import pyTFM plugin fails
alexlib opened this issue · 11 comments
alexlib commented
On Python 3.10 (Windows 10, miniconda3)
import TFM_addon.TFM_addon
Traceback (most recent call last):
File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 420, in add_script
self.script_launcher.activateScript(self.selected_script)
File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 501, in activateScript
if script.activate(self, silent=silent):
File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 230, in activate
raise err
File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 224, in activate
self.addon_module = import_module(folder + "." + basefilename)
File "C:\Users\alex\miniconda3\envs\pytfm\lib\importlib\__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 883, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\pyTFM\TFM_addon\TFM_addon.py", line 4, in <module>
from pyTFM.TFM_functions_for_clickpoints import * # must be on top because of some matplotlib backend issues
File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\pyTFM\TFM_functions_for_clickpoints.py", line 10, in <module>
from pyTFM.frame_shift_correction import *
File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\pyTFM\frame_shift_correction.py", line 12, in <module>
from skimage.feature import register_translation
ImportError: cannot import name 'register_translation' from 'skimage.feature' (C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\skimage\feature\__init__.py)
alexlib commented
On Python 3.10 (Windows 10, miniconda3)
import TFM_addon.TFM_addon Traceback (most recent call last): File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 420, in add_script self.script_launcher.activateScript(self.selected_script) File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 501, in activateScript if script.activate(self, silent=silent): File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 230, in activate raise err File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\clickpoints\modules\ScriptLauncher.py", line 224, in activate self.addon_module = import_module(folder + "." + basefilename) File "C:\Users\alex\miniconda3\envs\pytfm\lib\importlib\__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "<frozen importlib._bootstrap>", line 1050, in _gcd_import File "<frozen importlib._bootstrap>", line 1027, in _find_and_load File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 688, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 883, in exec_module File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\pyTFM\TFM_addon\TFM_addon.py", line 4, in <module> from pyTFM.TFM_functions_for_clickpoints import * # must be on top because of some matplotlib backend issues File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\pyTFM\TFM_functions_for_clickpoints.py", line 10, in <module> from pyTFM.frame_shift_correction import * File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\pyTFM\frame_shift_correction.py", line 12, in <module> from skimage.feature import register_translation ImportError: cannot import name 'register_translation' from 'skimage.feature' (C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\skimage\feature\__init__.py)
see
https://scikit-image.org/docs/0.19.x/release_notes.html#api-changes
in 0.19.1 the register_translation is removed
The deprecated skimage.feature.masked_register_translation function has been removed (use skimage.registration.phase_cross_correlation instead).
alexlib commented
please remove those lines
https://github.com/fabrylab/pyTFM/search?q=register_translation
since it fails the pyTFM plugin loading into clickpoints
rgerum commented
The new function was already used, but the import of register_translation was still present. I removed the import.
You can update to the current github version with:
pip install git+https://github.com/fabrylab/pyTFM --upgrade
The quamash problem with clickpoints was also fixed in december, you can update to the github version with:
pip install git+https://github.com/fabrylab/clickpoints/ --upgrade
alexlib commented
@rgerum
I see you closed the issue, but I still experience issues with the installation, both on Windows 10 and on WSL under Windows 10 - using the commands you suggested.
(pytfm) alex@DESKTOP-OV3L1FT:/mnt/c/Users/alex$ clickpoints
args ['/home/alex/anaconda3/envs/pytfm/bin/clickpoints']
ClickPoints 1.9.10
Using Python 3.10.2 final 64bit
Using PyQt5 5.15.6
/home/alex/anaconda3/envs/pytfm/lib/python3.10/site-packages/_distutils_hack/__init__.py:30: UserWarning: Setuptools is replacing distutils.
warnings.warn("Setuptools is replacing distutils.")
Traceback (most recent call last):
File "/home/alex/anaconda3/envs/pytfm/bin/clickpoints", line 8, in <module>
sys.exit(main())
File "/home/alex/anaconda3/envs/pytfm/lib/python3.10/site-packages/clickpoints/launch.py", line 78, in main
from clickpoints.Core import ClickPointsWindow
File "/home/alex/anaconda3/envs/pytfm/lib/python3.10/site-packages/clickpoints/Core.py", line 54, in <module>
from clickpoints.modules.Timeline import Timeline
File "/home/alex/anaconda3/envs/pytfm/lib/python3.10/site-packages/clickpoints/modules/Timeline.py", line 34, in <module>
from quamash import QEventLoop
ModuleNotFoundError: No module named 'quamash'
when I manually add quamash by
pip install quamash
I end up with
(pytfm) alex@DESKTOP-OV3L1FT:/mnt/c/Users/alex$ clickpoints
args ['/home/alex/anaconda3/envs/pytfm/bin/clickpoints']
ClickPoints 1.9.10
Using Python 3.10.2 final 64bit
Using PyQt5 5.15.6
/home/alex/anaconda3/envs/pytfm/lib/python3.10/site-packages/_distutils_hack/__init__.py:30: UserWarning: Setuptools is replacing distutils.
warnings.warn("Setuptools is replacing distutils.")
Traceback (most recent call last):
File "/home/alex/anaconda3/envs/pytfm/bin/clickpoints", line 8, in <module>
sys.exit(main())
File "/home/alex/anaconda3/envs/pytfm/lib/python3.10/site-packages/clickpoints/launch.py", line 78, in main
from clickpoints.Core import ClickPointsWindow
File "/home/alex/anaconda3/envs/pytfm/lib/python3.10/site-packages/clickpoints/Core.py", line 54, in <module>
from clickpoints.modules.Timeline import Timeline
File "/home/alex/anaconda3/envs/pytfm/lib/python3.10/site-packages/clickpoints/modules/Timeline.py", line 34, in <module>
from quamash import QEventLoop
File "/home/alex/anaconda3/envs/pytfm/lib/python3.10/site-packages/quamash/__init__.py", line 594, in <module>
from ._unix import _SelectorEventLoop
File "/home/alex/anaconda3/envs/pytfm/lib/python3.10/site-packages/quamash/_unix.py", line 44, in <module>
class _SelectorMapping(collections.Mapping):
AttributeError: module 'collections' has no attribute 'Mapping'
alexlib commented
rgerum commented
Hmm strange, clickpoints should not use quamash at all. It should use qasync instead.
So this line that is referenced in your error message is in the repository
from qasync import QEventLoop
So maybe you did not execute the pip install command in the right virtual environment? Or it did not get installed properly. I should make a new release to have this problem fixed for people installing it over pypi.
alexlib commented
i'm repeating the installation for the 5th time, removing and creating a new environment every time. things get wrong in a different way if I install first clickpoints -> stuck at a new error
(pytfm) PS C:\Users\alex> clickpoints
args ['C:\\Users\\alex\\miniconda3\\envs\\pytfm\\Scripts\\clickpoints']
ClickPoints 1.9.10
Using Python 3.10.2 final 64bit
Using PyQt5 5.15.6
C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\_distutils_hack\__init__.py:30: UserWarning: Setuptools is replacing distutils.
warnings.warn("Setuptools is replacing distutils.")
LoadConfig ['C:\\Users\\alex\\miniconda3\\envs\\pytfm\\Scripts\\clickpoints'] False
Traceback (most recent call last):
File "C:\Users\alex\miniconda3\envs\pytfm\lib\runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\alex\miniconda3\envs\pytfm\lib\runpy.py", line 86, in _run_code
exec(code, run_globals)
File "C:\Users\alex\miniconda3\envs\pytfm\Scripts\clickpoints.exe\__main__.py", line 7, in <module>
File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\clickpoints\launch.py", line 102, in main
window = ClickPointsWindow(config, app)
File "C:\Users\alex\miniconda3\envs\pytfm\lib\site-packages\clickpoints\Core.py", line 112, in __init__
self.move(x, y*0.5)
TypeError: arguments did not match any overloaded call:
move(self, QPoint): argument 1 has unexpected type 'float'
move(self, int, int): argument 1 has unexpected type 'float'
or if I start from pyTFM (that installs clickpoints from pypi probably) and then get to the errors I reported above.
rgerum commented
Ok this is a bug that has also been recently fixed.
I now made a new release. So hopefully it should now be installed correctly over pypi.
alexlib commented
@rgerum please note that there is some difference in the way pip implements the requirements if someone installs it through pyTFM or through clickpoints. What I mean is that if I start with
pip install git+https://github.com/fabrylab/clickpoints
or
pip install git+https://github.com/fabrylab/pytfm
I end up with different errors. Probably it requires somewhat more precise version instructions to pip.
rgerum commented
well i guess that by installing pytfm with pip and git it installs the pypi clickpoint version, which should now work as I made a release. But if you have any suggestions on what I can improve to make the installation process easier, I am happy to hear that.
alexlib commented
it works with the fresh installation
(pytfm) PS C:\Users\alex\Downloads> pip install git+https://github.com/fabrylab/pyTFM.git --no-cache-dir --force-reinstall
Collecting git+https://github.com/fabrylab/pyTFM.git
Cloning https://github.com/fabrylab/pyTFM.git to c:\users\alex\appdata\local\temp\pip-req-build-e246tk_h
Running command git clone --filter=blob:none --quiet https://github.com/fabrylab/pyTFM.git 'C:\Users\alex\AppData\Local\Temp\pip-req-build-e246tk_h'
Resolved https://github.com/fabrylab/pyTFM.git to commit 5d18dac13d3ad04dfe8193c990c159786f99d432
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Building wheels for collected packages: pyTFM, openpiv, peewee
Building wheel for pyTFM (setup.py) ... done
Created wheel for pyTFM: filename=pyTFM-1.3.3-py3-none-any.whl size=105954 sha256=aa1faebd810675a653b0967f85afb243539e5121c54f5f9099c6561c6ddfb7e4
Stored in directory: C:\Users\alex\AppData\Local\Temp\pip-ephem-wheel-cache-ga0p6sz_\wheels\b9\73\02\3d4274efb7e4bdbe098893d1d7fe479b5fa2a8f9b014e3b57f
Building wheel for openpiv (pyproject.toml) ... done
Created wheel for openpiv: filename=OpenPIV-0.22.0-cp310-cp310-win_amd64.whl size=24498239 sha256=f4c73d00848ecadd95e357576c29c16185de4929639aea2e1f8b9551b664c12e
Stored in directory: C:\Users\alex\AppData\Local\Temp\pip-ephem-wheel-cache-ga0p6sz_\wheels\9a\86\4d\ef1407a747f067a9793f97f4ccc6b6e35a6427e9134573abee
Building wheel for peewee (setup.py) ... done
Created wheel for peewee: filename=peewee-3.14.8-py3-none-any.whl size=131197 sha256=e04ed0865cd50b68299b290b73b7ea0a9735d9c2041a562ae3d3443fb13a6097
Stored in directory: C:\Users\alex\AppData\Local\Temp\pip-ephem-wheel-cache-ga0p6sz_\wheels\03\16\b8\eb39dd476609f95323e082720c03aabc47e27fa2dbc910b04d
Successfully built pyTFM openpiv peewee
Installing collected packages: sortedcontainers, PyQt5-Qt5, peewee, easygui, commonmark, smmap, six, qasync, pyyaml, python-utils, PyQt5-sip, pyparsing, pygments, psutil, pillow, numpy, networkx, natsort, kiwisolver, imageio-ffmpeg, fonttools, cython, cycler, colorama, tqdm, tifffile, scipy, rich, qimage2ndarray, PyWavelets, python-dateutil, pyqt5, progressbar2, packaging, imageio, imagecodecs, gitdb, scikit-image, qtpy, meshio, matplotlib, GitPython, solidspy, qtawesome, openpiv, clickpoints, pyTFM
Successfully installed GitPython-3.1.26 PyQt5-Qt5-5.15.2 PyQt5-sip-12.9.1 PyWavelets-1.2.0 clickpoints-1.9.11 colorama-0.4.4 commonmark-0.9.1 cycler-0.11.0 cython-0.29.27 easygui-0.98.2 fonttools-4.29.1 gitdb-4.0.9 imagecodecs-2021.11.20 imageio-2.15.0 imageio-ffmpeg-0.4.5 kiwisolver-1.3.2 matplotlib-3.5.1 meshio-5.3.0 natsort-8.1.0 networkx-2.6.3 numpy-1.22.2 openpiv-0.22.0 packaging-21.3 peewee-3.14.8 pillow-9.0.1 progressbar2-4.0.0 psutil-5.9.0 pyTFM-1.3.3 pygments-2.11.2 pyparsing-3.0.7 pyqt5-5.15.6 python-dateutil-2.8.2 python-utils-3.1.0 pyyaml-6.0 qasync-0.23.0 qimage2ndarray-1.8.3 qtawesome-1.1.1 qtpy-2.0.1 rich-11.2.0 scikit-image-0.19.1 scipy-1.8.0 six-1.16.0 smmap-5.0.0 solidspy-1.0.16 sortedcontainers-2.4.0 tifffile-2022.2.9 tqdm-4.62.3