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spyder-ide / spyder

Official repository for Spyder - The Scientific Python Development Environment
https://www.spyder-ide.org
MIT License
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PyimageJ open() #22316

Open Preston-Hunter opened 1 month ago

Preston-Hunter commented 1 month ago

Description

What steps will reproduce the problem?

import os import imagej ij = imagej.init(mode='interactive') web_image = ij.io().open('https://wsr.imagej.net/images/Cell_Colony.jpg')

works from anaconda command powershell. does not work in spyder. successive runs fail as well until i replace/redeclare the web_image variable

Traceback

Exception in comms call get_namespace_view:
  File "C:\ProgramData\anaconda3\Lib\site-packages\spyder_kernels\comms\commbase.py", line 317, in _comm_message
    buffer = cloudpickle.loads(msg['buffers'][0],
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jpype'
Exception in comms call get_var_properties:
  File "C:\ProgramData\anaconda3\Lib\site-packages\spyder_kernels\comms\commbase.py", line 317, in _comm_message
    buffer = cloudpickle.loads(msg['buffers'][0],
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jpype'
Exception in comms call get_namespace_view:
  File "C:\ProgramData\anaconda3\Lib\site-packages\spyder_kernels\comms\commbase.py", line 317, in _comm_message
    buffer = cloudpickle.loads(msg['buffers'][0],
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jpype'
Exception in comms call get_var_properties:
  File "C:\ProgramData\anaconda3\Lib\site-packages\spyder_kernels\comms\commbase.py", line 317, in _comm_message
    buffer = cloudpickle.loads(msg['buffers'][0],
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'jpype'

Versions

Dependencies

# Mandatory:
atomicwrites >=1.2.0                             :  1.4.0 (OK)
chardet >=2.0.0                                  :  4.0.0 (OK)
cloudpickle >=0.5.0                              :  2.2.1 (OK)
cookiecutter >=1.6.0                             :  2.5.0 (OK)
diff_match_patch >=20181111                      :  20200713 (OK)
intervaltree >=3.0.2                             :  3.1.0 (OK)
IPython >=7.31.1,<9.0.0,!=8.8.0,!=8.9.0,!=8.10.0 :  8.20.0 (OK)
jedi >=0.17.2,<0.19.0                            :  0.18.1 (OK)
jellyfish >=0.7                                  :  1.0.1 (OK)
jsonschema >=3.2.0                               :  4.19.2 (OK)
keyring >=17.0.0                                 :  23.13.1 (OK)
nbconvert >=4.0                                  :  7.10.0 (OK)
numpydoc >=0.6.0                                 :  1.5.0 (OK)
paramiko >=2.4.0                                 :  2.8.1 (OK)
parso >=0.7.0,<0.9.0                             :  0.8.3 (OK)
pexpect >=4.4.0                                  :  4.8.0 (OK)
pickleshare >=0.4                                :  0.7.5 (OK)
psutil >=5.3                                     :  5.9.0 (OK)
pygments >=2.0                                   :  2.15.1 (OK)
pylint >=2.5.0,<3.0                              :  2.16.2 (OK)
pylint_venv >=2.1.1                              :  2.3.0 (OK)
pyls_spyder >=0.4.0                              :  0.4.0 (OK)
pylsp >=1.7.2,<1.8.0                             :  1.7.2 (OK)
pylsp_black >=1.2.0                              :  1.2.1 (OK)
qdarkstyle >=3.0.2,<3.2.0                        :  3.0.2 (OK)
qstylizer >=0.2.2                                :  0.2.2 (OK)
qtawesome >=1.2.1                                :  1.2.2 (OK)
qtconsole >=5.4.2,<5.5.0                         :  5.4.2 (OK)
qtpy >=2.1.0                                     :  2.4.1 (OK)
rtree >=0.9.7                                    :  1.0.1 (OK)
setuptools >=49.6.0                              :  68.2.2 (OK)
sphinx >=0.6.6                                   :  5.0.2 (OK)
spyder_kernels >=2.4.3,<2.5.0                    :  2.4.4 (OK)
textdistance >=4.2.0                             :  4.2.1 (OK)
three_merge >=0.1.1                              :  0.1.1 (OK)
watchdog >=0.10.3                                :  2.1.6 (OK)
zmq >=22.1.0                                     :  25.1.2 (OK)

# Optional:
cython >=0.21                                    :  None (NOK)
matplotlib >=3.0.0                               :  3.8.0 (OK)
numpy >=1.7                                      :  1.26.4 (OK)
pandas >=1.1.1                                   :  2.1.4 (OK)
scipy >=0.17.0                                   :  1.11.4 (OK)
sympy >=0.7.3                                    :  1.12 (OK)
dalthviz commented 1 month ago

Hi @Preston-Hunter thank you for issue report! As a workaround, I think you should be able to check from the Variable Explorer options menu the Exclude unsupported data types to prevent the error messages. Also, seems like this is related to #20635 so a look over the suggestions there could be worthy too.

Let us know if the info above helps!