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3D U-Net TensorFlow workspace for BraTS 2020 #108

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merged 67 commits into from Aug 5, 2021
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6c3f998
3D U-Net for BraTS
tonyreina Jun 19, 2021
f41eb9b
Remove
tonyreina Jun 20, 2021
3505463
Update moving UNet
tonyreina Jun 20, 2021
56c0108
Refactoring define_model
tonyreina Jun 20, 2021
c4ec443
Working copy of 3D U-Net for BraTS
tonyreina Jun 22, 2021
dd60cba
Update data.yaml
tonyreina Jun 22, 2021
bd1b2f2
Update tf_3dunet_model.py
tonyreina Jun 22, 2021
cb34ac7
Update define_model.py
tonyreina Jun 22, 2021
833040b
Crop dimension, input and output dimensions
tonyreina Jun 22, 2021
03037da
Update plan.yaml
tonyreina Jun 22, 2021
a3e9b28
Bug fix for num_classes
tonyreina Jun 22, 2021
b7ed09f
Merge branch 'intel:develop' into develop
tonyreina Jun 22, 2021
51edb4f
Update README.md
tonyreina Jun 22, 2021
80c2055
Adding split_directory script
tonyreina Jun 22, 2021
f2905d4
Update define_model.py
tonyreina Jun 22, 2021
65d93f8
Update split_directory.sh
tonyreina Jun 22, 2021
ee56d7a
Update README.md
tonyreina Jun 22, 2021
572f6ce
Update split_directory.sh
tonyreina Jun 22, 2021
f492536
More parameters passed to model definition from plan.yaml
tonyreina Jun 22, 2021
c363445
More parameters passed to model definition from plan.yaml
tonyreina Jun 22, 2021
3a19a48
Update README.md
tonyreina Jun 22, 2021
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tonyreina Jun 22, 2021
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tonyreina Jun 22, 2021
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tonyreina Jun 22, 2021
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tonyreina Jun 22, 2021
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tonyreina Jun 22, 2021
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tonyreina Jun 22, 2021
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tonyreina Jun 22, 2021
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Update plan
tonyreina Jun 22, 2021
53f9e76
Updating check
tonyreina Jun 22, 2021
4e83cc9
Updating check
tonyreina Jun 22, 2021
6998a49
Bug fix in define_model. Changed some defaults
tonyreina Jun 22, 2021
d384814
Update cols.yaml
tonyreina Jun 22, 2021
f692dad
Update data.yaml
tonyreina Jun 22, 2021
691377d
Update plan.yaml
tonyreina Jun 22, 2021
c8af978
Modifiying data directory
tonyreina Jun 22, 2021
24ee1c2
Update tasks_fast_estimator.yaml
tonyreina Jun 23, 2021
85e873d
Update tf_brats_dataloader.py
tonyreina Jun 24, 2021
fdcccb9
Update plan.yaml
tonyreina Jun 24, 2021
cf3e446
Possible bug with db_stored_rounds. If it is 1, then it causes error …
tonyreina Jun 24, 2021
8fa804f
Update tf_3dunet_model.py
tonyreina Jun 24, 2021
80f95cd
Update __init__.py
tonyreina Jun 24, 2021
cf2f9ae
Update tf_brats_dataloader.py
tonyreina Jun 24, 2021
ae0e45b
_init__.py updated
tonyreina Jun 24, 2021
b7b85bf
_init__.py updated
tonyreina Jun 24, 2021
72648c7
Trying to get __init__ to work
tonyreina Jun 24, 2021
e1d1853
Missing files
tonyreina Jun 24, 2021
82c3c7f
Update test_hello_federation.sh
tonyreina Jun 24, 2021
412cc83
Update runner_keras.py
tonyreina Jun 24, 2021
74044e1
Update runner_keras.py
tonyreina Jun 24, 2021
60221b0
Flake8 fixes
tonyreina Jun 27, 2021
b0ae9bb
Merge branch 'develop' of github.com:tonyreina/openfl into develop
tonyreina Jun 27, 2021
4e6bed7
Update cert check on collaborator
tonyreina Jun 27, 2021
f119544
Merge branch 'intel:develop' into develop
tonyreina Jul 6, 2021
8c7f372
Flake8 fixes
tonyreina Jul 7, 2021
6b1a9b6
Merge branch 'intel:develop' into develop
tonyreina Jul 7, 2021
99f4f85
Flake8
tonyreina Jul 7, 2021
38cb5fe
Requested changes: tensorflow->tf; add check for existing directory; …
tonyreina Jul 8, 2021
f3517aa
Adding error exception if no BraTS files are found.
tonyreina Jul 12, 2021
50b7964
Merge branch 'intel:develop' into develop
tonyreina Jul 12, 2021
3a36158
Adding error exception if no BraTS files are found.
tonyreina Jul 12, 2021
61b2804
Bash shell correction for shard directories.
tonyreina Jul 13, 2021
93d10cb
Merge branch 'develop' into tonyreina:develop
itrushkin Aug 4, 2021
100675d
Update test_hello_federation.sh
tonyreina Aug 5, 2021
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11 changes: 10 additions & 1 deletion openfl-workspace/tf_3dunet_brats/src/dataloader.py
Expand Up @@ -36,7 +36,16 @@ def __init__(self, crop_dim,

self.create_file_list()

self.ds_train, self.ds_val, self.ds_test = self.get_dataset()
if self.num_files > 0:
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self.ds_train, self.ds_val, self.ds_test = self.get_dataset()

else:

self.ds_train = None
self.ds_val = None
self.ds_test = None
raise ValueError(f'ERROR: No BraTS datafiles found under directory {self.data_path}')

def create_file_list(self):
"""
Expand Down