https://lumicks-pylake.readthedocs.io/en/v0.8.2/install.html#updating
https://github.com/JamesLiWan/MultimerizationCode/blob/main/C_Trap-Multimer-photontrack.ipynb
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Fix which pylake we should use for the legacy-code.
Yep – you’re absolutely right, the channel parameter was added in pylake v0.9.0. If you look at the changelog: v0.9.0 (Jul 29 2021) introduces unit support and other updates, which also aligns with introducing the channel argument in track_greedy() Versions before v0.9.0, like v0.8.2 (Apr 30 2021), use the old signature: track_greedy(kymograph, line_width, pixel_threshold, …) with no channel argument. Since your code uses track_greedy(data, …) without specifying channel, you should install: pylake v0.8.2 -
Create mamba environment for pylake v0.8.2
mamba env remove -n pylake_082_clean mamba env create -f pylake_082_env.yml name: pylake_082_clean channels: - conda-forge - defaults dependencies: - python=3.8 - pip - jupyterlab - ipywidgets - numpy - matplotlib - h5py - pandas - scipy mamba activate pylake_082_clean #IMPORTANT: mamba install -c conda-forge lumicks.pylake=0.8.2 mamba install -c conda-forge numpy matplotlib ipywidgets scipy scikit-image pandas python -c "import lumicks.pylake; print(lumicks.pylake.__version__)" mamba install notebook=6 #+ ipython_genutils 0.2.0 pyhd8ed1ab_1 conda-forge Cached #+ nbclassic 1.1.0 pyhd8ed1ab_0 conda-forge Cached #+ notebook 6.5.7 pyha770c72_0 conda-forge Cached #Downgrade: #───────────────────────────────────────────────────────────────────── #- jupyter_client 8.6.3 pyhd8ed1ab_0 conda-forge Cached #+ jupyter_client 7.4.9 pyhd8ed1ab_0 conda-forge Cached jupyter notebook --version #pip show notebook (pylake_082_clean) jhuang@WS-2290C:/mnt/md1/DATA/Data_Vero_Kymographs$ mamba list jupyter # packages in environment at /home/jhuang/mambaforge/envs/pylake_082_clean: # # Name Version Build Channel jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge jupyter_client 7.4.9 pyhd8ed1ab_0 conda-forge jupyter_core 5.8.1 pyh31011fe_0 conda-forge jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge jupyter_server 2.14.2 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge jupyterlab 4.3.0 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge jupyterlab_server 2.27.3 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 3.0.13 pyhd8ed1ab_0 conda-forge (pylake_082_clean) jhuang@WS-2290C:/mnt/md1/DATA/Data_Vero_Kymographs$ mamba list notebook # packages in environment at /home/jhuang/mambaforge/envs/pylake_082_clean: # # Name Version Build Channel notebook 6.5.7 pyha770c72_0 conda-forge notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge #Note that Notebook v6.x and Notebook v7 is different, we have to notebook v6 More Detailed Breakdown: #Version Backend Used Notes #Notebook v6.x and below notebook (classic Tornado-based server) No jupyter_server dependency #Notebook v7+ Uses jupyter_server under the hood Required dependency -
Install extension for the recognization of %%javascript, %matplotlib inline, and %matplotlib notebook
mamba install widgetsnbextension -c conda-forge jupyter nbextension enable --py widgetsnbextension --sys-prefix #ModuleNotFoundError: No module named 'ipympl', but we don't need it! jupyter nbextension enable --py ipympl --sys-prefix jupyter nbextension list -
BUG_1: ModuleNotFoundError: No module named ‘matplotlib_venn’
mamba install -c conda-forge matplotlib-venn -
BUG_2: TypeError: init() got an unexpected keyword argument ‘drawtype’
#indicates that your version of Matplotlib is too new, and it no longer supports the drawtype argument in matplotlib.widgets.RectangleSelector. Only <= 3.4.3 supprts drawtype! mamba list matplotlib # packages in environment at /home/jhuang/mambaforge/envs/pylake_082_clean: # # Name Version Build Channel #matplotlib 3.7.3 py38h578d9bd_0 conda-forge #matplotlib-base 3.7.3 py38h58ed7fa_0 conda-forge #matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge #matplotlib-venn 1.1.1 pyhd8ed1ab_0 conda-forge #DEBUG: # MODIFIED: Delete "drawtype='box'," in kymowidget.py self.area_selector = RectangleSelector(self._axes, self.track_kymo, useblit=True, button=[3], minspanx=5, minspany=5, spancoords='pixels', interactive=False) -
OPTIONAL_BUG (NOT_DONE): [W 13:13:49.115 NotebookApp] Error loading server extension jupyterlab
#Traceback (most recent call last): # File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/notebook/notebookapp.py", line 2050, in init_server_extensions # func(self) # File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/jupyterlab/serverextension.py", line 71, in load_jupyter_server_extension # extension.initialize() # File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/jupyterlab/labapp.py", line 921, in initialize # super().initialize() # File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/jupyter_server/extension/application.py", line 437, in initialize # self._prepare_handlers() # File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/jupyter_server/extension/application.py", line 327, in _prepare_handlers # self.initialize_handlers() # File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/jupyterlab/labapp.py", line 735, in initialize_handlers # page_config["token"] = self.serverapp.identity_provider.token #AttributeError: 'NotebookApp' object has no attribute 'identity_provider' jupyter serverextension disable jupyterlab mamba remove jupyterlab (or pip uninstall jupyterlab) -
Run notebook on (pylake_082_clean) jhuang@WS-2290C:/mnt/md1/DATA/Data_Vero_Kymographs/MultimerizationCode-main_v082
(pylake_082_clean) jhuang@WS-2290C:/mnt/md1/DATA/Data_Vero_Kymographs/MultimerizationCode-main_v082$ jupyter notebook #jupyter notebook --no-browser --port=8888