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CAMP-TUM network contributions: Quicknat and Daf3D (Project-MONAI#6306)
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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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12 people authored and drbeh committed Jun 26, 2023
1 parent 6cc5020 commit 9f44549
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4 changes: 4 additions & 0 deletions .gitignore
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# profiling results
*.prof
runs

*.gz

*.pth
2 changes: 1 addition & 1 deletion monai/networks/blocks/denseblock.py
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from __future__ import annotations

from collections.abc import Sequence
from typing import Sequence

import torch
import torch.nn as nn
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2 changes: 2 additions & 0 deletions monai/networks/nets/__init__.py
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from .basic_unet import BasicUNet, BasicUnet, Basicunet, basicunet
from .basic_unetplusplus import BasicUNetPlusPlus, BasicUnetPlusPlus, BasicunetPlusPlus, basicunetplusplus
from .classifier import Classifier, Critic, Discriminator
from .daf3d import DAF3D
from .densenet import (
DenseNet,
Densenet,
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from .hovernet import Hovernet, HoVernet, HoVerNet, HoverNet
from .milmodel import MILModel
from .netadapter import NetAdapter
from .quicknat import Quicknat
from .regressor import Regressor
from .regunet import GlobalNet, LocalNet, RegUNet
from .resnet import (
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