Package Loading issue in Jupyter Notebook

[natalier11]

Hi there!

I've gotten the EZtrack Jupyter Notebook to work in the past and even analyzed videos but I'm running into a bit of an error now. After setting up the environment, downloading the zip, and opening jupyter notebook, I try to run the first step on the "LocationTracking_Individual.ipynb" file. When I run the cell containing all the necessary packages, it returns a message saying "WARNING:param.Dimension: Use method 'get_param_values' via param namespace" about 50 times, followed by "WARNING:param.ParameterizedMetaclass: Use method 'params' via param namespace" another 50 times, and then "WARNING:param.BokehRenderer: Use method 'params' via param namespace WARNING:param.NotebookArchive: Use method 'params' via param namespace" I've never run into this before and I thought I might ignore it and continue with my video analysis but it seems to affect step 3. When I try to run the Load Video and Crop Frame step, this pops up: I'm not sure if the video is potentially too long or there is some other issue going on. Help would be much appreciated! Thank you!

[ZachPenn]

Hi,

Sorry to hear you're having issues. I have a feeling this might have to do with package versions, as opposed to an issue with your video. Did you follow the install instructions, including package versions in the install? In any event, from terminal, could you activate the conda environment, enter the command conda list and then copy the output of that command here?

[natalier11]

Thanks for responding! I followed the install instructions provided by the github (I thought I did it wrong the first time so actually uninstalled everything and did it again with the github instructions). Here is the list of packages I have installed at the moment that I obtained from the terminal:

Name Version Build Channel

argon2-cffi 20.1.0 py36h779f372_2 conda-forge async_generator 1.10 py_0 conda-forge attrs 20.2.0 pyh9f0ad1d_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.1 py_0 conda-forge blas 1.0 mkl bleach 3.2.1 pyh9f0ad1d_0 conda-forge bokeh 1.2.0 py36_0 conda-forge ca-certificates 2020.6.20 hecda079_0 conda-forge certifi 2020.6.20 py36hd36e781_2 conda-forge cffi 1.14.3 py36h2e103f8_1 conda-forge colorama 0.4.4 pyh9f0ad1d_0 conda-forge cycler 0.10.0 py_2 conda-forge decorator 4.4.2 py_0 conda-forge defusedxml 0.6.0 py_0 conda-forge entrypoints 0.3 py36h9f0ad1d_1002 conda-forge freetype 2.10.4 h546665d_0 conda-forge holoviews 1.12.3 py_2 conda-forge icc_rt 2019.0.0 h0cc432a_1 icu 58.2 ha925a31_3 importlib-metadata 2.0.0 py_1 conda-forge importlib_metadata 2.0.0 1 conda-forge intel-openmp 2020.2 254 ipykernel 5.3.4 py36h7b7c402_1 conda-forge ipython 7.16.1 py36h95af2a2_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.5.1 pyh9f0ad1d_1 conda-forge jedi 0.17.2 py36h9f0ad1d_1 conda-forge jinja2 2.11.2 pyh9f0ad1d_0 conda-forge jpeg 9d h8ffe710_0 conda-forge jsonschema 3.2.0 py_2 conda-forge jupyter 1.0.0 py_2 conda-forge jupyter_client 6.1.7 py_0 conda-forge jupyter_console 6.2.0 py_0 conda-forge jupyter_core 4.6.3 py36h9f0ad1d_2 conda-forge jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge kiwisolver 1.3.0 py36he95197e_0 conda-forge libblas 3.8.0 20_mkl conda-forge libcblas 3.8.0 20_mkl conda-forge liblapack 3.8.0 20_mkl conda-forge libpng 1.6.37 h1d00b33_2 conda-forge libsodium 1.0.18 h62dcd97_1 conda-forge libtiff 4.1.0 h885aae3_6 conda-forge libwebp 0.5.2 7 conda-forge lz4-c 1.9.2 h62dcd97_2 conda-forge m2w64-gcc-libgfortran 5.3.0 6 m2w64-gcc-libs 5.3.0 7 m2w64-gcc-libs-core 5.3.0 7 m2w64-gmp 6.1.0 2 m2w64-libwinpthread-git 5.0.0.4634.697f757 2 markupsafe 1.1.1 py36hc753bc4_2 conda-forge matplotlib 3.1.1 py36_2 conda-forge matplotlib-base 3.1.1 py36h2981e6d_2 conda-forge mistune 0.8.4 py36h779f372_1002 conda-forge mkl 2020.2 256 msys2-conda-epoch 20160418 1 nbclient 0.5.1 py_0 conda-forge nbconvert 6.0.7 py36h9f0ad1d_2 conda-forge nbformat 5.0.8 py_0 conda-forge nest-asyncio 1.4.1 py_0 conda-forge notebook 6.1.4 py36h9f0ad1d_1 conda-forge numpy 1.19.2 py36hc5bf2d3_1 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge opencv 3.4.3 py36h597e314_201 conda-forge openssl 1.0.2u hfa6e2cd_0 conda-forge packaging 20.4 pyh9f0ad1d_0 conda-forge pandas 0.23.0 py36_1 conda-forge pandoc 2.11.0.4 hf4a77e7_0 conda-forge pandocfilters 1.4.2 py_1 conda-forge param 1.10.0 py_0 conda-forge parso 0.7.1 pyh9f0ad1d_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 8.0.1 py36he4e95fe_0 conda-forge pip 20.2.4 py_0 conda-forge prometheus_client 0.8.0 pyh9f0ad1d_0 conda-forge prompt-toolkit 3.0.8 py_0 conda-forge prompt_toolkit 3.0.8 0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pygments 2.7.2 py_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyqt 5.6.0 py36h764d66f_1008 conda-forge pyrsistent 0.17.3 py36h779f372_1 conda-forge python 3.6.11 h6f26aa1_2_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.6 1_cp36m conda-forge pytz 2020.1 pyh9f0ad1d_0 conda-forge pyviz_comms 0.7.6 pyh9f0ad1d_0 conda-forge pywin32 228 py36h779f372_0 conda-forge pywinpty 0.5.7 py36h9f0ad1d_1 conda-forge pyyaml 5.3.1 py36hc753bc4_1 conda-forge pyzmq 19.0.2 py36h274d426_2 conda-forge qt 5.6.2 vc14h6f8c307_12 qtconsole 4.7.7 pyh9f0ad1d_0 conda-forge qtpy 1.9.0 py_0 conda-forge scipy 1.2.1 py36h29ff71c_0 send2trash 1.5.0 py_0 conda-forge setuptools 49.6.0 py36hd36e781_2 conda-forge sip 4.18.1 py36h6538335_1000 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge sqlite 3.33.0 he774522_1 conda-forge terminado 0.9.1 py36h9f0ad1d_1 conda-forge testpath 0.4.4 py_0 conda-forge tk 8.6.10 he774522_1 conda-forge tornado 6.1 py36h68aa20f_0 conda-forge traitlets 4.3.3 py36h9f0ad1d_1 conda-forge vc 14.1 h869be7e_1 conda-forge vs2015_runtime 14.16.27012 h30e32a0_2 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.35.1 pyh9f0ad1d_0 conda-forge widgetsnbextension 3.5.1 py36h9f0ad1d_4 conda-forge wincertstore 0.2 py36h9f0ad1d_1005 conda-forge winpty 0.4.3 4 conda-forge xz 5.2.5 h62dcd97_1 conda-forge yaml 0.2.5 he774522_0 conda-forge zeromq 4.3.2 ha925a31_4 conda-forge zipp 3.4.0 py_0 conda-forge zlib 1.2.11 h62dcd97_1010 conda-forge zstd 1.4.5 h1f3a1b7_2 conda-forge

[ZachPenn]

Can I also ask what operating system and browser you are using?

[natalier11]

I am using Windows 10 and Mozilla for my browser.

[ZachPenn]

I will be looking further into this over the next few days when I can get some time. It is a problem that is specific to Windows and has to do with package dependencies, rather than ezTrack code. This may take me a few days.

Zach

[natalier11]

No problem! Thanks for your assistance!

[ZachPenn]

I think the issue can be resolved by updating a couple of packages. For some reason I had better luck uninstalling the ezTrack environment and then reinstalling than simply updating the specific packages.

If you are unfamiliar with removing environments, you can use the following command: conda remove --name ezTrack --all

Subsequently, reinstall the ezTrack conda environment with the following command: conda create -y -n ezTrack -c conda-forge python=3.6 pandas=0.23.0 matplotlib=3.1.1 opencv=3.4.3 jupyter=1.0.0 holoviews=1.13.5 scipy=1.2.1 bokeh=2.1.1

So far this has been tested on Windows using Chrome and Mozilla Firefox browsers and on Mac using Chrome.

Please let me know if this works for you and thanks for bringing this to my attention.

[natalier11]

Hi there! I was able to uninstall the environments adreinstall them with your command line no problem. However, now when I try to run the first cell in the notebook, I get an error message that says: Javascript error adding output! TypeError: t.slice is not a function See your browser Javascript console for more details.

I've never received this type of error message on anything and I'm not sure how to fix this. Let me know if you have any ideas.

[natalier11]

The cell seems to run even with that error but once I get to step 3, it shows the following output: It also shows this message in the anaconda prompt when I run step 3: [IPKernelApp] WARNING | No such comm: hv-extension-comm

I am not sure if this has to do with the environments again.

[ZachPenn]

Definitely has something to do with the environment. This is the same issue I had when I at first tried to update the packages without uninstalling the environment first, but I suppose that's not the solution. Will look into this more.

[ZachPenn]

I have now tested ezTrack with the updated conda environment install instructions that I provided you on two computers running Windows and with four browsers (Chrome, Edge, Firefox, and Explorer). I only get the error you describe when using Internet Explorer. ezTrack works on all other browsers. Were you using Internet Explorer?

[natalier11]

That's really odd because I've only ever used Firefox through this whole process. Let me try Chrome and see if that may help.

[natalier11]

It appears that using Chrome works with no issues!! Thanks so much for all your help, I really appreciate it!