'adata = sm.tl.spatial_distance' runs into ValueError: need at most x handles....

[josenimo]

Dear Scimap developer,

I am looking forward to analyzing my images with your package, so far every step of the way has worked but now the spatial distance is running into an ValueError

the command:

adata = sm.tl.spatial_distance (adata, 
                               x_coordinate='X_centroid', y_coordinate='Y_centroid', 
                               z_coordinate=None, 
                               phenotype='phenotype', 
                               subset=None, 
                               imageid='imageid', 
                               label='spatial_distance')

the stack trace:

Exception in thread ExecutorManagerThread:
Traceback (most recent call last):
  File "C:\Users\Administrator\Jose_BI\Anaconda\envs\scimap\lib\threading.py", line 932, in _bootstrap_inner
    self.run()
  File "C:\Users\Administrator\Jose_BI\Anaconda\envs\scimap\lib\site-packages\joblib\externals\loky\process_executor.py", line 557, in run
    result_item, is_broken, bpe = self.wait_result_broken_or_wakeup()
  File "C:\Users\Administrator\Jose_BI\Anaconda\envs\scimap\lib\site-packages\joblib\externals\loky\process_executor.py", line 611, in wait_result_broken_or_wakeup
    ready = wait(readers + worker_sentinels)
  File "C:\Users\Administrator\Jose_BI\Anaconda\envs\scimap\lib\multiprocessing\connection.py", line 879, in wait
    ready_handles = _exhaustive_wait(waithandle_to_obj.keys(), timeout)
  File "C:\Users\Administrator\Jose_BI\Anaconda\envs\scimap\lib\multiprocessing\connection.py", line 811, in _exhaustive_wait
    res = _winapi.WaitForMultipleObjects(L, False, timeout)
ValueError: need at most 63 handles, got a sequence of length 129

conda list

# packages in environment at C:\Users\Administrator\Jose_BI\Anaconda\envs\scimap:
#
# Name                    Version                   Build  Channel
aiobotocore               2.4.0                    pypi_0    pypi
aiofiles                  22.1.0                   pypi_0    pypi
aiohttp                   3.8.3                    pypi_0    pypi
aioitertools              0.11.0                   pypi_0    pypi
aiosignal                 1.2.0                    pypi_0    pypi
aiosqlite                 0.18.0                   pypi_0    pypi
alabaster                 0.7.12                   pypi_0    pypi
anndata                   0.7.8                    pypi_0    pypi
anyio                     3.6.2                    pypi_0    pypi
appdirs                   1.4.4                    pypi_0    pypi
argon2-cffi               21.3.0                   pypi_0    pypi
argon2-cffi-bindings      21.2.0                   pypi_0    pypi
arrow                     1.2.3                    pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
asttokens                 2.0.8                    pypi_0    pypi
async-timeout             4.0.2                    pypi_0    pypi
atomicwrites              1.4.1                    pypi_0    pypi
attrs                     22.1.0                   pypi_0    pypi
babel                     2.10.3                   pypi_0    pypi
backcall                  0.2.0                    pypi_0    pypi
beautifulsoup4            4.11.1                   pypi_0    pypi
bleach                    5.0.1                    pypi_0    pypi
botocore                  1.27.59                  pypi_0    pypi
build                     0.8.0                    pypi_0    pypi
bzip2                     1.0.8                h8ffe710_4    conda-forge
ca-certificates           2022.9.24            h5b45459_0    conda-forge
cachey                    0.2.1                    pypi_0    pypi
certifi                   2022.9.24                pypi_0    pypi
cffi                      1.15.1                   pypi_0    pypi
charset-normalizer        2.1.1                    pypi_0    pypi
click                     8.1.3                    pypi_0    pypi
colorama                  0.4.5                    pypi_0    pypi
commonmark                0.9.1                    pypi_0    pypi
contourpy                 1.0.5                    pypi_0    pypi
cycler                    0.11.0                   pypi_0    pypi
cython                    0.29.28                  pypi_0    pypi
dask                      2.30.0                   pypi_0    pypi
debugpy                   1.6.3                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
defusedxml                0.7.1                    pypi_0    pypi
docstring-parser          0.15                     pypi_0    pypi
docutils                  0.19                     pypi_0    pypi
entrypoints               0.4                      pypi_0    pypi
executing                 1.1.0                    pypi_0    pypi
fasteners                 0.18                     pypi_0    pypi
fastjsonschema            2.16.2                   pypi_0    pypi
fonttools                 4.37.4                   pypi_0    pypi
fqdn                      1.5.1                    pypi_0    pypi
freetype-py               2.3.0                    pypi_0    pypi
frozenlist                1.3.1                    pypi_0    pypi
fsspec                    2022.8.2                 pypi_0    pypi
gensim                    4.2.0                    pypi_0    pypi
ghp-import                2.1.0                    pypi_0    pypi
h5py                      3.7.0                    pypi_0    pypi
heapdict                  1.0.1                    pypi_0    pypi
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idna                      3.4                      pypi_0    pypi
igraph                    0.10.1                   pypi_0    pypi
imageio                   2.22.1                   pypi_0    pypi
imageio-ffmpeg            0.4.8                    pypi_0    pypi
imagesize                 1.4.1                    pypi_0    pypi
importlib-metadata        5.0.0                    pypi_0    pypi
importlib-resources       5.9.0                    pypi_0    pypi
ipykernel                 6.16.0                   pypi_0    pypi
ipython                   8.5.0                    pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
ipywidgets                8.0.2                    pypi_0    pypi
isoduration               20.11.0                  pypi_0    pypi
jedi                      0.18.1                   pypi_0    pypi
jinja2                    3.1.2                    pypi_0    pypi
jmespath                  1.0.1                    pypi_0    pypi
joblib                    1.2.0                    pypi_0    pypi
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jsonpointer               2.3                      pypi_0    pypi
jsonschema                4.17.3                   pypi_0    pypi
jupyter                   1.0.0                    pypi_0    pypi
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jupyterlab-widgets        3.0.3                    pypi_0    pypi
kiwisolver                1.4.4                    pypi_0    pypi
leidenalg                 0.9.0                    pypi_0    pypi
libffi                    3.4.2                h8ffe710_5    conda-forge
libsqlite                 3.39.4               hcfcfb64_0    conda-forge
libzlib                   1.2.12               hcfcfb64_4    conda-forge
llvmlite                  0.38.1                   pypi_0    pypi
magicgui                  0.5.1                    pypi_0    pypi
markdown                  3.3.7                    pypi_0    pypi
markupsafe                2.1.1                    pypi_0    pypi
matplotlib                3.6.0                    pypi_0    pypi
matplotlib-inline         0.1.6                    pypi_0    pypi
mergedeep                 1.3.4                    pypi_0    pypi
mistune                   2.0.4                    pypi_0    pypi
mkdocs                    1.4.0                    pypi_0    pypi
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mkdocs-material-extensions 1.0.3                    pypi_0    pypi
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numcodecs                 0.10.2                   pypi_0    pypi
numpy                     1.22.4                   pypi_0    pypi
numpydoc                  1.4.0                    pypi_0    pypi
ome-zarr                  0.6.0                    pypi_0    pypi
openssl                   3.0.5                hcfcfb64_2    conda-forge
packaging                 21.3                     pypi_0    pypi
pandas                    1.5.0                    pypi_0    pypi
pandocfilters             1.5.0                    pypi_0    pypi
parso                     0.8.3                    pypi_0    pypi
patsy                     0.5.2                    pypi_0    pypi
pep517                    0.13.0                   pypi_0    pypi
phenograph                1.5.7                    pypi_0    pypi
pickleshare               0.7.5                    pypi_0    pypi
pillow                    9.2.0                    pypi_0    pypi
pint                      0.19.2                   pypi_0    pypi
pip                       22.2.2             pyhd8ed1ab_0    conda-forge
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plotly                    4.14.3                   pypi_0    pypi
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prompt-toolkit            3.0.31                   pypi_0    pypi
psutil                    5.9.2                    pypi_0    pypi
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pure-eval                 0.2.2                    pypi_0    pypi
py                        1.11.0                   pypi_0    pypi
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pydantic                  1.10.2                   pypi_0    pypi
pygments                  2.13.0                   pypi_0    pypi
pymdown-extensions        9.6                      pypi_0    pypi
pynndescent               0.5.7                    pypi_0    pypi
pyopengl                  3.1.6                    pypi_0    pypi
pyparsing                 3.0.9                    pypi_0    pypi
pyqt5                     5.15.9                   pypi_0    pypi
pyqt5-qt5                 5.15.2                   pypi_0    pypi
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pyqtgraph                 0.13.1                   pypi_0    pypi
pyrsistent                0.18.1                   pypi_0    pypi
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rich                      12.6.0                   pypi_0    pypi
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scanpy                    1.9.1                    pypi_0    pypi
scikit-image              0.19.3                   pypi_0    pypi
scikit-learn              1.1.2                    pypi_0    pypi
scimap                    0.22.9                   pypi_0    pypi
scipy                     1.9.1                    pypi_0    pypi
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session-info              1.0.0                    pypi_0    pypi
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six                       1.16.0                   pypi_0    pypi
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sqlite                    3.39.4               hcfcfb64_0    conda-forge
stack-data                0.5.1                    pypi_0    pypi
statsmodels               0.13.2                   pypi_0    pypi
stdlib-list               0.8.0                    pypi_0    pypi
superqt                   0.3.5                    pypi_0    pypi
terminado                 0.16.0                   pypi_0    pypi
texttable                 1.6.4                    pypi_0    pypi
threadpoolctl             3.1.0                    pypi_0    pypi
tifffile                  2020.12.8                pypi_0    pypi
tinycss2                  1.1.1                    pypi_0    pypi
tk                        8.6.12               h8ffe710_0    conda-forge
tomli                     2.0.1                    pypi_0    pypi
toolz                     0.12.0                   pypi_0    pypi
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ucrt                      10.0.20348.0         h57928b3_0    conda-forge
umap-learn                0.5.3                    pypi_0    pypi
uri-template              1.2.0                    pypi_0    pypi
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vc                        14.2                 hac3ee0b_8    conda-forge
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https://filetransfer.mdc-berlin.de/scimap_spatial_bug/
I am uploading my raw data, the adata object, the phenotyping table, and the gates. as well as the entire jupyter notebook. Thank you for your help!

Edit:
I was able to run it in my laptop, but not my workstation.. something about windows is messing it up.
I will update if I figure it out

[ajitjohnson]

Dear @josenimo I think it is the parallelization function that is giving you trouble. I am not able to download your data btw. Requires a username and password.

[josenimo]

Dear @ajitjohnson, thank you, do you have any idea where I could look for help about this windows issue? Since I was able to run it in my laptop, I think this problem is just for my workstation setup.

Thank you for scimap, it is a great tool!

Here are the files:
https://filetransfer.mdc-berlin.de/?u=HqR4M6kQ&p=PnKfYP7Y
Username: HqR4M6kQ
Password: PnKfYP7Y