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CAMP-TUM network contributions: Quicknat and Daf3D #6306

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merged 84 commits into from
Jun 24, 2023
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99f4c5d
initial commit, reformatted original files
Feb 5, 2023
f796381
initial commit, reformated original monai files
Feb 5, 2023
f03baae
initial commit, reformated original monai files
Feb 5, 2023
916b58b
blocks and network structures for daf3d
Feb 6, 2023
6717c12
basic code reformatting
Feb 8, 2023
a3864ed
unit test and greater input variability
Feb 9, 2023
d86c80b
quicknat network and quicknat test
Feb 16, 2023
3627c8e
quicknat network and quicknat test
Feb 17, 2023
3cac0dc
Merge branch '5921-Quicknat' into 5921-TUM-CAMP-Networks-Contribution
Feb 20, 2023
c52c351
Merge branch '5921-DAF3D' into 5921-TUM-CAMP-Networks-Contribution
Feb 20, 2023
dc24c46
Merge branch 'dev' into 5921-TUM-CAMP-Networks-Contribution
Feb 20, 2023
df7a97c
reset to non-variable blocks, not all format tests passing yet
Feb 20, 2023
2ad7e27
fixed return in training mode
Feb 20, 2023
90bb7c6
Merge branch '5921-DAF3D' into 5921-TUM-CAMP-Networks-Contribution
Feb 24, 2023
a63d8c6
Merge branch 'dev' into 5921-TUM-CAMP-Networks-Contribution
Feb 24, 2023
01ad50f
included convConcatDenseBlock, Encoder, Decoder, bottleneck
ge96lip Feb 24, 2023
d1448c5
added classifier block
ge96lip Feb 24, 2023
75ac889
added skipwithidx
ge96lip Feb 24, 2023
da124bc
added Bottleneck, ConvConcatDenseBloc, Decoder, Encoder to init
ge96lip Feb 24, 2023
33e15f2
SkipConnectionWithIdx to init
ge96lip Feb 24, 2023
c7929b0
from .quicknat import Quicknat to init
ge96lip Feb 24, 2023
9f3aba6
final changes
ge96lip Feb 24, 2023
fdf4f09
Merge branch '5921-Quicknat' into 5921-TUM-CAMP-Networks-Contribution
Feb 24, 2023
0d2782d
ClassifierBlock imported from blocks.convolutions
Feb 24, 2023
73688eb
Black reformating of Quicknat
Feb 24, 2023
c55aca8
Update with dev branch
Apr 5, 2023
14fba3b
Merge branch '5921-TUM-CAMP-Networks-Contribution' into dev
Apr 5, 2023
cb863a3
Merge branch 'Project-MONAI:dev' into dev
vgonzalezd Apr 5, 2023
734bc19
Squeeze import using monai.utils.optional_import
Apr 6, 2023
b5c27ed
Ortography error
Apr 6, 2023
8bce035
Merge remote-tracking branch 'upstream/dev' into dev
Apr 6, 2023
ed906f9
Merge branch '5921-TUM-CAMP-Networks-Contribution' into dev
Apr 6, 2023
bdc5b52
Update .gitignore deleting absolut paths
vgonzalezd Jun 20, 2023
161161d
Update monai/networks/blocks/backbone_fpn_utils.py
vgonzalezd Jun 20, 2023
65929b0
Update convolutions.py
vgonzalezd Jun 20, 2023
bc9dbc2
Update monai/networks/blocks/denseblock.py
vgonzalezd Jun 20, 2023
cc12a67
Updated the constructor of ConvConcatDense
ge96lip Jun 20, 2023
082f25d
Update monai/networks/layers/simplelayers.py
vgonzalezd Jun 20, 2023
64be058
Update import squeeze_and_excitation
ge96lip Jun 20, 2023
0eb7ee7
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 20, 2023
54c9683
rearranged daf3d blocks into daf3d main file
Jun 20, 2023
1f8cfb3
merged all changes
Jun 20, 2023
aab1dcf
set the optional import to the other imports at the beginning
ge96lip Jun 20, 2023
c0a144f
fixed codeformat
Jun 20, 2023
9adb4d3
deleted @export("monai.networks.nets") from quicknat.py
ge96lip Jun 20, 2023
785ddc7
Merge branch 'dev' of github.com:vgonzalezd/MONAI into dev
Jun 20, 2023
5f88e73
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 20, 2023
c2ee13f
fixed codeformat
Jun 20, 2023
eb1ee70
merge
Jun 20, 2023
f1a4740
excluding ClassifierBlock in convolutions.py
ge96lip Jun 21, 2023
34d4031
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 21, 2023
5c54a70
Included ClassifiertBlock into quicknat.py
ge96lip Jun 21, 2023
55f2f5c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 21, 2023
994a71c
Included SkipConnectionWithIdx into Quicknat
ge96lip Jun 21, 2023
69aa7b0
took out all quicknat specific blocks
ge96lip Jun 21, 2023
3c51089
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 21, 2023
0641547
Quicknat specific blocks included
ge96lip Jun 21, 2023
73cc2db
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 21, 2023
fcd3b48
small adaptions to import
ge96lip Jun 21, 2023
fbe7db5
deleted SkipConnectionsWithIdx
ge96lip Jun 21, 2023
aca8b31
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 21, 2023
321e13e
deleted old reverences to quicknat specific blocks denseblock.py
ge96lip Jun 21, 2023
5cfd78f
deleted SkipConnectionWithIdx from __init__.py as it now is in quickn…
ge96lip Jun 21, 2023
e4d88b2
codeformat and block initialization according to new class arrangement
Jun 21, 2023
fcee6f6
Skip Quicknat test if squeeze-and-excitation not installed
Al3xand1a Jun 21, 2023
32973d6
Skip daf3d test if torch vision not installed
Al3xand1a Jun 21, 2023
15caa82
Update test_daf3d.py typo
Al3xand1a Jun 21, 2023
bafce62
type check for default se_layer and dropout layer in quicknat.py line…
ge96lip Jun 22, 2023
6b01218
codeformat
Jun 22, 2023
3599a43
Merge branch 'dev' of github.com:vgonzalezd/MONAI into dev
Jun 22, 2023
5c259b5
deleted enable_test_dropout() in quicknat.py
ge96lip Jun 22, 2023
e0f2139
Merge branch 'dev' of github.com:vgonzalezd/MONAI into dev
Jun 22, 2023
20e29df
codeformat
Jun 22, 2023
6f29896
fixed mypy issues in daf3d
Al3xand1a Jun 24, 2023
f007315
codeformat and mypy in daf3d
Jun 24, 2023
cebf558
workaround for type check
ge96lip Jun 24, 2023
bd8e997
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 24, 2023
d75bd8d
Update monai/networks/nets/daf3d.py
Al3xand1a Jun 24, 2023
a0daad1
Added import of Optional
Al3xand1a Jun 24, 2023
82b8edd
Merge branch 'dev' into dev
wyli Jun 24, 2023
fd3196b
Update tests/test_daf3d.py
wyli Jun 24, 2023
999cf95
Update daf3d.py
Al3xand1a Jun 24, 2023
83dafd9
changed the default assignment for se_layer and dropout2d
ge96lip Jun 24, 2023
0b8fd2d
cleaned up code quicknat.py
ge96lip Jun 24, 2023
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4 changes: 4 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -150,3 +150,7 @@ tests/testing_data/CT_2D_head_moving.mha
# profiling results
*.prof
runs

*.gz

*.pth
2 changes: 1 addition & 1 deletion monai/networks/blocks/denseblock.py
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@

from __future__ import annotations

from collections.abc import Sequence
from typing import Sequence

import torch
import torch.nn as nn
Expand Down
2 changes: 2 additions & 0 deletions monai/networks/nets/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
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,
Expand Down Expand Up @@ -51,6 +52,7 @@
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 (
Expand Down
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