search

labsyspharm / scimap

Spatial Single-Cell Analysis Toolkit
https://scimap.xyz/
MIT License
74 stars 26 forks source link

'adata = sm.tl.spatial_distance' runs into ValueError: need at most x handles.... #44

Closed josenimo closed 1 year ago

josenimo commented 1 year ago

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 hsluv 5.0.3 pypi_0 pypi 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 json5 0.9.11 pypi_0 pypi jsonpointer 2.3 pypi_0 pypi jsonschema 4.17.3 pypi_0 pypi jupyter 1.0.0 pypi_0 pypi jupyter-client 8.0.2 pypi_0 pypi jupyter-console 6.4.4 pypi_0 pypi jupyter-core 5.2.0 pypi_0 pypi jupyter-events 0.5.0 pypi_0 pypi jupyter-server 2.2.1 pypi_0 pypi jupyter-server-fileid 0.6.0 pypi_0 pypi jupyter-server-terminals 0.4.4 pypi_0 pypi jupyter-server-ydoc 0.6.1 pypi_0 pypi jupyter-ydoc 0.2.2 pypi_0 pypi jupyterlab 3.6.1 pypi_0 pypi jupyterlab-pygments 0.2.2 pypi_0 pypi jupyterlab-server 2.19.0 pypi_0 pypi 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 mkdocs-material 7.3.6 pypi_0 pypi mkdocs-material-extensions 1.0.3 pypi_0 pypi more-itertools 8.14.0 pypi_0 pypi multidict 6.0.2 pypi_0 pypi napari 0.4.16 pypi_0 pypi napari-brightness-contrast 0.1.8 pypi_0 pypi napari-console 0.0.6 pypi_0 pypi napari-ome-zarr 0.4.0 pypi_0 pypi napari-plugin-engine 0.2.0 pypi_0 pypi napari-svg 0.1.6 pypi_0 pypi napari-tools-menu 0.1.19 pypi_0 pypi natsort 8.2.0 pypi_0 pypi nbclassic 0.5.1 pypi_0 pypi nbclient 0.7.0 pypi_0 pypi nbconvert 7.2.1 pypi_0 pypi nbformat 5.7.0 pypi_0 pypi nest-asyncio 1.5.6 pypi_0 pypi networkx 2.8.7 pypi_0 pypi notebook 6.4.12 pypi_0 pypi notebook-shim 0.2.2 pypi_0 pypi npe2 0.6.1 pypi_0 pypi numba 0.55.2 pypi_0 pypi 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 pkgutil-resolve-name 1.3.10 pypi_0 pypi platformdirs 2.6.2 pypi_0 pypi plotly 4.14.3 pypi_0 pypi pluggy 0.13.1 pypi_0 pypi prometheus-client 0.14.1 pypi_0 pypi prompt-toolkit 3.0.31 pypi_0 pypi psutil 5.9.2 pypi_0 pypi psygnal 0.4.2 pypi_0 pypi pure-eval 0.2.2 pypi_0 pypi py 1.11.0 pypi_0 pypi pycparser 2.21 pypi_0 pypi 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 pyqt5-sip 12.11.1 pypi_0 pypi pyqtgraph 0.13.1 pypi_0 pypi pyrsistent 0.18.1 pypi_0 pypi pytest 5.4.3 pypi_0 pypi pytest-xvfb 2.0.0 pypi_0 pypi python 3.8.13 hcf16a7b_0_cpython conda-forge python-dateutil 2.8.2 pypi_0 pypi python-json-logger 2.0.4 pypi_0 pypi pytomlpp 1.0.11 pypi_0 pypi pytz 2022.4 pypi_0 pypi pyvirtualdisplay 3.0 pypi_0 pypi pywavelets 1.4.1 pypi_0 pypi pywin32 304 pypi_0 pypi pywinpty 2.0.8 pypi_0 pypi pyyaml 6.0 pypi_0 pypi pyyaml-env-tag 0.1 pypi_0 pypi pyzmq 24.0.1 pypi_0 pypi qtconsole 5.3.2 pypi_0 pypi qtpy 2.2.1 pypi_0 pypi requests 2.28.1 pypi_0 pypi retrying 1.3.3 pypi_0 pypi rfc3339-validator 0.1.4 pypi_0 pypi rfc3986-validator 0.1.1 pypi_0 pypi rich 12.6.0 pypi_0 pypi s3fs 2022.8.2 pypi_0 pypi 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 seaborn 0.11.2 pypi_0 pypi send2trash 1.8.0 pypi_0 pypi session-info 1.0.0 pypi_0 pypi setuptools 65.4.1 pyhd8ed1ab_0 conda-forge shapely 1.8.4 pypi_0 pypi six 1.16.0 pypi_0 pypi sklearn 0.0 pypi_0 pypi smart-open 6.2.0 pypi_0 pypi sniffio 1.3.0 pypi_0 pypi snowballstemmer 2.2.0 pypi_0 pypi soupsieve 2.3.2.post1 pypi_0 pypi sphinx 5.2.3 pypi_0 pypi sphinxcontrib-applehelp 1.0.2 pypi_0 pypi sphinxcontrib-devhelp 1.0.2 pypi_0 pypi sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi sphinxcontrib-jsmath 1.0.1 pypi_0 pypi sphinxcontrib-qthelp 1.0.3 pypi_0 pypi sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi 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 tornado 6.2 pypi_0 pypi tqdm 4.64.1 pypi_0 pypi traitlets 5.9.0 pypi_0 pypi typer 0.6.1 pypi_0 pypi typing-extensions 4.3.0 pypi_0 pypi 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 urllib3 1.26.12 pypi_0 pypi vc 14.2 hac3ee0b_8 conda-forge vispy 0.10.0 pypi_0 pypi vs2015_runtime 14.29.30139 h890b9b1_8 conda-forge watchdog 2.1.9 pypi_0 pypi wcwidth 0.2.5 pypi_0 pypi webcolors 1.12 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi websocket-client 1.5.1 pypi_0 pypi wheel 0.37.1 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.3 pypi_0 pypi wrapt 1.14.1 pypi_0 pypi xlrd 1.2.0 pypi_0 pypi xz 5.2.6 h8d14728_0 conda-forge y-py 0.5.5 pypi_0 pypi yarl 1.8.1 pypi_0 pypi ypy-websocket 0.8.2 pypi_0 pypi zarr 2.10.3 pypi_0 pypi zipp 3.8.1 pypi_0 pypi ```

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 commented 1 year ago

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 commented 1 year ago

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