels:
--> 645         sdata.labels[key] = _robust_transform(sdata.labels[key], cs)
    647 if members["has_points"].values[0]:
    648     for key in sdata.points:

File ~/opt/anaconda3/envs/spatialdata-env/lib/python3.9/site-packages/spatialdata_plot/pl/utils.py:1145, in _robust_transform(element, cs)
   1143 for _, t in enumerate(transformations):
   1144     if isinstance(t, sd.transformations.transformations.Translation):
-> 1145         element = _translate_image(image=element, translation=t)
   1147     elif isinstance(t, sd.transformations.transformations.Affine):
   1148         # edge case, waiting for Luca to decompose affine into components
   1149         # element = transform(element, t)
   (...)
   1156         # element = _robust_transform(element, cs)
   1157         # print(element.shape)
   1158         pass

File ~/opt/anaconda3/envs/spatialdata-env/lib/python3.9/site-packages/spatialdata_plot/pl/utils.py:1099, in _translate_image(image, translation)
...
    807 )
    809 y_axis_name = "y"
    810 if axis_names and "y" in axis_names:

IndexError: tuple index out of range

This is my environment:

abseil-cpp                20211102.0           he9d5cce_0  
aiobotocore               2.5.4                    pypi_0    pypi
aiofiles                  22.1.0           py39hecd8cb5_0  
aiohttp                   3.8.5                    pypi_0    pypi
aioitertools              0.11.0                   pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
aiosqlite                 0.18.0           py39hecd8cb5_0  
alabaster                 0.7.12             pyhd3eb1b0_0  
anndata                   0.9.2                    pypi_0    pypi
anyio                     3.5.0            py39hecd8cb5_0  
app-model                 0.2.0              pyhd8ed1ab_0    conda-forge
appdirs                   1.4.4              pyhd3eb1b0_0  
appnope                   0.1.2           py39hecd8cb5_1001  
argon2-cffi               21.3.0             pyhd3eb1b0_0  
argon2-cffi-bindings      21.2.0           py39hca72f7f_0  
arrow-cpp                 11.0.0               h89a8245_1  
asciitree                 0.3.3                      py_2  
asttokens                 2.0.5              pyhd3eb1b0_0  
async-timeout             4.0.3                    pypi_0    pypi
attrs                     22.1.0           py39hecd8cb5_0  
aws-c-common              0.6.8                h6c40b1e_1  
aws-c-event-stream        0.1.6                hcec6c5f_6  
aws-checksums             0.1.11               h6c40b1e_2  
aws-sdk-cpp               1.8.185              h1a8d504_1  
babel                     2.11.0           py39hecd8cb5_0  
backcall                  0.2.0              pyhd3eb1b0_0  
beautifulsoup4            4.12.2           py39hecd8cb5_0  
blas                      1.0                         mkl  
bleach                    4.1.0              pyhd3eb1b0_0  
blosc                     1.21.3               hcec6c5f_0  
bokeh                     3.2.1            py39h20db666_0  
boost-cpp                 1.73.0              hca72f7f_12  
botocore                  1.31.17                  pypi_0    pypi
bottleneck                1.3.5            py39h67323c0_0  
brotli                    1.0.9                hca72f7f_7  
brotli-bin                1.0.9                hca72f7f_7  
brotlipy                  0.7.0           py39h9ed2024_1003  
brunsli                   0.1                  h23ab428_0  
bzip2                     1.0.8                h1de35cc_0  
c-ares                    1.19.0               h6c40b1e_0  
ca-certificates           2023.05.30           hecd8cb5_0  
cachey                    0.2.1              pyh9f0ad1d_0    conda-forge
certifi                   2023.7.22        py39hecd8cb5_0  
cffi                      1.15.1           py39h6c40b1e_3  
cfitsio                   3.470                hbd21bf8_7  
charls                    2.2.0                h23ab428_0  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
click                     8.0.4            py39hecd8cb5_0  
click-plugins             1.1.1                    pypi_0    pypi
cligj                     0.7.2                    pypi_0    pypi
cloudpickle               2.2.1            py39hecd8cb5_0  
colorama                  0.4.6            py39hecd8cb5_0  
colorcet                  3.0.1                    pypi_0    pypi
comm                      0.1.2            py39hecd8cb5_0  
contourpy                 1.0.5            py39haf03e11_0  
cryptography              41.0.2           py39h3b477ad_0  
cycler                    0.11.0                   pypi_0    pypi
cytoolz                   0.12.0           py39hca72f7f_0  
dask                      2023.6.0         py39hecd8cb5_0  
dask-core                 2023.6.0         py39hecd8cb5_0  
dask-image                2023.8.1                 pypi_0    pypi
datashader                0.15.2                   pypi_0    pypi
datashape                 0.5.2                    pypi_0    pypi
debugpy                   1.6.7            py39hcec6c5f_0  
decorator                 5.1.1              pyhd3eb1b0_0  
defusedxml                0.7.1              pyhd3eb1b0_0  
distributed               2023.6.0         py39hecd8cb5_0  
docstring_parser          0.15               pyhd8ed1ab_0    conda-forge
docutils                  0.17.1           py39hecd8cb5_1  
entrypoints               0.4              py39hecd8cb5_0  
executing                 0.8.3              pyhd3eb1b0_0  
expat                     2.4.9                he9d5cce_0  
fasteners                 0.16.3             pyhd3eb1b0_0  
fiona                     1.9.4.post1              pypi_0    pypi
fontconfig                2.14.1               hb0a0c50_2  
fonttools                 4.42.1                   pypi_0    pypi
freetype                  2.12.1               hd8bbffd_0  
freetype-py               2.2.0              pyhd3eb1b0_0  
frozenlist                1.4.0                    pypi_0    pypi
fsspec                    2023.4.0         py39hecd8cb5_0  
geopandas                 0.13.2                   pypi_0    pypi
gflags                    2.2.2                h0a44026_0  
giflib                    5.2.1                h6c40b1e_3  
glog                      0.5.0                h23ab428_0  
greenlet                  2.0.2                    pypi_0    pypi
grpc-cpp                  1.48.2               h4ed1731_1  
h5py                      3.9.0                    pypi_0    pypi
heapdict                  1.0.1              pyhd3eb1b0_0  
hsluv                     5.0.3            py39hecd8cb5_0  
icu                       58.2                 h0a44026_3  
idna                      3.4              py39hecd8cb5_0  
imagecodecs               2021.8.26        py39h8a96914_2  
imageio                   2.31.1           py39hecd8cb5_0  
imagesize                 1.4.1            py39hecd8cb5_0  
importlib-metadata        6.0.0            py39hecd8cb5_0  
importlib-resources       6.0.1                    pypi_0    pypi
importlib_metadata        6.0.0                hd3eb1b0_0  
in-n-out                  0.1.8              pyhd8ed1ab_0    conda-forge
intel-openmp              2023.1.0         ha357a0b_43547  
ipykernel                 6.25.0           py39h20db666_0  
ipython                   8.12.2           py39hecd8cb5_0  
ipython_genutils          0.2.0              pyhd3eb1b0_1  
jedi                      0.18.1           py39hecd8cb5_1  
jinja2                    3.1.2            py39hecd8cb5_0  
jmespath                  1.0.1                    pypi_0    pypi
joblib                    1.3.2                    pypi_0    pypi
jpeg                      9e                   h6c40b1e_1  
json5                     0.9.6              pyhd3eb1b0_0  
jsonschema                4.17.3           py39hecd8cb5_0  
jupyter-cache             0.6.1                    pypi_0    pypi
jupyter_client            7.4.9            py39hecd8cb5_0  
jupyter_core              5.3.0            py39hecd8cb5_0  
jupyter_events            0.6.3            py39hecd8cb5_0  
jupyter_server            1.23.4           py39hecd8cb5_0  
jupyter_server_fileid     0.9.0            py39hecd8cb5_0  
jupyter_server_ydoc       0.8.0            py39hecd8cb5_1  
jupyter_ydoc              0.2.4            py39hecd8cb5_0  
jupyterlab                3.6.3            py39hecd8cb5_0  
jupyterlab_pygments       0.1.2                      py_0  
jupyterlab_server         2.22.0           py39hecd8cb5_0  
jxrlib                    1.1                  haf1e3a3_2  
kiwisolver                1.4.4            py39hcec6c5f_0  
krb5                      1.20.1               h428f121_1  
lazy_loader               0.2              py39hecd8cb5_0  
lcms2                     2.12                 hf1fd2bf_0  
lerc                      3.0                  he9d5cce_0  
libaec                    1.0.4                hb1e8313_1  
libboost                  1.73.0              h3fa6bed_12  
libbrotlicommon           1.0.9                hca72f7f_7  
libbrotlidec              1.0.9                hca72f7f_7  
libbrotlienc              1.0.9                hca72f7f_7  
libcurl                   8.1.1                hf20ceda_2  
libcxx                    14.0.6               h9765a3e_0  
libdeflate                1.17                 hb664fd8_0  
libedit                   3.1.20221030         h6c40b1e_0  
libev                     4.33                 h9ed2024_1  
libevent                  2.1.12               h04015c4_1  
libffi                    3.4.4                hecd8cb5_0  
libgfortran               5.0.0           11_3_0_hecd8cb5_28  
libgfortran5              11.3.0              h9dfd629_28  
libiconv                  1.16                 hca72f7f_2  
libnghttp2                1.52.0               h9beae6a_1  
libpng                    1.6.39               h6c40b1e_0  
libprotobuf               3.20.3               hfff2838_0  
libsodium                 1.0.18               h1de35cc_0  
libssh2                   1.10.0               h04015c4_2  
libthrift                 0.15.0               h70b4b81_2  
libtiff                   4.5.0                hcec6c5f_2  
libwebp                   1.2.4                hf6ce154_1  
libwebp-base              1.2.4                h6c40b1e_1  
libxml2                   2.10.4               h930c0e2_0  
libxslt                   1.1.37               h6d1eb0e_0  
libzopfli                 1.0.3                hb1e8313_0  
llvm-openmp               14.0.6               h0dcd299_0  
llvmlite                  0.40.1                   pypi_0    pypi
locket                    1.0.0            py39hecd8cb5_0  
loguru                    0.7.0                    pypi_0    pypi
lxml                      4.9.2            py39h6c40b1e_0  
lz4                       4.3.2            py39h6c40b1e_0  
lz4-c                     1.9.4                hcec6c5f_0  
magicgui                  0.7.2              pyhd8ed1ab_0    conda-forge
markdown-it-py            2.2.0            py39hecd8cb5_1  
markupsafe                2.1.1            py39hca72f7f_0  
matplotlib                3.7.2                    pypi_0    pypi
matplotlib-inline         0.1.6            py39hecd8cb5_0  
matplotlib-scalebar       0.8.1                    pypi_0    pypi
mdit-py-plugins           0.3.5                    pypi_0    pypi
mdurl                     0.1.0            py39hecd8cb5_0  
mistune                   0.8.4           py39h9ed2024_1000  
mkl                       2023.1.0         h8e150cf_43559  
mkl-service               2.4.0            py39h6c40b1e_1  
mkl_fft                   1.3.6            py39h07fba90_1  
mkl_random                1.2.2            py39h07fba90_1  
msgpack-python            1.0.3            py39haf03e11_0  
multidict                 6.0.4                    pypi_0    pypi
multipledispatch          1.0.0                    pypi_0    pypi
multiscale-spatial-image  0.11.2                   pypi_0    pypi
mypy_extensions           0.4.3            py39hecd8cb5_1  
myst-nb                   0.17.2                   pypi_0    pypi
myst-parser               0.18.1                   pypi_0    pypi
napari                    0.4.18             pyhd8ed1ab_2    conda-forge
napari-console            0.0.8              pyhd8ed1ab_0    conda-forge
napari-matplotlib         1.0.2                    pypi_0    pypi
napari-plugin-engine      0.2.0              pyhd8ed1ab_2    conda-forge
napari-spatialdata        0.2.6                    pypi_0    pypi
napari-svg                0.1.10             pyhd8ed1ab_0    conda-forge
natsort                   8.4.0                    pypi_0    pypi
nbclassic                 0.5.5            py39hecd8cb5_0  
nbclient                  0.5.13           py39hecd8cb5_0  
nbconvert                 6.5.4            py39hecd8cb5_0  
nbformat                  5.7.0            py39hecd8cb5_0  
ncurses                   6.4                  hcec6c5f_0  
nest-asyncio              1.5.6            py39hecd8cb5_0  
networkx                  3.1              py39hecd8cb5_0  
notebook                  6.5.4            py39hecd8cb5_1  
notebook-shim             0.2.2            py39hecd8cb5_0  
npe2                      0.7.2              pyhd8ed1ab_0    conda-forge
numba                     0.57.1                   pypi_0    pypi
numcodecs                 0.11.0           py39hcec6c5f_0  
numexpr                   2.8.4            py39h47b59a4_1  
numpy                     1.23.4                   pypi_0    pypi
numpydoc                  1.5.0            py39hecd8cb5_0  
ome-zarr                  0.8.0                    pypi_0    pypi
openjpeg                  2.4.0                h66ea3da_0  
openssl                   3.0.10               hca72f7f_1  
orc                       1.7.4                h995b336_1  
packaging                 23.0             py39hecd8cb5_0  
pandas                    2.0.3            py39h3ea8b11_0  
pandocfilters             1.5.0              pyhd3eb1b0_0  
param                     1.13.0                   pypi_0    pypi
parso                     0.8.3              pyhd3eb1b0_0  
partd                     1.2.0              pyhd3eb1b0_1  
patsy                     0.5.3                    pypi_0    pypi
pexpect                   4.8.0              pyhd3eb1b0_3  
pickleshare               0.7.5           pyhd3eb1b0_1003  
pillow                    9.4.0            py39hcec6c5f_0  
pims                      0.6.1                    pypi_0    pypi
pint                      0.22               pyhd8ed1ab_1    conda-forge
pip                       23.2.1           py39hecd8cb5_0  
platformdirs              3.10.0           py39hecd8cb5_0  
pooch                     1.4.0              pyhd3eb1b0_0  
prometheus_client         0.14.1           py39hecd8cb5_0  
prompt-toolkit            3.0.36           py39hecd8cb5_0  
psutil                    5.9.0            py39hca72f7f_0  
psygnal                   0.9.2              pyhd8ed1ab_0    conda-forge
ptyprocess                0.7.0              pyhd3eb1b0_2  
pure_eval                 0.2.2              pyhd3eb1b0_0  
pyarrow                   11.0.0           py39h7122ad0_0  
pycparser                 2.21               pyhd3eb1b0_0  
pyct                      0.5.0                    pypi_0    pypi
pydantic                  1.10.8           py39h6c40b1e_0  
pygeos                    0.14                     pypi_0    pypi
pygments                  2.15.1           py39hecd8cb5_1  
pynndescent               0.5.10                   pypi_0    pypi
pyopengl                  3.1.1a1          py39hecd8cb5_0  
pyopenssl                 23.2.0           py39hecd8cb5_0  
pyparsing                 3.0.9                    pypi_0    pypi
pyproj                    3.6.0                    pypi_0    pypi
pyproject_hooks           1.0.0            py39hecd8cb5_0  
pyqt5                     5.15.9                   pypi_0    pypi
pyqt5-qt5                 5.15.2                   pypi_0    pypi
pyqt5-sip                 12.12.2                  pypi_0    pypi
pyrsistent                0.18.0           py39hca72f7f_0  
pysocks                   1.7.1            py39hecd8cb5_0  
python                    3.9.17               h5ee71fb_0  
python-build              0.10.0           py39hecd8cb5_0  
python-dateutil           2.8.2              pyhd3eb1b0_0  
python-fastjsonschema     2.16.2           py39hecd8cb5_0  
python-json-logger        2.0.7            py39hecd8cb5_0  
python-lmdb               1.4.1            py39hcec6c5f_0  
python-tzdata             2023.3             pyhd3eb1b0_0  
pytz                      2022.7           py39hecd8cb5_0  
pywavelets                1.4.1            py39h6c40b1e_0  
pyyaml                    6.0              py39h6c40b1e_1  
pyzmq                     23.2.0           py39he9d5cce_0  
qtconsole-base            5.4.3              pyha770c72_0    conda-forge
qtpy                      2.2.0            py39hecd8cb5_0  
re2                       2022.04.01           he9d5cce_0  
readline                  8.2                  hca72f7f_0  
requests                  2.31.0           py39hecd8cb5_0  
rfc3339-validator         0.1.4            py39hecd8cb5_0  
rfc3986-validator         0.1.1            py39hecd8cb5_0  
rich                      13.3.5           py39hecd8cb5_0  
s3fs                      2023.4.0                 pypi_0    pypi
scanpy                    1.9.3                    pypi_0    pypi
scikit-image              0.19.3           py39hcec6c5f_1  
scikit-learn              1.3.0                    pypi_0    pypi
scipy                     1.11.1           py39hdb2ea58_0  
seaborn                   0.12.2                   pypi_0    pypi
send2trash                1.8.0              pyhd3eb1b0_1  
session-info              1.0.0                    pypi_0    pypi
setuptools                68.0.0           py39hecd8cb5_0  
shapely                   2.0.1                    pypi_0    pypi
shellingham               1.5.0            py39hecd8cb5_0  
six                       1.16.0             pyhd3eb1b0_1  
slicerator                1.1.0                    pypi_0    pypi
snappy                    1.1.9                he9d5cce_0  
sniffio                   1.2.0            py39hecd8cb5_1  
snowballstemmer           2.2.0              pyhd3eb1b0_0  
sortedcontainers          2.4.0              pyhd3eb1b0_0  
soupsieve                 2.4              py39hecd8cb5_0  
spatial-image             0.3.0                    pypi_0    pypi
spatialdata               0.0.12                   pypi_0    pypi
spatialdata-plot          0.0.4                    pypi_0    pypi
sphinx                    4.4.0              pyhd3eb1b0_0  
sphinx-copybutton         0.5.2                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.2              pyhd3eb1b0_0  
sphinxcontrib-devhelp     1.0.2              pyhd3eb1b0_0  
sphinxcontrib-htmlhelp    2.0.0              pyhd3eb1b0_0  
sphinxcontrib-jsmath      1.0.1              pyhd3eb1b0_0  
sphinxcontrib-qthelp      1.0.3              pyhd3eb1b0_0  
sphinxcontrib-serializinghtml 1.1.5              pyhd3eb1b0_0  
sqlalchemy                2.0.20                   pypi_0    pypi
sqlite                    3.41.2               h6c40b1e_0  
stack_data                0.2.0              pyhd3eb1b0_0  
statsmodels               0.14.0                   pypi_0    pypi
stdlib-list               0.9.0                    pypi_0    pypi
superqt                   0.5.0              pyh9208f05_0    conda-forge
tabulate                  0.9.0                    pypi_0    pypi
tbb                       2021.8.0             ha357a0b_0  
tblib                     1.7.0              pyhd3eb1b0_0  
terminado                 0.17.1           py39hecd8cb5_0  
threadpoolctl             3.2.0                    pypi_0    pypi
tifffile                  2021.7.2           pyhd3eb1b0_2  
tinycss2                  1.2.1            py39hecd8cb5_0  
tk                        8.6.12               h5d9f67b_0  
tomli                     2.0.1            py39hecd8cb5_0  
tomli-w                   1.0.0              pyhd3eb1b0_0  
toolz                     0.12.0           py39hecd8cb5_0  
tornado                   6.3.2            py39h6c40b1e_0  
tqdm                      4.65.0           py39h01d92e1_0  
traitlets                 5.7.1            py39hecd8cb5_0  
typer                     0.9.0            py39hecd8cb5_0  
typing-extensions         4.5.0                    pypi_0    pypi
tzdata                    2023c                h04d1e81_0  
umap-learn                0.5.3                    pypi_0    pypi
urllib3                   1.26.16          py39hecd8cb5_0  
utf8proc                  2.6.1                h9ed2024_0  
vispy                     0.12.1           py39h3017f15_0  
wcwidth                   0.2.5              pyhd3eb1b0_0  
webencodings              0.5.1            py39hecd8cb5_1  
websocket-client          0.58.0           py39hecd8cb5_4  
wheel                     0.38.4           py39hecd8cb5_0  
wrapt                     1.14.1           py39hca72f7f_0  
xarray                    2022.12.0                pypi_0    pypi
xarray-dataclasses        1.6.0                    pypi_0    pypi
xarray-datatree           0.0.12                   pypi_0    pypi
xarray-schema             0.0.3                    pypi_0    pypi
xarray-spatial            0.3.7                    pypi_0    pypi
xyzservices               2022.9.0         py39hecd8cb5_1  
xz                        5.4.2                h6c40b1e_0  
y-py                      0.5.9            py39h7242b5c_0  
yaml                      0.2.5                haf1e3a3_0  
yarl                      1.9.2                    pypi_0    pypi
ypy-websocket             0.8.2            py39hecd8cb5_0  
zarr                      2.13.3           py39hecd8cb5_0  
zeromq                    4.3.4                h23ab428_0  
zfp                       0.5.5                he9d5cce_6  
zict                      2.2.0            py39hecd8cb5_0  
zipp                      3.11.0           py39hecd8cb5_0  
zlib                      1.2.13               h4dc903c_0  
zstd                      1.5.5                hc035e20_0  

[LucaMarconato]

Hi Nils, thanks for the kind feedback and for reporting this bug.

I think this behavior is due to this bug that I have reported here: https://github.com/scverse/spatialdata-plot/issues/146. In such a case, we are working on the solution and it should be fixed soon 😊

[LucaMarconato]

I just checked, the bug is not present anymore, probably thanks to the fix mentioned above.