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InsightSoftwareConsortium / ITKElastix

An ITK Python interface to elastix, a toolbox for rigid and nonrigid registration of images
Apache License 2.0
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Latest ITKElastix crashes #265

Closed dzenanz closed 7 months ago

dzenanz commented 1 year ago

Similar to #258, it crashes silently on my computer. This is enough to trigger it:

print("Pre-loading ITK DLLs")
_ = itk.ElastixRegistrationMethod

I tried these versions:

Only the latest version crashes for me. This is Python 3.9.13 on Windows 11.

dzenanz commented 1 year ago

This is the output produced:

Connected to pydev debugger (build 232.10227.11)
Pre-loading ITK DLLs

Process finished with exit code -1073741819 (0xC0000005)
dzenanz commented 12 months ago

Starting from a fresh virtual environment did not help. Here is a log:

M:\Work>python -m venv .venv

M:\Work>.venv\Scripts\activate

(.venv) M:\Work>cd mri-segmentation

(.venv) M:\Work\mri-segmentation>pip install -r requirements.txt
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Collecting argon2-cffi-bindings
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Collecting types-python-dateutil>=2.8.10
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Installing collected packages: webencodings, wcwidth, types-python-dateutil, pywin32, pure-eval, json5, ipython-genutils, fastjsonschema, zstandard, zipp, websocket-client, webcolors, urllib3, uri-template, typing-extensions, traitlets, tornado, tomli, tinycss2, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, pyzmq, pyyaml, pywinpty, python-json-logger, pyparsing, pygments, pycparser, psutil, prompt-toolkit, prometheus-client, platformdirs, pillow, parso, param, pandocfilters, packaging, overrides, numpy, nest-asyncio, mistune, MarkupSafe, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, idna, fqdn, executing, exceptiongroup, defusedxml, decorator, debugpy, cycler, colorama, charset-normalizer, certifi, babel, attrs, traittypes, tqdm, terminado, rfc3339-validator, requests, referencing, python-dateutil, pyct, matplotlib-inline, jupyter-core, jinja2, jedi, itk-core, importlib-metadata, comm, cffi, bleach, beautifulsoup4, async-lru, asttokens, anyio, stack-data, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, itk-numerics, itk-meshtopolydata, itk-io, colorcet, arrow, argon2-cffi-bindings, jsonschema, itk-iomeshstl, itk-filtering, isoduration, ipython, argon2-cffi, nbformat, itk-segmentation, itk-registration, ipykernel, nbclient, jupyter-events, itk, nbconvert, itk-elastix, itk-cuberille, notebook, jupyter-server, widgetsnbextension, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, ipywidgets, ipympl, ipydatawidgets, itkwidgets
Successfully installed MarkupSafe-2.1.3 anyio-4.1.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.1.0 babel-2.13.1 beautifulsoup4-4.12.2 bleach-6.1.0 certifi-2023.11.17 cffi-1.16.0 charset-normalizer-3.3.2 colorama-0.4.6 colorcet-3.0.1 comm-0.2.0 cycler-0.12.1 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 exceptiongroup-1.2.0 executing-2.0.1 fastjsonschema-2.19.0 fqdn-1.5.1 idna-3.6 importlib-metadata-7.0.0 ipydatawidgets-4.3.2 ipykernel-6.27.1 ipympl-0.8.8 ipython-8.18.1 ipython-genutils-0.2.0 ipywidgets-7.8.1 isoduration-20.11.0 itk-5.4rc2 itk-core-5.4rc2 itk-cuberille-2.6.0 itk-elastix-0.19.1 itk-filtering-5.4rc2 itk-io-5.4rc2 itk-iomeshstl-2.3.0 itk-meshtopolydata-0.10.0 itk-numerics-5.4rc2 itk-registration-5.4rc2 itk-segmentation-5.4rc2 itkwidgets-0.32.6 jedi-0.19.1 jinja2-3.1.2 json5-0.9.14 jsonpointer-2.4 jsonschema-4.20.0 jsonschema-specifications-2023.11.2 jupyter-client-8.6.0 jupyter-core-5.5.0 jupyter-events-0.9.0 jupyter-lsp-2.2.1 jupyter-server-2.11.2 jupyter-server-terminals-0.4.4 jupyterlab-4.0.9 jupyterlab-pygments-0.3.0 jupyterlab-server-2.25.2 jupyterlab-widgets-1.1.7 kiwisolver-1.4.5 matplotlib-3.3.1 matplotlib-inline-0.1.6 mistune-3.0.2 nbclient-0.9.0 nbconvert-7.12.0 nbformat-5.9.2 nest-asyncio-1.5.8 notebook-6.4.13 notebook-shim-0.2.3 numpy-1.26.2 overrides-7.4.0 packaging-23.2 pandocfilters-1.5.0 param-2.0.1 parso-0.8.3 pillow-10.1.0 platformdirs-4.1.0 prometheus-client-0.19.0 prompt-toolkit-3.0.41 psutil-5.9.6 pure-eval-0.2.2 pycparser-2.21 pyct-0.5.0 pygments-2.17.2 pyparsing-3.1.1 python-dateutil-2.8.2 python-json-logger-2.0.7 pywin32-306 pywinpty-2.0.12 pyyaml-6.0.1 pyzmq-25.1.2 referencing-0.31.1 requests-2.31.0 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.13.2 send2trash-1.8.2 six-1.16.0 sniffio-1.3.0 soupsieve-2.5 stack-data-0.6.3 terminado-0.18.0 tinycss2-1.2.1 tomli-2.0.1 tornado-6.4 tqdm-4.66.1 traitlets-5.6.0 traittypes-0.2.1 types-python-dateutil-2.8.19.14 typing-extensions-4.8.0 uri-template-1.3.0 urllib3-2.1.0 wcwidth-0.2.12 webcolors-1.13 webencodings-0.5.1 websocket-client-1.7.0 widgetsnbextension-3.6.6 zipp-3.17.0 zstandard-0.22.0
WARNING: You are using pip version 22.0.4; however, version 23.3.1 is available.
You should consider upgrading via the 'M:\Work\.venv\Scripts\python.exe -m pip install --upgrade pip' command.

(.venv) M:\Work\mri-segmentation>python
Python 3.9.13 (tags/v3.9.13:6de2ca5, May 17 2022, 16:36:42) [MSC v.1929 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import itk
>>> _ = itk.ElastixRegistrationMethod

(.venv) M:\Work\mri-segmentation>

Non-Elastix related things work, e.g. image = itk.imread("C:/a/100.jpg").

thewtex commented 12 months ago

Note that itk-5.3.0 is being brought in, which is not compatible with itk-elastix 0.19.1.

dzenanz commented 12 months ago

That might be coming from my system installation. Let me try to clean it up to see whether that fixes the problem.

dzenanz commented 12 months ago

Clearing the system installation, and manually installing ITK 5.4RC2 first, did not help. Log:

M:\Work>python -m venv .venv

M:\Work>.venv\Scripts\activate

(.venv) M:\Work>cd mri-segmentation

(.venv) M:\Work\mri-segmentation>pip install itk==5.4rc2
Collecting itk==5.4rc2
  Using cached itk-5.4rc2-cp39-cp39-win_amd64.whl (8.6 kB)
Collecting numpy
  Using cached numpy-1.26.2-cp39-cp39-win_amd64.whl (15.8 MB)
Collecting itk-filtering==5.4rc2
  Using cached itk_filtering-5.4rc2-cp39-cp39-win_amd64.whl (24.3 MB)
Collecting itk-io==5.4rc2
  Using cached itk_io-5.4rc2-cp39-cp39-win_amd64.whl (8.5 MB)
Collecting itk-core==5.4rc2
  Using cached itk_core-5.4rc2-cp39-cp39-win_amd64.whl (37.5 MB)
Collecting itk-segmentation==5.4rc2
  Using cached itk_segmentation-5.4rc2-cp39-cp39-win_amd64.whl (5.2 MB)
Collecting itk-registration==5.4rc2
  Using cached itk_registration-5.4rc2-cp39-cp39-win_amd64.whl (9.5 MB)
Collecting itk-numerics==5.4rc2
  Using cached itk_numerics-5.4rc2-cp39-cp39-win_amd64.whl (20.6 MB)
Installing collected packages: numpy, itk-core, itk-numerics, itk-io, itk-filtering, itk-segmentation, itk-registration, itk
Successfully installed itk-5.4rc2 itk-core-5.4rc2 itk-filtering-5.4rc2 itk-io-5.4rc2 itk-numerics-5.4rc2 itk-registration-5.4rc2 itk-segmentation-5.4rc2 numpy-1.26.2
WARNING: You are using pip version 22.0.4; however, version 23.3.1 is available.
You should consider upgrading via the 'M:\Work\.venv\Scripts\python.exe -m pip install --upgrade pip' command.

(.venv) M:\Work\mri-segmentation>pip install -r requirements.txt
Collecting itk-elastix>=0.18.0
  Using cached itk_elastix-0.19.1-cp39-cp39-win_amd64.whl (7.8 MB)
Collecting itk-iomeshstl>=2.3.0
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Collecting itk-cuberille>=2.6.0
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Collecting itkwidgets>=0.32.0
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Collecting jupyterlab>=2.2.0
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Requirement already satisfied: numpy in m:\Work\.venv\lib\site-packages (from -r requirements.txt (line 6)) (1.26.2)
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Requirement already satisfied: itk>=5.4rc2 in m:\Work\.venv\lib\site-packages (from itk-elastix>=0.18.0->-r requirements.txt (line 1)) (5.4rc2)
Requirement already satisfied: itk-io>=5.3.0 in m:\Work\.venv\lib\site-packages (from itk-iomeshstl>=2.3.0->-r requirements.txt (line 2)) (5.4rc2)
Collecting ipympl>=0.4.1
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Requirement already satisfied: itk-filtering>=5.3.0 in m:\Work\.venv\lib\site-packages (from itkwidgets>=0.32.0->-r requirements.txt (line 4)) (5.4rc2)
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Requirement already satisfied: itk-numerics>=5.3.0 in m:\Work\.venv\lib\site-packages (from itkwidgets>=0.32.0->-r requirements.txt (line 4)) (5.4rc2)
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Requirement already satisfied: itk-core>=5.3.0 in m:\Work\.venv\lib\site-packages (from itkwidgets>=0.32.0->-r requirements.txt (line 4)) (5.4rc2)
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Requirement already satisfied: itk-segmentation==5.4rc2 in m:\Work\.venv\lib\site-packages (from itk>=5.4rc2->itk-elastix>=0.18.0->-r requirements.txt (line 1)) (5.4rc2)
Requirement already satisfied: itk-registration==5.4rc2 in m:\Work\.venv\lib\site-packages (from itk>=5.4rc2->itk-elastix>=0.18.0->-r requirements.txt (line 1)) (5.4rc2)
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Collecting requests>=2.31
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Collecting jsonschema>=4.18.0
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Installing collected packages: webencodings, wcwidth, types-python-dateutil, pywin32, pure-eval, json5, ipython-genutils, fastjsonschema, zstandard, zipp, websocket-client, webcolors, urllib3, uri-template, typing-extensions, traitlets, tornado, tomli, tinycss2, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, pyzmq, pyyaml, pywinpty, python-json-logger, pyparsing, pygments, pycparser, psutil, prompt-toolkit, prometheus-client, platformdirs, pillow, parso, param, pandocfilters, packaging, overrides, nest-asyncio, mistune, MarkupSafe, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, idna, fqdn, executing, exceptiongroup, defusedxml, decorator, debugpy, cycler, colorama, charset-normalizer, certifi, babel, attrs, traittypes, tqdm, terminado, rfc3339-validator, requests, referencing, python-dateutil, pyct, matplotlib-inline, jupyter-core, jinja2, jedi, itk-meshtopolydata, importlib-metadata, comm, cffi, bleach, beautifulsoup4, async-lru, asttokens, anyio, stack-data, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, itk-iomeshstl, colorcet, arrow, argon2-cffi-bindings, jsonschema, isoduration, ipython, argon2-cffi, nbformat, ipykernel, nbclient, jupyter-events, itk-elastix, itk-cuberille, nbconvert, notebook, jupyter-server, widgetsnbextension, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, ipywidgets, ipympl, ipydatawidgets, itkwidgets
Successfully installed MarkupSafe-2.1.3 anyio-4.1.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.1.0 babel-2.13.1 beautifulsoup4-4.12.2 bleach-6.1.0 certifi-2023.11.17 cffi-1.16.0 charset-normalizer-3.3.2 colorama-0.4.6 colorcet-3.0.1 comm-0.2.0 cycler-0.12.1 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 exceptiongroup-1.2.0 executing-2.0.1 fastjsonschema-2.19.0 fqdn-1.5.1 idna-3.6 importlib-metadata-7.0.0 ipydatawidgets-4.3.2 ipykernel-6.27.1 ipympl-0.8.8 ipython-8.18.1 ipython-genutils-0.2.0 ipywidgets-7.8.1 isoduration-20.11.0 itk-cuberille-2.6.0 itk-elastix-0.19.1 itk-iomeshstl-2.3.0 itk-meshtopolydata-0.10.0 itkwidgets-0.32.6 jedi-0.19.1 jinja2-3.1.2 json5-0.9.14 jsonpointer-2.4 jsonschema-4.20.0 jsonschema-specifications-2023.11.2 jupyter-client-8.6.0 jupyter-core-5.5.0 jupyter-events-0.9.0 jupyter-lsp-2.2.1 jupyter-server-2.11.2 jupyter-server-terminals-0.4.4 jupyterlab-4.0.9 jupyterlab-pygments-0.3.0 jupyterlab-server-2.25.2 jupyterlab-widgets-1.1.7 kiwisolver-1.4.5 matplotlib-3.3.1 matplotlib-inline-0.1.6 mistune-3.0.2 nbclient-0.9.0 nbconvert-7.12.0 nbformat-5.9.2 nest-asyncio-1.5.8 notebook-6.4.13 notebook-shim-0.2.3 overrides-7.4.0 packaging-23.2 pandocfilters-1.5.0 param-2.0.1 parso-0.8.3 pillow-10.1.0 platformdirs-4.1.0 prometheus-client-0.19.0 prompt-toolkit-3.0.41 psutil-5.9.6 pure-eval-0.2.2 pycparser-2.21 pyct-0.5.0 pygments-2.17.2 pyparsing-3.1.1 python-dateutil-2.8.2 python-json-logger-2.0.7 pywin32-306 pywinpty-2.0.12 pyyaml-6.0.1 pyzmq-25.1.2 referencing-0.31.1 requests-2.31.0 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.13.2 send2trash-1.8.2 six-1.16.0 sniffio-1.3.0 soupsieve-2.5 stack-data-0.6.3 terminado-0.18.0 tinycss2-1.2.1 tomli-2.0.1 tornado-6.4 tqdm-4.66.1 traitlets-5.6.0 traittypes-0.2.1 types-python-dateutil-2.8.19.14 typing-extensions-4.8.0 uri-template-1.3.0 urllib3-2.1.0 wcwidth-0.2.12 webcolors-1.13 webencodings-0.5.1 websocket-client-1.7.0 widgetsnbextension-3.6.6 zipp-3.17.0 zstandard-0.22.0
WARNING: You are using pip version 22.0.4; however, version 23.3.1 is available.
You should consider upgrading via the 'M:\Work\.venv\Scripts\python.exe -m pip install --upgrade pip' command.

(.venv) M:\Work\mri-segmentation>python
Python 3.9.13 (tags/v3.9.13:6de2ca5, May 17 2022, 16:36:42) [MSC v.1929 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import itk
>>> _ = itk.ElastixRegistrationMethod

(.venv) M:\Work\mri-segmentation>
dzenanz commented 7 months ago

0.19.2 with ITK 5.4RC4 solves the crash.