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Merge dev into geometric #8026

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f6f9e81
Use int16 instead of int8 in `LabelStats` (#7489)
KumoLiu Feb 23, 2024
20512d3
auto updates (#7495)
monai-bot Feb 26, 2024
7cfa2c9
Add sample_std parameter to RandGaussianNoise. (#7492)
bakert1 Feb 26, 2024
9830525
Add __repr__ and __str__ to Metrics baseclass (#7487)
MathijsdeBoer Feb 28, 2024
02c7f53
Bump al-cheb/configure-pagefile-action from 1.3 to 1.4 (#7510)
dependabot[bot] Mar 1, 2024
e9e2738
Add arm support (#7500)
KumoLiu Mar 3, 2024
95f69de
Fix error in "test_bundle_trt_export" (#7524)
KumoLiu Mar 10, 2024
6b7568d
Fix typo in the PerceptualNetworkType Enum (#7548)
SomeUserName1 Mar 15, 2024
ec63e06
Update to use `log_sigmoid` in `FocalLoss` (#7534)
KumoLiu Mar 18, 2024
35c93fd
Update integration_segmentation_3d result for PyTorch2403 (#7551)
KumoLiu Mar 22, 2024
c649934
Add Barlow Twins loss for representation learning (#7530)
Lucas-rbnt Mar 22, 2024
c3a7383
Stein's Unbiased Risk Estimator (SURE) loss and Conjugate Gradient (#…
cxlcl Mar 22, 2024
c86e790
auto updates (#7577)
monai-bot Mar 25, 2024
97678fa
Remove nested error propagation on `ConfigComponent` instantiate (#7569)
surajpaib Mar 26, 2024
e5bebfc
2872 implementation of mixup, cutmix and cutout (#7198)
juampatronics Mar 26, 2024
2716b6a
Remove device count cache when import monai (#7581)
KumoLiu Mar 27, 2024
c9fed96
Fixing gradient in sincos positional encoding in monai/networks/block…
Lucas-rbnt Mar 27, 2024
ba3c72c
Fix inconsistent alpha parameter/docs for RandGibbsNoise/RandGibbsNoi…
johnzielke Mar 27, 2024
7c0b10e
Fix bundle_root for NNIGen (#7586)
mingxin-zheng Mar 27, 2024
2d463a7
Auto3DSeg algo_template hash update (#7589)
monai-bot Mar 27, 2024
15d2abf
Utilizing subprocess for nnUNet training. (#7576)
KumoLiu Apr 1, 2024
ec4d946
typo fix (#7595)
scalyvladimir Apr 1, 2024
a7c2589
auto updates (#7599)
monai-bot Apr 1, 2024
c885100
7540 change bundle workflow args (#7549)
yiheng-wang-nv Apr 1, 2024
264b9e4
Add "properties_path" in BundleWorkflow (#7542)
KumoLiu Apr 1, 2024
bbaaf4c
Auto3DSeg algo_template hash update (#7603)
monai-bot Apr 1, 2024
5ec7305
ENH: generate_label_classes_crop_centers: warn only if ratio of missi…
lorinczszabolcs Apr 2, 2024
763347d
Update base image to 2403 (#7600)
KumoLiu Apr 3, 2024
195d7dd
simplification of the sincos positional encoding in patchembedding.py…
Lucas-rbnt Apr 4, 2024
625967c
harmonization and clarification of dice losses variants docs and asso…
Lucas-rbnt Apr 5, 2024
c0b9cc0
Implementation of intensity clipping transform: bot hard and soft app…
Lucas-rbnt Apr 5, 2024
87152d1
Fix typo in `SSIMMetric` (#7612)
KumoLiu Apr 8, 2024
e9a5bfe
auto updates (#7614)
monai-bot Apr 10, 2024
54a6991
Fix test error in `test_soft_clipping_one_sided_high` (#7624)
KumoLiu Apr 11, 2024
3856c45
Fix deprecated warning in ruff (#7625)
KumoLiu Apr 11, 2024
da3ecdd
7601 fix mlflow artifacts (#7604)
binliunls Apr 12, 2024
1268488
Uninstall opencv included in base image (#7626)
KumoLiu Apr 12, 2024
9e2904a
Add checks for num_fold and fail early if wrong (#7634)
mingxin-zheng Apr 12, 2024
0497448
Auto3DSeg algo_template hash update (#7642)
monai-bot Apr 15, 2024
605ffe1
Auto3DSeg algo_template hash update (#7643)
monai-bot Apr 15, 2024
bff4b15
Remove source code of numcodecs in the Dockerfile (#7644)
KumoLiu Apr 15, 2024
16d4e2f
Remove memory_pool_limit in trt config (#7647)
KumoLiu Apr 16, 2024
d6e6b24
Add version requirement for mlflow (#7659)
KumoLiu Apr 19, 2024
ffd4454
Auto3DSeg algo_template hash update (#7674)
monai-bot Apr 19, 2024
224c47a
Fixed four test issues within test code. (#7662)
freddiewanah Apr 19, 2024
7a6b69f
Adapt to use assert raises (#7670)
freddiewanah Apr 19, 2024
03a5fa6
MedicalNetPerceptualSimilarity: Add multi-channel (#7568)
SomeUserName1 Apr 19, 2024
c6bf8e9
Workaround for B909 in flake8-bugbear (#7691)
KumoLiu Apr 22, 2024
178ebc8
Fix AttributeError in 'PerceptualLoss' (#7693)
KumoLiu Apr 22, 2024
ac9b186
Always convert input to C-order in distance_transform_edt (#7675)
KumoLiu Apr 23, 2024
a59676f
Auto3DSeg algo_template hash update (#7695)
monai-bot Apr 23, 2024
ec6aa33
Merge similar test components with parameterized (#7663)
freddiewanah Apr 23, 2024
dc58e5c
Add ResNet backbones for FlexibleUNet (#7571)
k-sukharev Apr 23, 2024
1c07a17
Refactored test assertions that have suboptimal tests with numbers (#…
freddiewanah Apr 23, 2024
07a78d2
Auto3DSeg algo_template hash update (#7700)
monai-bot Apr 24, 2024
c3e4457
Update pycln version (#7704)
KumoLiu Apr 24, 2024
bfe09b8
Refactored others type of subotimal asserts (#7672)
freddiewanah Apr 24, 2024
8c709de
Fix download failing on FIPS machines (#7698)
MattTheCuber Apr 25, 2024
6a130cc
7713 Update TRT parameter (#7714)
binliunls Apr 26, 2024
4c193ea
Fix itk install error when python=3.8 (#7719)
KumoLiu Apr 29, 2024
5650899
auto updates (#7723)
monai-bot Apr 29, 2024
e1a69b0
Auto3DSeg algo_template hash update (#7728)
monai-bot Apr 30, 2024
fe733b0
Propagate kernel size through attention Attention-UNet (#7734)
Pkaps25 May 7, 2024
ecaf5a1
Fixed misguiding weight mode documentation (#7746)
simojens May 7, 2024
32b7754
Enhance logging logic in `ConfigWorkflow` (#7745)
KumoLiu May 8, 2024
f278e51
Add version requirement for filelock and nni (#7744)
KumoLiu May 8, 2024
d83fa56
Add dimensionality of heads argument to SABlock (#7664)
NabJa May 8, 2024
258f56d
Add activation parameter to ResNet (#7749)
Pkaps25 May 9, 2024
4af2306
Revert version requirement for mlflow (#7742)
KumoLiu May 10, 2024
ab4bd43
auto updates (#7760)
monai-bot May 13, 2024
daf2e71
Fix HTTPError when Too Many Requests for huggingface hub (#7765)
KumoLiu May 13, 2024
1bcf97f
Add direct links to github source code to docs (#7738)
johnzielke May 16, 2024
5e9ac1b
Fix matplotlib 3.9.0 has no attribute 'get_cmap` (#7780)
KumoLiu May 17, 2024
7429e2a
Fix doc source links for read the docs (#7779)
johnzielke May 17, 2024
d0d1292
Restrict Auto3DSeg fold input based on datalist (#7778)
mingxin-zheng May 17, 2024
25e78a2
7753 update changelog for v1.3.1 (#7773)
KumoLiu May 17, 2024
b16f54a
Pin transformer's version (#7782)
KumoLiu May 18, 2024
96bfda0
Skip failed tests (#7783)
KumoLiu May 20, 2024
244148d
Add function in monai.transforms.utils.py (#7712)
ytl0623 May 21, 2024
66a2fae
7753 update releasing 1.3.1 (#7788)
KumoLiu May 21, 2024
373c003
Add norm param to ResNet (#7752)
Pkaps25 May 23, 2024
e5afa43
Fix tests/test_warp.py (#7794)
KumoLiu May 23, 2024
ad6a433
Fix Resnet (#7805)
KumoLiu May 27, 2024
94ab632
auto updates (#7807)
monai-bot May 27, 2024
762b525
Fix precision issue in TestClipIntensityPercentiles3D (#7808)
KumoLiu May 28, 2024
a0935d9
Fix negative strides issue in `NrrdReader` (#7809)
KumoLiu May 28, 2024
0d7f772
Ensure deterministic in MixUp, CutMix, CutOut (#7813)
KumoLiu May 30, 2024
4029c42
Refactor Dataset to use Compose for transforms (#7784)
surajpaib May 31, 2024
7449c4d
change blossom-ci to ACL security format (#7843)
YanxuanLiu Jun 13, 2024
08d5728
Fixing Numpy requirements to exclude 2.0 (#7859)
ericspod Jun 19, 2024
e801540
Change deprecated scipy.ndimage namespaces in optional imports (#7847)
alkamid Jun 25, 2024
e92949d
Cherry pick #7859 for 1.3.2 (#7873)
KumoLiu Jun 25, 2024
59a7211
Update changelog for hotfix 1.3.2 (#7877)
KumoLiu Jun 25, 2024
bef5eb8
7870 update releasing 1.3.2 (#7879)
KumoLiu Jun 26, 2024
586c659
Fix 'load_module()' deprecated in Python 3.12 (#7881)
KumoLiu Jun 27, 2024
ac84a4e
Fix Ruff type check issue (#7885)
KumoLiu Jun 28, 2024
06cbd70
fix implementation mistakes and add conjugate gradients solver (#7876)
MrGranddy Jun 28, 2024
2f62b81
Add alpha parameter to DiceFocalLoss (#7841)
kephale Jun 29, 2024
55386e0
Adding Tailored ControlNet Implementations into Generative Model Appl…
guopengf Jul 1, 2024
2c7a26b
Integrating a Tailored Auto-Encoder Model into Generative Model Appli…
dongyang0122 Jul 1, 2024
15d0771
Integrating a Tailored Diffusion U-Net Model into Generative Model Ap…
dongyang0122 Jul 2, 2024
410109a
Maisi morphological funcs (#7893)
Can-Zhao Jul 2, 2024
58106a6
Remove use of deprecated python 3.12 strtobool (#7900)
hjmjohnson Jul 3, 2024
3b9683c
Clean disk space in conda test pipeline (#7902)
KumoLiu Jul 4, 2024
64ea76d
Fix deprecated argument in 'scipy.sparse.linalg.cg' (#7897)
KumoLiu Jul 6, 2024
3a0c2d5
auto updates (#7903)
monai-bot Jul 8, 2024
8cfbcba
Replace deprecated pkgutil.find_loader use (#7906)
hjmjohnson Jul 9, 2024
9554f47
Fix docstring indentation in `SaveImage` (#7913)
MathijsdeBoer Jul 11, 2024
14b086b
7908 drop python 3.8 (#7909)
KumoLiu Jul 12, 2024
848005d
Fix failing unit-test test_wsireader (#7905)
hjmjohnson Jul 14, 2024
ac86ed4
Merge tag '1.3.2' into dev
KumoLiu Jul 15, 2024
4fbe800
Fix wsireader get mpp issue (#7921)
KumoLiu Jul 16, 2024
50d5180
Support download bundles from ngc private registry (#7907)
KumoLiu Jul 17, 2024
bdbfa3e
Revert change in blossom-ci yml (#7927)
KumoLiu Jul 18, 2024
85ab9f4
Try to fix experiment already exist issue in `MLFlowHandler` (#7916)
KumoLiu Jul 18, 2024
7e4f141
Fix incorrect repo name during bundle download (#7929)
KumoLiu Jul 18, 2024
46e2b0e
Fix load pretrain weight issue in ResNet (#7924)
KumoLiu Jul 18, 2024
d020fac
Merge genaidev Into Dev (#7886)
ericspod Jul 19, 2024
7a8680e
Fix mypy issue introduced in 1.11.0 (#7941)
KumoLiu Jul 22, 2024
37917e0
Make ViT and Unetr to be torchscript comaptible (#7937)
KumoLiu Jul 23, 2024
316934a
Add checks for monai bundles after download and warn if incompatible …
mingxin-zheng Jul 24, 2024
12d00ce
Cleanup warnings when collecting tests (#7914)
hjmjohnson Jul 24, 2024
3f0c768
Fix Incompatible types in assignment issue (#7950)
KumoLiu Jul 25, 2024
2e53df7
Adding metadata schema to the code base itself (#7409)
ericspod Jul 25, 2024
54019e4
Addition of norm_eps (#7962)
virginiafdez Jul 30, 2024
f1ef3e8
Rename `optional_packages_version` to `required_packages_version` (#7…
KumoLiu Jul 30, 2024
139b62c
Fix outdated link in the docs (#7971)
KumoLiu Aug 1, 2024
1ece8a5
7982-fix-ci-issue (#7983)
yiheng-wang-nv Aug 2, 2024
ae5a04d
7973-add-ngc-prefix (#7974)
yiheng-wang-nv Aug 3, 2024
56ee32e
Fix: Small logic mistake in the `AsDiscrete.__call__` method (#7984)
dcfidalgo Aug 3, 2024
6c23fd0
Flash attention (#7977)
virginiafdez Aug 6, 2024
49a1e34
7994-enhance-mlpblock (#7995)
yiheng-wang-nv Aug 7, 2024
660891f
Initial commit -- Adding calibration loss specific to segmentation (#…
Bala93 Aug 8, 2024
4a3117f
Ensure location as tuple in wsireader (#8007)
KumoLiu Aug 9, 2024
0bb05d7
Add label smoothing param in DiceCELoss (#8000)
ytl0623 Aug 9, 2024
069519d
Add include_fc and `use_combined_linear` argument in the `SABlock` (#…
KumoLiu Aug 9, 2024
6be7b13
Replaced package "pkg_resources" with "packaging" (#7953)
K-Rilla Aug 9, 2024
f848002
Add utils for vista3d (#7999)
yiheng-wang-nv Aug 9, 2024
6243031
Adding a network CellSamWrapper (#7981)
myron Aug 10, 2024
250c18d
Refactor DiffusionModelUNetMaisi (#7989)
guopengf Aug 12, 2024
7a6f680
Remove segment-anything in setup.cfg (#8010)
KumoLiu Aug 12, 2024
6858114
Refactor AutoencoderKlMaisi (#7993)
guopengf Aug 13, 2024
9dbfe16
Refactor ControlNetMaisi (#8005)
guopengf Aug 13, 2024
34ce94d
Fix ci issue in test_vit (#8013)
KumoLiu Aug 13, 2024
4877767
Fix module can not import correctly issue (#8015)
KumoLiu Aug 14, 2024
e85580a
Fix 'torch.device' object has no attribute 'gpu_id' issue in trt expo…
KumoLiu Aug 15, 2024
77304dd
Add vista network (#7987)
heyufan1995 Aug 15, 2024
7b9a523
NACLLoss memory management (#8020)
Bala93 Aug 15, 2024
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NACLLoss memory management (#8020)
Fixes # .

### Description

Calling contiguous after applying the permute option to work with view
operation in apply_filter
(https://github.com/Project-MONAI/MONAI/blob/59a7211070538586369afd4a01eca0a7fe2e742e/monai/networks/layers/simplelayers.py#L293).

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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.

---------

Signed-off-by: Balamurali <balamuralim.1993@gmail.com>
Signed-off-by: bala93 <balamuralim.1993@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Co-authored-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
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4 people authored Aug 15, 2024
commit 7b9a523c97ff9e7f1fad7fb2a761ce5322947500
4 changes: 2 additions & 2 deletions monai/losses/nacl_loss.py
Original file line number Diff line number Diff line change
Expand Up @@ -95,11 +95,11 @@ def get_constr_target(self, mask: torch.Tensor) -> torch.Tensor:
rmask: torch.Tensor

if self.dim == 2:
oh_labels = F.one_hot(mask.to(torch.int64), num_classes=self.nc).contiguous().permute(0, 3, 1, 2).float()
oh_labels = F.one_hot(mask.to(torch.int64), num_classes=self.nc).permute(0, 3, 1, 2).contiguous().float()
rmask = self.svls_layer(oh_labels)

if self.dim == 3:
oh_labels = F.one_hot(mask.to(torch.int64), num_classes=self.nc).contiguous().permute(0, 4, 1, 2, 3).float()
oh_labels = F.one_hot(mask.to(torch.int64), num_classes=self.nc).permute(0, 4, 1, 2, 3).contiguous().float()
rmask = self.svls_layer(oh_labels)

return rmask
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1 change: 1 addition & 0 deletions tests/test_nacl_loss.py
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@

TEST_CASES = [
[{"classes": 3, "dim": 2}, {"inputs": inputs, "targets": targets}, 1.1442],
[{"classes": 3, "dim": 2}, {"inputs": inputs.repeat(4, 1, 1, 1), "targets": targets.repeat(4, 1, 1)}, 1.1442],
[{"classes": 3, "dim": 2, "kernel_ops": "gaussian"}, {"inputs": inputs, "targets": targets}, 1.1433],
[{"classes": 3, "dim": 2, "kernel_ops": "gaussian", "sigma": 0.5}, {"inputs": inputs, "targets": targets}, 1.1469],
[{"classes": 3, "dim": 2, "distance_type": "l2"}, {"inputs": inputs, "targets": targets}, 1.1269],
Expand Down
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