Add itkwidgets example in notebook by Nic-Ma · Pull Request #454 · Project-MONAI/tutorials

Nic-Ma · 2021-11-24T09:45:30Z

Description

This PR added itkwidgets example in the visualization tutorial.

Status

Ready

Checks

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

Signed-off-by: Nic Ma <[email protected]>

review-notebook-app · 2021-11-24T09:45:34Z

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Signed-off-by: Nic Ma <[email protected]>

ericspod · 2021-11-24T14:24:35Z

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 · 2021-11-24T14:48:17Z

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 · 2021-11-24T14:49:44Z

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

aylward · 2021-11-24T14:51:25Z

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 · 2021-11-24T15:16:54Z

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
appdirs 1.4.4 pyhd3eb1b0_0
argon2-cffi 20.1.0 py38h27cfd23_1
async_generator 1.10 pyhd3eb1b0_0
attrs 21.2.0 pyhd3eb1b0_0
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
blosc 1.21.0 h8c45485_0
bottleneck 1.3.2 py38heb32a55_1
brotli 1.0.9 he6710b0_2
brotlipy 0.7.0 py38h27cfd23_1003
brunsli 0.1 h2531618_0
bzip2 1.0.8 h7b6447c_0
c-ares 1.17.1 h27cfd23_0
ca-certificates 2021.10.26 h06a4308_2
cachetools 4.2.4 pypi_0 pypi
certifi 2021.10.8 py38h06a4308_0
cffi 1.14.6 py38h400218f_0
cfitsio 3.470 hf0d0db6_6
charls 2.2.0 h2531618_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
click 8.0.3 pyhd3eb1b0_0
cloudpickle 2.0.0 pyhd3eb1b0_0
colorcet 2.0.6 pypi_0 pypi
coverage 5.5 py38h27cfd23_2
cryptography 35.0.0 py38hd23ed53_0
cudatoolkit 10.2.89 hfd86e86_1
cupy-cuda102 9.5.0 pypi_0 pypi
cycler 0.10.0 py38_0
cytoolz 0.11.0 py38h7b6447c_0
dask-core 2021.10.0 pyhd3eb1b0_0
dbus 1.13.18 hb2f20db_0
debugpy 1.4.1 py38h295c915_0
decorator 5.1.0 pyhd3eb1b0_0
defusedxml 0.7.1 pyhd3eb1b0_0
entrypoints 0.3 py38_0
expat 2.4.1 h2531618_2
fastrlock 0.8 pypi_0 pypi
ffmpeg 4.3 hf484d3e_0 pytorch
flake8 3.9.2 pyhd3eb1b0_0
fontconfig 2.13.1 h6c09931_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.11.0 h70c0345_0
fsspec 2021.8.1 pyhd3eb1b0_0
giflib 5.2.1 h7b6447c_0
glib 2.69.1 h5202010_0
gmp 6.2.1 h2531618_2
gnutls 3.6.15 he1e5248_0
google-auth 2.3.3 pypi_0 pypi
google-auth-oauthlib 0.4.6 pypi_0 pypi
grpcio 1.42.0 pypi_0 pypi
gst-plugins-base 1.14.0 h8213a91_2
gstreamer 1.14.0 h28cd5cc_2
icu 58.2 he6710b0_3
idna 3.2 pyhd3eb1b0_0
imagecodecs 2021.8.26 py38h4cda21f_0
imageio 2.9.0 pyhd3eb1b0_0
importlab 0.6.1 pypi_0 pypi
importlib-metadata 4.8.1 py38h06a4308_0
importlib_metadata 4.8.1 hd3eb1b0_0
intel-openmp 2021.4.0 h06a4308_3561
ipydatawidgets 4.2.0 pypi_0 pypi
ipykernel 6.4.1 py38h06a4308_1
ipympl 0.8.2 pypi_0 pypi
ipython 7.29.0 py38hb070fc8_0
ipython_genutils 0.2.0 pyhd3eb1b0_1
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
jedi 0.18.0 py38h06a4308_1
jinja2 3.0.2 pyhd3eb1b0_0
joblib 1.1.0 pyhd3eb1b0_0
jpeg 9d h7f8727e_0
json5 0.9.6 pyhd3eb1b0_0
jsonschema 3.2.0 pyhd3eb1b0_2
jupyter_client 7.0.1 pyhd3eb1b0_0
jupyter_core 4.8.1 py38h06a4308_0
jupyter_server 1.4.1 py38h06a4308_0
jupyterlab 3.2.1 pyhd3eb1b0_1
jupyterlab-widgets 1.0.2 pypi_0 pypi
jupyterlab_pygments 0.1.2 py_0
jupyterlab_server 2.8.2 pyhd3eb1b0_0
jxrlib 1.1 h7b6447c_2
kiwisolver 1.3.1 py38h2531618_0
krb5 1.19.2 hac12032_0
lame 3.100 h7b6447c_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.35.1 h7274673_9
lerc 3.0 h295c915_0
libaec 1.0.4 he6710b0_1
libcst 0.3.21 pypi_0 pypi
libcurl 7.78.0 h0b77cf5_0
libdeflate 1.8 h7f8727e_5
libedit 3.1.20210910 h7f8727e_0
libev 4.33 h7f8727e_1
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgfortran-ng 7.5.0 ha8ba4b0_17
libgfortran4 7.5.0 ha8ba4b0_17
libgomp 9.3.0 h5101ec6_17
libiconv 1.15 h63c8f33_5
libidn2 2.3.2 h7f8727e_0
libnghttp2 1.41.0 hf8bcb03_2
libpng 1.6.37 hbc83047_0
libsodium 1.0.18 h7b6447c_0
libssh2 1.9.0 h1ba5d50_1
libstdcxx-ng 9.3.0 hd4cf53a_17
libtasn1 4.16.0 h27cfd23_0
libtiff 4.2.0 h85742a9_0
libunistring 0.9.10 h27cfd23_0
libuuid 1.0.3 h7f8727e_2
libuv 1.40.0 h7b6447c_0
libwebp 1.2.0 h89dd481_0
libwebp-base 1.2.0 h27cfd23_0
libxcb 1.14 h7b6447c_0
libxml2 2.9.12 h03d6c58_0
libzopfli 1.0.3 he6710b0_0
locket 0.2.1 py38h06a4308_1
lz4-c 1.9.3 h295c915_1
markdown 3.3.6 pypi_0 pypi
markupsafe 2.0.1 py38h27cfd23_0
matplotlib 3.4.3 py38h06a4308_0
matplotlib-base 3.4.3 py38hbbc1b5f_0
matplotlib-inline 0.1.2 pyhd3eb1b0_2
mccabe 0.6.1 py38_1
mistune 0.8.4 py38h7b6447c_1000
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py38h7f8727e_0
mkl_fft 1.3.1 py38hd3c417c_0
mkl_random 1.2.2 py38h51133e4_0
monai 0.7.0 pypi_0 pypi
munkres 1.1.4 py_0
mypy 0.910 pyhd3eb1b0_0
mypy_extensions 0.4.3 py38_0
nbclassic 0.2.6 pyhd3eb1b0_0
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
pandocfilters 1.4.3 py38h06a4308_1
param 1.12.0 pypi_0 pypi
parameterized 0.8.1 pyhd3eb1b0_1
parso 0.8.2 pyhd3eb1b0_0
partd 1.2.0 pyhd3eb1b0_0
pathspec 0.7.0 py_0
pcre 8.45 h295c915_0
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 8.4.0 py38h5aabda8_0
pip 21.2.4 py38h06a4308_0
prometheus_client 0.11.0 pyhd3eb1b0_0
prompt-toolkit 3.0.20 pyhd3eb1b0_0
protobuf 3.19.1 pypi_0 pypi
psutil 5.8.0 py38h27cfd23_1
ptyprocess 0.7.0 pyhd3eb1b0_2
pyasn1 0.4.8 pypi_0 pypi
pyasn1-modules 0.2.8 pypi_0 pypi
pycodestyle 2.7.0 pyhd3eb1b0_0
pycparser 2.20 py_2
pyct 0.4.8 pypi_0 pypi
pyflakes 2.3.1 pyhd3eb1b0_0
pygments 2.10.0 pyhd3eb1b0_0
pyopenssl 21.0.0 pyhd3eb1b0_1
pyparsing 3.0.4 pyhd3eb1b0_0
pyqt 5.9.2 py38h05f1152_4
pyrsistent 0.18.0 py38heee7806_0
pysocks 1.7.1 py38h06a4308_0
python 3.8.12 h12debd9_0
python-dateutil 2.8.2 pyhd3eb1b0_0
pytorch 1.10.0 py3.8_cuda10.2_cudnn7.6.5_0 pytorch
pytorch-ignite 0.4.7 pypi_0 pypi
pytorch-mutex 1.0 cuda pytorch
pytype 2021.11.18 pypi_0 pypi
pytz 2021.3 pyhd3eb1b0_0
pywavelets 1.1.1 py38h7b6447c_2
pyyaml 6.0 py38h7f8727e_1
pyzmq 22.2.1 py38h295c915_1
qt 5.9.7 h5867ecd_1
readline 8.1 h27cfd23_0
regex 2021.8.3 py38h7f8727e_0
requests 2.26.0 pyhd3eb1b0_0
requests-oauthlib 1.3.0 pypi_0 pypi
rsa 4.8 pypi_0 pypi
scikit-image 0.18.3 py38h51133e4_0
scikit-learn 1.0.1 py38h51133e4_0
scipy 1.7.1 py38h292c36d_2
send2trash 1.8.0 pyhd3eb1b0_1
setuptools 58.0.4 py38h06a4308_0
sip 4.19.13 py38he6710b0_0
six 1.16.0 pyhd3eb1b0_0
snappy 1.1.8 he6710b0_0
sniffio 1.2.0 py38h06a4308_1
sqlite 3.36.0 hc218d9a_0
tabulate 0.8.9 pypi_0 pypi
tensorboard 2.7.0 pypi_0 pypi
tensorboard-data-server 0.6.1 pypi_0 pypi
tensorboard-plugin-wit 1.8.0 pypi_0 pypi
terminado 0.9.4 py38h06a4308_0
testpath 0.5.0 pyhd3eb1b0_0
threadpoolctl 2.2.0 pyh0d69192_0
tifffile 2021.7.2 pyhd3eb1b0_2
tk 8.6.11 h1ccaba5_0
toml 0.10.2 pyhd3eb1b0_0
toolz 0.11.1 pyhd3eb1b0_0
torchinfo 1.5.3 pypi_0 pypi
torchvision 0.11.1 py38_cu102 pytorch
tornado 6.1 py38h27cfd23_0
traitlets 5.1.0 pyhd3eb1b0_0
traittypes 0.2.1 pypi_0 pypi
typed-ast 1.5.0 pypi_0 pypi
typing-inspect 0.7.1 pypi_0 pypi
typing_extensions 3.10.0.2 pyh06a4308_0
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
wheel 0.37.0 pyhd3eb1b0_1
widgetsnbextension 3.5.2 pypi_0 pypi
xz 5.2.5 h7b6447c_0
yaml 0.2.5 h7b6447c_0
zeromq 4.3.4 h2531618_0
zfp 0.5.5 h2531618_6
zipp 3.6.0 pyhd3eb1b0_0
zlib 1.2.11 h7b6447c_3
zstandard 0.16.0 pypi_0 pypi
zstd 1.4.9 haebb681_0

aylward · 2021-11-24T15:54:05Z

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

aylward · 2021-11-24T15:59:06Z

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 · 2021-11-24T16:09:29Z

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 · 2021-11-24T16:36:26Z

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

aylward · 2021-11-24T17:36:52Z

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

Signed-off-by: Nic Ma <[email protected]>

Nic-Ma · 2021-11-24T23:57:28Z

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.

* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * Update spleen_segmentation_3d.ipynb (#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]> Co-authored-by: Dong Yang <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: nvahmadi <[email protected]> Co-authored-by: Vishwesh <[email protected]> Co-authored-by: vnath <[email protected]> Co-authored-by: myron <[email protected]> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * Update spleen_segmentation_3d.ipynb (#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]>

* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * Update spleen_segmentation_3d.ipynb (#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change arch code keys * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]>

* [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]>

* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (Project-MONAI#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * Update spleen_segmentation_3d.ipynb (Project-MONAI#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (Project-MONAI#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (Project-MONAI#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (Project-MONAI#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (Project-MONAI#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (Project-MONAI#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (Project-MONAI#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]> Co-authored-by: Dong Yang <[email protected]> Co-authored-by: Nic Ma <[email protected]> Co-authored-by: nvahmadi <[email protected]> Co-authored-by: Vishwesh <[email protected]> Co-authored-by: vnath <[email protected]> Co-authored-by: myron <[email protected]> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Yiheng Wang <[email protected]> Co-authored-by: Wenqi Li <[email protected]>

* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (Project-MONAI#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * Update spleen_segmentation_3d.ipynb (Project-MONAI#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (Project-MONAI#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (Project-MONAI#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (Project-MONAI#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (Project-MONAI#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (Project-MONAI#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (Project-MONAI#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]>

* initialize dints tutorials Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update README.md * Update README.md * update scripts Signed-off-by: dongy <[email protected]> * Change Dints interface * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Modify scripts for new Dints interface * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Test push * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update readme Signed-off-by: Dong Yang <[email protected]> * Add readme * Update readme * Change lr in search * update readme Signed-off-by: Dong Yang <[email protected]> * Enable single GPU * update readme Signed-off-by: Dong Yang <[email protected]> * Add visualization tutorial transform image (Project-MONAI#448) * [DLMED] add visualization tutorial Signed-off-by: Nic Ma <[email protected]> * [DLMED] add image Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] update notebook Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference image Signed-off-by: Nic Ma <[email protected]> * [DLMED] fix PEP error Signed-off-by: Nic Ma <[email protected]> * Update spleen_segmentation_3d.ipynb (Project-MONAI#455) The `pip install` statement is missing pytorch-ignite. Changing: `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm]"` to `!python -c "import monai" || pip install -q "monai-weekly[gdown, nibabel, tqdm, ignite]"` * Figures added, pretrained weights link added, minor fixes (Project-MONAI#456) * Figures added, pretrained weights link added, minor fixes Signed-off-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: vnath <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add itkwidgets example in notebook (Project-MONAI#454) * [DLMED] add itkwidgets Signed-off-by: Nic Ma <[email protected]> * [DLMED] add reference screenshot Signed-off-by: Nic Ma <[email protected]> * [DLMED] update to PLS orientation Signed-off-by: Nic Ma <[email protected]> * MIL example (Project-MONAI#431) * MIL example Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * mil tutorial update Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * small updates Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * updated images Signed-off-by: myron <[email protected]> * gdown for json Signed-off-by: myron <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README Signed-off-by: Behrooz <[email protected]> * Fix formatting and typos Signed-off-by: Behrooz <[email protected]> * small fixes Signed-off-by: myron <[email protected]> * stats Signed-off-by: myron <[email protected]> * pip install Signed-off-by: myron <[email protected]> * README fixes Signed-off-by: myron <[email protected]> Co-authored-by: am <am> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Behrooz <[email protected]> Co-authored-by: Nic Ma <[email protected]> * 450 update AsDiscrete (Project-MONAI#451) * update asdiscrete Signed-off-by: Yiheng Wang <[email protected]> * update postprocessing figures Signed-off-by: Yiheng Wang <[email protected]> * fix version error of mutual info Signed-off-by: Yiheng Wang <[email protected]> * update to use include in torchin Signed-off-by: Yiheng Wang <[email protected]> * 459 update nvidia flare 2.0 example (Project-MONAI#460) * update nvidia flare 2.0 example Signed-off-by: Yiheng Wang <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * enhance code format Signed-off-by: Yiheng Wang <[email protected]> * update folder and readme Signed-off-by: Yiheng Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Weights Link Updated (Project-MONAI#465) Signed-off-by: vnath <[email protected]> Co-authored-by: vnath <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes readme typos Signed-off-by: Wenqi Li <[email protected]> * update readmes Signed-off-by: Wenqi Li <[email protected]> * update readme Signed-off-by: Wenqi Li <[email protected]> * qa commit Signed-off-by: Wenqi Li <[email protected]> * link Signed-off-by: Wenqi Li <[email protected]> * Add plot arch_code utils * Fix bugs in search and update readme * Fix combination weights bug * Small typo update * Fix minor bug in train_dints * update scripts Signed-off-by: dongy <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: dongy <[email protected]> * Update Readme * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Change arch code keys * update scripts Signed-off-by: Dong Yang <[email protected]> * update scripts Signed-off-by: Dong Yang <[email protected]> Co-authored-by: dongy <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: heyufan1995 <[email protected]>

[DLMED] add itkwidgets

8aee1b6

Signed-off-by: Nic Ma <[email protected]>

[DLMED] add reference screenshot

cc2de4a

Signed-off-by: Nic Ma <[email protected]>

Nic-Ma requested review from aylward, ericspod, rijobro and wyli November 24, 2021 09:52

Nic-Ma mentioned this pull request Nov 24, 2021

transform documentation enhancements Project-MONAI/MONAI#2721

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aylward mentioned this pull request Nov 24, 2021

Display a clear warning when unsupported data is passed to the view command InsightSoftwareConsortium/itkwidgets#435

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wyli approved these changes Nov 24, 2021

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Nic-Ma added 2 commits November 25, 2021 07:54

[DLMED] update to PLS orientation

44fb189

Signed-off-by: Nic Ma <[email protected]>

Merge branch 'master' into add-itkwidgets-example

d8e4b43

Nic-Ma merged commit 54b47f9 into master Nov 25, 2021

Nic-Ma deleted the add-itkwidgets-example branch November 25, 2021 01:32

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