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TUM-CAMP-Networks-Contribution #5921

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vgonzalezd opened this issue Jan 31, 2023 · 1 comment · Fixed by #6306
Closed

TUM-CAMP-Networks-Contribution #5921

vgonzalezd opened this issue Jan 31, 2023 · 1 comment · Fixed by #6306
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@vgonzalezd
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@vgonzalezd
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We would like to contribute with 3 refactored networks codes in MONAI

DAF3D:
Wang, Y., Dou, H., Hu, X., Zhu, L., Yang, X., Xu, M., ... & Ni, D. (2019). Deep attentive features for prostate segmentation in 3D transrectal ultrasound. IEEE transactions on medical imaging, 38(12), 2768-2778.
https://github.com/wulalago/DAF3D/blob/master/README.md

QuickNAT:
Roy, A. G., Conjeti, S., Navab, N., Wachinger, C., & Alzheimer's Disease Neuroimaging Initiative. (2019). QuickNAT: A fully convolutional network for quick and accurate segmentation of neuroanatomy. NeuroImage, 186, 713-727.
https://www.sciencedirect.com/science/article/abs/pii/S1053811918321232

IFSSnet:
Al Chanti, D., Duque, V. G., Crouzier, M., Nordez, A., Lacourpaille, L., & Mateus, D. (2021). IFSS-Net: Interactive few-shot siamese network for faster muscle segmentation and propagation in volumetric ultrasound. IEEE transactions on medical imaging, 40(10), 2615-2628.
https://hal.science/hal-03197457/document
@wyli
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wyli commented Jan 31, 2023

please let us know if you have any questions, the contributing guide has some info about creating pull requests in MONAI https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md#preparing-pull-requests

@vgonzalezd vgonzalezd mentioned this issue Apr 5, 2023
Merged
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wyli pushed a commit that referenced this issue Jun 24, 2023
@vgonzalezd @ge96lip
@ericspod @pre-commit-ci @Al3xand1a
CAMP-TUM network contributions: Quicknat and Daf3D (#6306)
0ffe55a 
Fixes #5921 

### Description

@Al3xand1a and @ge96lip implement DAF3D[1] and Quicknat[2] networks and
test them in open-source and local datasets. We use as a baseline the
pytorch codes available in [3] and [4]
We are quite confident about the implementation, but feel free to
contact us if you find errors. For any questions send us an email to
ge45qix@mytum.de

We have some questions for the contribution:
For Quicknat:
1) we add the sequential class file in the networks folder because we do
not know where to add it.
2) How do we include the squeeze and excitation requirement (sse and
Csse) if it comes from a GitHub repository?

https://github.com/ai-med/nn-common-modules/releases/download/v1.1/nn_common_modules-1.3-py3-none-any.whl
For Daf3D
3) Are the overwritten blocks fine as they are? or do they have to be
more flexible?
For both:
We run this command line (`./runtests.sh --quick --unittests
--disttests`) but the error we are getting is not related to our
changes, so we run our unit_test independently and they work. Same with
documentation.
 
[1] Deep Attentive Features for Prostate Segmentation in 3D Transrectal
Ultrasound.
Yi Wang, Haoran Dou, Xiaowei Hu, Lei Zhu, Xin Yang, Ming Xu, Jing Qin,
Pheng-Ann Heng, Tianfu Wang, and Dong Ni.
IEEE Transactions on Medical Imaging, 2019.
[2] Roy, A. G., Conjeti, S., Navab, N., Wachinger, C., & Alzheimer's
Disease Neuroimaging Initiative. (2019). QuickNAT: A fully convolutional
network for quick and accurate segmentation of neuroanatomy. NeuroImage,
186, 713-727.
[3] https://github.com/ai-med/quickNAT_pytorch
[4] https://github.com/wulalago/DAF3D

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: ge96lip <73938628+ge96lip@users.noreply.github.com>
Signed-off-by: vanessagd.2395 <vanessa.gonzalez-duque@eleves.ec-nantes.fr>
Signed-off-by: Al3xand1a <98582325+Al3xand1a@users.noreply.github.com>
Co-authored-by: Alexandra Marquardt <alexandra@MBPvonAlexandra.fritz.box>
Co-authored-by: Carlotta <carlotta.hoelzle@icloud.com>
Co-authored-by: Alexandra Marquardt <alexandra@w223-2e-v4.eduroam.dynamic.rbg.tum.de>
Co-authored-by: Vanessa <vanessa.gonzalezduque@ls2n.fr>
Co-authored-by: ge96lip <73938628+ge96lip@users.noreply.github.com>
Co-authored-by: “Vanessa <“vanessa.gonzalezduque@ls2n.fr”>
Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alexandra Marquardt <alexandra@w192-1i-v4.eduroam.dynamic.rbg.tum.de>
Co-authored-by: Al3xand1a <98582325+Al3xand1a@users.noreply.github.com>
Co-authored-by: Alexandra Marquardt <alexandra@w217-4n-v4.eduroam.dynamic.rbg.tum.de>
bhashemian pushed a commit to bhashemian/MONAI that referenced this issue Jun 26, 2023
@vgonzalezd @ge96lip
@ericspod @pre-commit-ci @Al3xand1a @bhashemian
CAMP-TUM network contributions: Quicknat and Daf3D (Project-MONAI#6306)
9f44549 
Fixes Project-MONAI#5921 

### Description

@Al3xand1a and @ge96lip implement DAF3D[1] and Quicknat[2] networks and
test them in open-source and local datasets. We use as a baseline the
pytorch codes available in [3] and [4]
We are quite confident about the implementation, but feel free to
contact us if you find errors. For any questions send us an email to
ge45qix@mytum.de

We have some questions for the contribution:
For Quicknat:
1) we add the sequential class file in the networks folder because we do
not know where to add it.
2) How do we include the squeeze and excitation requirement (sse and
Csse) if it comes from a GitHub repository?

https://github.com/ai-med/nn-common-modules/releases/download/v1.1/nn_common_modules-1.3-py3-none-any.whl
For Daf3D
3) Are the overwritten blocks fine as they are? or do they have to be
more flexible?
For both:
We run this command line (`./runtests.sh --quick --unittests
--disttests`) but the error we are getting is not related to our
changes, so we run our unit_test independently and they work. Same with
documentation.
 
[1] Deep Attentive Features for Prostate Segmentation in 3D Transrectal
Ultrasound.
Yi Wang, Haoran Dou, Xiaowei Hu, Lei Zhu, Xin Yang, Ming Xu, Jing Qin,
Pheng-Ann Heng, Tianfu Wang, and Dong Ni.
IEEE Transactions on Medical Imaging, 2019.
[2] Roy, A. G., Conjeti, S., Navab, N., Wachinger, C., & Alzheimer's
Disease Neuroimaging Initiative. (2019). QuickNAT: A fully convolutional
network for quick and accurate segmentation of neuroanatomy. NeuroImage,
186, 713-727.
[3] https://github.com/ai-med/quickNAT_pytorch
[4] https://github.com/wulalago/DAF3D

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] New tests added to cover the changes.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: ge96lip <73938628+ge96lip@users.noreply.github.com>
Signed-off-by: vanessagd.2395 <vanessa.gonzalez-duque@eleves.ec-nantes.fr>
Signed-off-by: Al3xand1a <98582325+Al3xand1a@users.noreply.github.com>
Co-authored-by: Alexandra Marquardt <alexandra@MBPvonAlexandra.fritz.box>
Co-authored-by: Carlotta <carlotta.hoelzle@icloud.com>
Co-authored-by: Alexandra Marquardt <alexandra@w223-2e-v4.eduroam.dynamic.rbg.tum.de>
Co-authored-by: Vanessa <vanessa.gonzalezduque@ls2n.fr>
Co-authored-by: ge96lip <73938628+ge96lip@users.noreply.github.com>
Co-authored-by: “Vanessa <“vanessa.gonzalezduque@ls2n.fr”>
Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alexandra Marquardt <alexandra@w192-1i-v4.eduroam.dynamic.rbg.tum.de>
Co-authored-by: Al3xand1a <98582325+Al3xand1a@users.noreply.github.com>
Co-authored-by: Alexandra Marquardt <alexandra@w217-4n-v4.eduroam.dynamic.rbg.tum.de>
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CAMP-TUM network contributions: Quicknat and Daf3D vgonzalezd/MONAI
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@wyli @vgonzalezd