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4587 mri utils#4690

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wyli merged 76 commits into
Project-MONAI:devfrom
mersad95zd:4587-mri-utils
Jul 13, 2022
Merged

4587 mri utils#4690
wyli merged 76 commits into
Project-MONAI:devfrom
mersad95zd:4587-mri-utils

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@mersad95zd

@mersad95zd mersad95zd commented Jul 13, 2022

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Fixes # .

Description

mri_utils contains required utils for MRI reconstruction

Status

Work in progress

Types of changes

  • 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).
  • New tests added to cover the changes.
  • Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

mersad95zd and others added 30 commits June 21, 2022 07:45
@mersad95zd
mri utils added
e0d20e5 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
fft_utils with its unit test added
aecedaa 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@Can-Zhao
Merge branch 'dev' into 00-mri-utils
41c93b0
@mersad95zd
fft_utils updated with monai data converter
1e0e39c 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch '00-mri-utils' of https://github.com/mersad95zd/MONAI in…
34b9da9 
…to 00-mri-utils
@mersad95zd
updated fft_util's docstring
a452ddc 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
apps.rst updated with fft_utils docstrings under the reconstruction m…
962f5f8 
…odule

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
fft_utils docstring updated by adding dimension hins
829992c 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
fft_utils docstring updated by removing redundant output type
8536cd3 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
test_fft_utils.py moved to the tests folder
ae346ee 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch 'dev' into 00-mri-utils
41aa0c7
@mersad95zd
Merge branch 'dev' into 00-mri-utils
89f5c99
@mersad95zd
created fft_utils_t, the torch-only version of fft_utils
58086b3 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch '00-mri-utils' of https://github.com/mersad95zd/MONAI in…
9928973 
…to 00-mri-utils
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
0c3f067 
for more information, see https://pre-commit.ci
@mersad95zd
fft_utils_t updated with type ignore for mypy
f48dc5a 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch '00-mri-utils' of https://github.com/mersad95zd/MONAI in…
e4773b4 
…to 00-mri-utils
@mersad95zd
docs/source/networks.rst updated with fft_utils_t
7a61979 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
4fd131f 
for more information, see https://pre-commit.ci
@mersad95zd
manual fix for fft_utils_t output data types
d4ce1fb 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch '00-mri-utils' of https://github.com/mersad95zd/MONAI in…
eb2b420 
…to 00-mri-utils
@mersad95zd
initial mri_transforms added under apps/reconstruction
4793885 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
PR1 files deleted
5b4e2ad 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch '4587-mri-transforms' of https://github.com/mersad95zd/M…
378e63e 
…ONAI into 4587-mri-transforms
@mersad95zd
with PR1 files to avoid error
a986290 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch '4587-mri-transforms' of https://github.com/mersad95zd/M…
3941149 
…ONAI into 4587-mri-transforms
@mersad95zd
PR1 included
b78b541 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
PR1 files finally removed
0be3d34 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch 'dev' into 4587-mri-transforms
cc42c3b
@mersad95zd
putting test_mri_transforms under apps for now
00c9a7c 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
new utils added: complex_mul and complex_conj
e97bb1b 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch '4587-mri-transforms' of https://github.com/mersad95zd/M…
dd52ae0 
…ONAI into 4587-mri-transforms
@mersad95zd
mypy issue with mri_utils unittest resolved
b723274 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
a separate PR for mri_utils
2766330 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd mersad95zd requested review from Can-Zhao, Nic-Ma and wyli July 13, 2022 16:41
Can-Zhao
Can-Zhao reviewed Jul 13, 2022
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Comment thread monai/apps/reconstruction/mri_utils.py Outdated
mersad95zd and others added 2 commits July 13, 2022 09:47
@mersad95zd
minor update to enum keys
318a425 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch 'dev' into 4587-mri-utils
063b987
@mersad95zd mersad95zd marked this pull request as ready for review July 13, 2022 16:50
Can-Zhao
Can-Zhao approved these changes Jul 13, 2022
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@Can-Zhao Can-Zhao left a comment •
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Looks good to me. @wyli @Nic-Ma Do you feel convert_to_tensor_complex() can be moved to monai.utils.type_conversion.py ? If it is not ready, I was also thinking whether it would be better to put all the complex value util funcs to complex_utils.py.

@mersad95zd
minor docstring fix
cadcdba 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch '4587-mri-utils' of https://github.com/mersad95zd/MONAI …
cca7afa 
…into 4587-mri-utils
Can-Zhao
Can-Zhao reviewed Jul 13, 2022
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Comment thread docs/source/transforms.rst Outdated
@wyli

wyli commented Jul 13, 2022 •
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thanks, it looks great, I think we keep convert_to_tensor_complex in apps for now, we can create a ticket (feature request) for considering merge the util into monai.utils. I'll merge this one if existing comments addressed, tests pass

Can-Zhao
Can-Zhao reviewed Jul 13, 2022
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Comment thread monai/apps/reconstruction/mri_utils.py Outdated
mersad95zd and others added 2 commits July 13, 2022 10:49
@mersad95zd
separated complex utils
3e1f305 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
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Can-Zhao
Can-Zhao reviewed Jul 13, 2022
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Comment thread monai/apps/reconstruction/complex_utils.py
mersad95zd and others added 5 commits July 13, 2022 10:58
@mersad95zd
docs updated
0b2b53d 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
Merge branch '4587-mri-utils' of https://github.com/mersad95zd/MONAI …
c4f66e8 
…into 4587-mri-utils
@mersad95zd
docs updated
a550e1a 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd
compelx_utils docstring updated
4108997 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@wyli
Merge branch 'dev' into 4587-mri-utils
498705f
@wyli

wyli commented Jul 13, 2022

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/build

@wyli wyli enabled auto-merge (squash) July 13, 2022 18:33
wyli
wyli reviewed Jul 13, 2022
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Comment thread monai/apps/reconstruction/complex_utils.py
@wyli wyli merged commit d99857c into Project-MONAI:dev Jul 13, 2022
@mersad95zd mersad95zd deleted the 4587-mri-utils branch July 13, 2022 20:02
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@wyli wyli wyli left review comments
@Can-Zhao Can-Zhao Can-Zhao approved these changes
@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma Nic-Ma is a code owner

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3 participants

@mersad95zd @wyli @Can-Zhao