Add itkwidgets example in notebook

[Nic-Ma]

Description

This PR added itkwidgets example in the visualization tutorial.

Status

Ready

Checks

• Notebook runs automatically ./runner [-p <regex_pattern>]

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[ericspod]

I'm not getting any display with view from itkwidgets. With the following in a cell:

import monai
from itkwidgets import view
img,seg=monai.data.create_test_image_3d(128,128,128,5)
view(image=img*255, label_image=seg * 255, gradient_opacity=0.4)

I get no output as a result in Jupyter or Jupyterlab 3.1.7. I installed the itkwidgets package on top of whatever else was needed for MONAI 0.7.0 so am I missing something? It might just be a Jupyter version issue as discussed, all my Jupyter versions are:

IPython          : 7.29.0
ipykernel        : 6.4.1
ipywidgets       : 7.6.5
jupyter_client   : 7.0.1
jupyter_core     : 4.8.1
jupyter_server   : 1.4.1
jupyterlab       : 3.2.1
nbclient         : 0.5.3
nbconvert        : 6.1.0
nbformat         : 5.1.3
notebook         : 6.4.5
qtconsole        : not installed
traitlets        : 5.1.0

[aylward]

Regretfully Jupyter Lab 3 isn't supported, but it should work in notebooks.

Do the controls show up? If so, please try switching to a 2D view (click on one of the cubes that has a yellow, red, or green face to switch to a 2D view). Let me know if a 2D image shows.

If only a line of text appears, then I'll checkout your specific versions. I'm running conda on Windows and the versions are a bit behind yours on some of those packages...I can dig into it.

[aylward]

We might want to also show off the checkerboard command for 2D/3D image comparison:

[aylward]

Ah - just saw that you're creating 5-channel data. Can you try sending only one channel to the view() command:

import monai
from itkwidgets import view
img,seg=monai.data.create_test_image_3d(128,128,128,5)
view(image=img[:,:,:,0]*255, label_image=seg[:,:,:,0]*255, gradient_opacity=0.4)

We really should generate a warning if invalid data is passed to it!!! I'll file an issue.

[ericspod]

Hi @aylward,
I ran the cell again and both image and segmentation have shape (128,128,128) so I don't think it's a channel problem, I get no output at all. In Jupyter Notebook I tried adding a 1-size channel to the beginning and end without success for the whole volumes and 2D slices thereof. If I try it again in Jupyterlab it does say "loading widget..." as output but no more. You mentioned earlier lab 3 isn't supported so it's fair enough. I'm on Ubuntu 20.04.3 LTS.

My library versions for Python 3.8.12

• _libgcc_mutex 0.1 main
• _openmp_mutex 4.5 1_gnu
• absl-py 1.0.0 pypi_0 pypi
• anyio 2.2.0 py38h06a4308_1
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• babel 2.9.1 pyhd3eb1b0_0
• backcall 0.2.0 pyhd3eb1b0_0
• black 19.10b0 py_0
• blas 1.0 mkl
• bleach 4.0.0 pyhd3eb1b0_0
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• brunsli 0.1 h2531618_0
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• ca-certificates 2021.10.26 h06a4308_2
• cachetools 4.2.4 pypi_0 pypi
• certifi 2021.10.8 py38h06a4308_0
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• cfitsio 3.470 hf0d0db6_6
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• click 8.0.3 pyhd3eb1b0_0
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• cupy-cuda102 9.5.0 pypi_0 pypi
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• importlab 0.6.1 pypi_0 pypi
• importlib-metadata 4.8.1 py38h06a4308_0
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• intel-openmp 2021.4.0 h06a4308_3561
• ipydatawidgets 4.2.0 pypi_0 pypi
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• ipympl 0.8.2 pypi_0 pypi
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• ipywidgets 7.6.5 pypi_0 pypi
• isort 5.9.3 pyhd3eb1b0_0
• itk-core 5.2.1.post1 pypi_0 pypi
• itk-filtering 5.2.1.post1 pypi_0 pypi
• itk-meshtopolydata 0.7.1 pypi_0 pypi
• itk-numerics 5.2.1.post1 pypi_0 pypi
• itkwidgets 0.32.1 pypi_0 pypi
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• jupyterlab-widgets 1.0.2 pypi_0 pypi
• jupyterlab_pygments 0.1.2 py_0
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• jxrlib 1.1 h7b6447c_2
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• libev 4.33 h7f8727e_1
• libffi 3.3 he6710b0_2
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• libgfortran-ng 7.5.0 ha8ba4b0_17
• libgfortran4 7.5.0 ha8ba4b0_17
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• monai 0.7.0 pypi_0 pypi
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• mypy_extensions 0.4.3 py38_0
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• nbclient 0.5.3 pyhd3eb1b0_0
• nbconvert 6.1.0 py38h06a4308_0
• nbformat 5.1.3 pyhd3eb1b0_0
• ncurses 6.3 heee7806_1
• nest-asyncio 1.5.1 pyhd3eb1b0_0
• nettle 3.7.3 hbbd107a_1
• networkx 2.6.3 pyhd3eb1b0_0
• nibabel 3.2.1 pypi_0 pypi
• ninja 1.10.2.2 pypi_0 pypi
• notebook 6.4.5 py38h06a4308_0
• numexpr 2.7.3 py38h22e1b3c_1
• numpy 1.21.2 py38h20f2e39_0
• numpy-base 1.21.2 py38h79a1101_0
• oauthlib 3.1.1 pypi_0 pypi
• olefile 0.46 pyhd3eb1b0_0
• openh264 2.1.0 hd408876_0
• openjpeg 2.4.0 h3ad879b_0
• openssl 1.1.1l h7f8727e_0
• packaging 21.0 pyhd3eb1b0_0
• pandas 1.3.4 py38h8c16a72_0
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• param 1.12.0 pypi_0 pypi
• parameterized 0.8.1 pyhd3eb1b0_1
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• pathspec 0.7.0 py_0
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• pillow 8.4.0 py38h5aabda8_0
• pip 21.2.4 py38h06a4308_0
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• python 3.8.12 h12debd9_0
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• pytype 2021.11.18 pypi_0 pypi
• pytz 2021.3 pyhd3eb1b0_0
• pywavelets 1.1.1 py38h7b6447c_2
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• tornado 6.1 py38h27cfd23_0
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• urllib3 1.26.7 pyhd3eb1b0_0
• wcwidth 0.2.5 pyhd3eb1b0_0
• webencodings 0.5.1 py38_1
• werkzeug 2.0.2 pypi_0 pypi
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• widgetsnbextension 3.5.2 pypi_0 pypi
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• zstd 1.4.9 haebb681_0

[aylward]

I've sent an invite to Matt McCormick to join this project. He might have insights.

[aylward]

Hmm - can you try with non-tensor data?

Perhaps try any of the examples at
https://github.com/InsightSoftwareConsortium/itkwidgets/tree/master/examples

Sorry for the inconvenience and thanks for your persistence!

[ericspod]

It was actually Numpy arrays and not tensors. I tried the following in Jupyter notebook which was taken from the 2D example but the only output I get is three instances of "libpng warning: sCAL: invalid unit".

from urllib.request import urlretrieve
import os
import itk
from itkwidgets import view

# Download data
file_name = 'cthead1.png'
if not os.path.exists(file_name):
    url = 'https://data.kitware.com/api/v1/file/57b5d9ef8d777f10f269538f/download'
    urlretrieve(url, file_name)

image = itk.imread(file_name)
view(image)

[ericspod]

Looking at the Javascript console I'm seeing some errors related to JQuery amongst other things:

[aylward]

Thanks! I've forwarded to Matt. Fingers crossed. S

…

On Wed, Nov 24, 2021, 10:36 AM Eric Kerfoot ***@***.***> wrote: Looking at the Javascript console I'm seeing some errors related to JQuery amongst other things: [image: image] <https://user-images.githubusercontent.com/17726042/143278211-cb8face2-125e-4361-a5e8-f111b0a21431.png> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#454 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACEJLYSKQGQVFL5NFB6NYLUNUIBJANCNFSM5IVTEAAQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[wyli]

Thanks, I think this could be an initial demo, and we can refine it later

[Nic-Ma]

Hi @ericspod @aylward @wyli ,

Thanks for the review and comments.
I updated the PR to use PLS orientation and it depends on PR Project-MONAI/MONAI#3385.
@wyli and I also verified the itkwidgets view online.

Thanks.