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4599 mri ssim loss#4600

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wyli merged 53 commits into
Project-MONAI:devfrom
mersad95zd:4599-mri-ssim-loss
Jul 8, 2022
Merged

4599 mri ssim loss#4600
wyli merged 53 commits into
Project-MONAI:devfrom
mersad95zd:4599-mri-ssim-loss

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@mersad95zd

@mersad95zd mersad95zd commented Jun 27, 2022 •
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Fixes # .

Description

SSIM loss function as a new feature:

  • ssim_loss.py under monai.apps.reconstruction
  • its unittest under tests
  • its docs under losses.rst/ReconstructionLosses/SSIMLoss

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>
Can-Zhao
Can-Zhao reviewed Jul 1, 2022
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Comment thread monai/apps/reconstruction/ssim_metric.py Outdated
Can-Zhao
Can-Zhao reviewed Jul 1, 2022
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Comment thread monai/apps/reconstruction/ssim_metric.py Outdated
@mersad95zd
ssim_metric now calls ssim_loss; moved metric to metrics; moved loss …
dec52e6 
…to losses

Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@mersad95zd mersad95zd requested a review from Can-Zhao July 1, 2022 12:40
Can-Zhao
Can-Zhao reviewed Jul 1, 2022
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Comment thread monai/losses/ssim_loss.py Outdated
Can-Zhao
Can-Zhao reviewed Jul 1, 2022
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Comment thread monai/losses/ssim_loss.py Outdated
Can-Zhao
Can-Zhao approved these changes Jul 1, 2022
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@Can-Zhao Can-Zhao left a comment

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Looks good to me. Thanks!

@wyli wyli requested review from Nic-Ma, ericspod and rijobro July 6, 2022 13:24
Nic-Ma
Nic-Ma approved these changes Jul 8, 2022
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@Nic-Ma Nic-Ma left a comment

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Looks good to me except for some minor comments inline.
@KumoLiu Could you please help double confirm the loss computation as you have experience in the 3D reconstruction?

Thanks in advance.

Comment thread docs/source/data.rst Outdated
Comment thread docs/source/losses.rst Outdated
Comment thread monai/losses/ssim_loss.py
Comment thread monai/metrics/regression.py
Comment thread monai/metrics/regression.py
@mersad95zd

mersad95zd commented Jul 8, 2022

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Looks good to me except for some minor comments inline. @KumoLiu Could you please help double confirm the loss computation as you have experience in the 3D reconstruction?

Thanks in advance.

Thanks Nic, I made those edits and pushed again.

@KumoLiu

KumoLiu commented Jul 8, 2022

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Hi @Nic-Ma,
Loss computation also seems good to me.
Thanks.

@wyli

wyli commented Jul 8, 2022

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thanks, could you help address this issue https://github.com/Project-MONAI/MONAI/runs/7246230319?check_suite_focus=true and I'll merge this PR.

Can-Zhao
Can-Zhao reviewed Jul 8, 2022
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Comment thread docs/source/losses.rst Outdated
Can-Zhao
Can-Zhao reviewed Jul 8, 2022
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Comment thread docs/source/transforms.rst Outdated
@mersad95zd
docs issue resolved
df76151 
Signed-off-by: mersad95zd <m.zalbagi@gmail.com>
@wyli

wyli commented Jul 8, 2022

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/build

@wyli wyli enabled auto-merge (squash) July 8, 2022 18:56
@wyli wyli merged commit 4071750 into Project-MONAI:dev Jul 8, 2022
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Reviewers

@Can-Zhao Can-Zhao Can-Zhao approved these changes
@Nic-Ma Nic-Ma Nic-Ma approved these changes
@rijobro rijobro Awaiting requested review from rijobro
@ericspod ericspod Awaiting requested review from ericspod ericspod is a code owner

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5 participants

@mersad95zd @KumoLiu @wyli @Nic-Ma @Can-Zhao