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Op mri #101

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michalozeryflato and others added 30 commits May 24, 2022 11:45
@michalozeryflato
initial code from Tal
32666cb
@michalozeryflato
initial running example
4b9f1bf
@michalozeryflato
backup running example (3 first ops)
1f6ddcd
@michalozeryflato
working on the third and forth operator
cb11fd9
@michalozeryflato
add initial version of duke dataset
f71b7c3
@michalozeryflato
initial version of complete MRI processing pipeline
92e0b01
@michalozeryflato
backup changes
5312017
@michalozeryflato
Merge branch 'fuse2' of github.com:IBM/fuse-med-ml into op_mri
a09a963
@michalozeryflato
fixing imports in duke_breast_cancer old code
b79d2a5
@michalozeryflato
backup changes - startting to work on adding labels + runner_duke
2b8beb9
data_cuaration for duke
75e7735
Merge branch 'op_mri' of github.com:IBM/fuse-med-ml into op_mri
346b37a
new version for data curation
5329ac4
add lesion properties operations
e7ab739
data curation file, contain pre-preprocessing functions
ee8e248
@michalozeryflato
backup fixes. runner_duke throws an exception:
6f4c512 
RuntimeError: Given groups=1, weight of size [16, 1, 3, 3, 3], expected input[2, 2, 9, 100, 100] to have 1 channels, but got 2 channels instead

Although input dimentions seems to match those of [Fuse1]processor code
@michalozeryflato
Merge branch 'op_mri' of github.com:IBM/fuse-med-ml into op_mri
7f46051 
� Conflicts:
�	fuseimg/datasets/duke.py
add radiomics Op
f83be44
add radiomics processing functions
c0875cc
add radiomics
5ede2f0
merge op
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''
c58337c
''
a06bbac
add radiomics op
dc9ad94
minor change
3ae6a41
delete=false
787a961
delete tmp file
007fab3
@michalozeryflato
backup first version of duke running example in Fuse2
344f688
@michalozeryflato
no global variables
df1efc5
@michalozeryflato
backup first version of duke running example in Fuse2
082797a
michalozeryflato and others added 26 commits June 28, 2022 08:26
@michalozeryflato
start re-org and cleaning of duke and prostate_x
c08977b
@michalozeryflato
clean prostate_x and duke code
e119b91
@michalozeryflato
minor delete of a comment
24f0135
@michalozeryflato
Merge remote-tracking branch 'origin/op_mri_v2' into op_mri_v2
76da4e2
@michalozeryflato
Merge pull request #120 from IBM/op_mri_v2
90da516 
Op mri v2
@michalozeryflato
ProstateX: remove dependency in Tal's processed file
1eb0289
@michalozeryflato
Merge branch 'op_mri' into op_mri_v2
f39825b
@michalozeryflato
Merge pull request #123 from IBM/op_mri_v2
1e877e0 
ProstateX: remove dependency in Tal's processed file
@michalozeryflato
fix the problem in prostate_x by removing 5 samples
97f0975
@michalozeryflato
Merge remote-tracking branch 'origin/fuse2' into op_mri
cb308da 
# Conflicts:
#	examples/fuse_examples/imaging/classification/duke_breast_cancer/run_train_3dpatch.py
#	examples/fuse_examples/imaging/classification/prostate_x/run_train_3dpatch.py
#	examples/fuse_examples/imaging/utils/backbone_3d_multichannel.py
#	fuse/data/ops/ops_common.py
#	fuseimg/data/ops/aug/geometry.py
#	requirements.txt
@michalozeryflato
create folds file keeping each patient's samples within the same fold.
4583832 
Allow CacheSampler not to use pipeline hash in the name of the cache directory. start cleaning the code
@michalozeryflato
handle pull request comments, such as using existing operations
3d90670
@michalozeryflato
Merge branch 'fuse2' of github.com:IBM/fuse-med-ml into op_mri
ea1522a 
� Conflicts:
�	fuse/data/utils/split.py
�	requirements.txt
@michalozeryflato
initial (non-working) version of runner_prostate_x with ManagerDefaul…
d98f01d 
…t replaced with LightningModuleDefault
@michalozeryflato
adding test code for duke; fixing mask in duke to be integer.
beef102
@michalozeryflato
fix user_path_home to be optional in duke and prostatex examples
b5e313c
@michalozeryflato
Merge branch 'fuse2' of github.com:IBM/fuse-med-ml into op_mri
aeecf25 
� Conflicts:
�	fuseimg/data/ops/aug/geometry.py
@michalozeryflato
cancel @run_in_subprocess - to locate errors
60d8a6e
@michalozeryflato
add test for prostatex
b754c0d
@michalozeryflato
return sub-process in test
4e9d35f
@michalozeryflato
modify run_multiprocessed.py to get subprocess error
68c8452
@michalozeryflato
run_multiprocessed.py: fixing printing of error
8f4e0f5
@michalozeryflato
debegging
a44c086
@mosheraboh
run tests with prev run in subprocess
6d7c8e8
@michalozeryflato
replace exmaples.fuse_examples with fuse_examples
15991bf
@michalozeryflato
Merge remote-tracking branch 'origin/op_mri' into op_mri
68cc65d
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@michalozeryflato @mosheraboh @SagiPolaczek