AddChannel, AsChannelFirst, AsChannelLast, EnsureChannelFirst, Identity, RepeatChannel by rijobro · Pull Request #2840 · Project-MONAI/MONAI

rijobro · 2021-08-25T10:56:22Z

Description

Torch transforms:
AddChannel, AsChannelFirst, AsChannelLast, EnsureChannelFirst, Identity, RepeatChannel.

Status

Ready

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
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.

Signed-off-by: Richard Brown <[email protected]>

…ty, RepeatChannel Signed-off-by: Richard Brown <[email protected]>

monai/transforms/utility/array.py

Signed-off-by: Richard Brown <[email protected]>

wyli · 2021-08-25T19:48:56Z

/build

madil90 · 2021-08-25T22:27:22Z

/build

wyli · 2021-08-26T07:16:09Z

/build

rijobro · 2021-08-26T09:10:55Z

@wyli could you help me with the blossom error? I'm not sure what version of python/pytorch/OS it's running to be able to replicate the error. (It's also strange that the displayed error hasn't shown up in any of the other checks.)

wyli · 2021-08-26T12:47:15Z

yes, I'm also aware of the bug yesterday, still couldn't figure it out. It looks like a shared testing file cache is dirty, I'm working on it.

according to the log the test is running for this commit 9266581 but I couldn't find the corresponding branch/PR. Do you know which branch that commit is pushed to?

rijobro · 2021-08-26T13:01:41Z

I deleted some of my branches after they were merged, so I can't find out which commit that one belonged to. Sorry!

That said, the error does look like it's related to this PR. I was just surprised that it didn't show up for the other testing environments.

Signed-off-by: Richard Brown <[email protected]>

wyli · 2021-08-26T13:09:13Z

/build

wyli · 2021-08-26T13:20:30Z

the last run error was

Details

======================================================================
FAIL: test_shape_3 (tests.test_as_channel_lastd.TestAsChannelLastd)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_lastd.py", line 36, in test_shape
    self.assertTupleEqual(result["image"].shape, expected_shape)
AssertionError: Tuples differ: torch.Size([2, 3, 1, 4]) != (2, 3, 4, 1)

First differing element 2:
1
4

- torch.Size([2, 3, 1, 4])
+ (2, 3, 4, 1)

======================================================================
FAIL: test_shape_4 (tests.test_as_channel_lastd.TestAsChannelLastd)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_lastd.py", line 36, in test_shape
    self.assertTupleEqual(result["image"].shape, expected_shape)
AssertionError: Tuples differ: torch.Size([1, 3, 2, 4]) != (1, 3, 4, 2)

First differing element 2:
2
4

- torch.Size([1, 3, 2, 4])
+ (1, 3, 4, 2)

======================================================================
FAIL: test_shape_5 (tests.test_as_channel_lastd.TestAsChannelLastd)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_lastd.py", line 36, in test_shape
    self.assertTupleEqual(result["image"].shape, expected_shape)
AssertionError: Tuples differ: torch.Size([1, 2, 4, 3]) != (1, 2, 3, 4)

First differing element 2:
4
3

- torch.Size([1, 2, 4, 3])
+ (1, 2, 3, 4)

======================================================================
FAIL: test_shape_6 (tests.test_as_channel_lastd.TestAsChannelLastd)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_lastd.py", line 36, in test_shape
    self.assertTupleEqual(result["image"].shape, expected_shape)
AssertionError: Tuples differ: torch.Size([2, 3, 1, 4]) != (2, 3, 4, 1)

First differing element 2:
1
4

- torch.Size([2, 3, 1, 4])
+ (2, 3, 4, 1)

======================================================================
FAIL: test_shape_7 (tests.test_as_channel_lastd.TestAsChannelLastd)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_lastd.py", line 36, in test_shape
    self.assertTupleEqual(result["image"].shape, expected_shape)
AssertionError: Tuples differ: torch.Size([1, 3, 2, 4]) != (1, 3, 4, 2)

First differing element 2:
2
4

- torch.Size([1, 3, 2, 4])
+ (1, 3, 4, 2)

======================================================================
FAIL: test_shape_8 (tests.test_as_channel_lastd.TestAsChannelLastd)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_lastd.py", line 36, in test_shape
    self.assertTupleEqual(result["image"].shape, expected_shape)
AssertionError: Tuples differ: torch.Size([1, 2, 4, 3]) != (1, 2, 3, 4)

First differing element 2:
4
3

- torch.Size([1, 2, 4, 3])
+ (1, 2, 3, 4)

======================================================================
FAIL: test_shape_3 (tests.test_as_channel_last.TestAsChannelLast)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_last.py", line 32, in test_shape
    self.assertTupleEqual(result.shape, expected_shape)
AssertionError: Tuples differ: torch.Size([2, 3, 1, 4]) != (2, 3, 4, 1)

First differing element 2:
1
4

- torch.Size([2, 3, 1, 4])
+ (2, 3, 4, 1)

======================================================================
FAIL: test_shape_4 (tests.test_as_channel_last.TestAsChannelLast)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_last.py", line 32, in test_shape
    self.assertTupleEqual(result.shape, expected_shape)
AssertionError: Tuples differ: torch.Size([1, 3, 2, 4]) != (1, 3, 4, 2)

First differing element 2:
2
4

- torch.Size([1, 3, 2, 4])
+ (1, 3, 4, 2)

======================================================================
FAIL: test_shape_5 (tests.test_as_channel_last.TestAsChannelLast)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_last.py", line 32, in test_shape
    self.assertTupleEqual(result.shape, expected_shape)
AssertionError: Tuples differ: torch.Size([1, 2, 4, 3]) != (1, 2, 3, 4)

First differing element 2:
4
3

- torch.Size([1, 2, 4, 3])
+ (1, 2, 3, 4)

======================================================================
FAIL: test_shape_6 (tests.test_as_channel_last.TestAsChannelLast)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_last.py", line 32, in test_shape
    self.assertTupleEqual(result.shape, expected_shape)
AssertionError: Tuples differ: torch.Size([2, 3, 1, 4]) != (2, 3, 4, 1)

First differing element 2:
1
4

- torch.Size([2, 3, 1, 4])
+ (2, 3, 4, 1)

======================================================================
FAIL: test_shape_7 (tests.test_as_channel_last.TestAsChannelLast)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_last.py", line 32, in test_shape
    self.assertTupleEqual(result.shape, expected_shape)
AssertionError: Tuples differ: torch.Size([1, 3, 2, 4]) != (1, 3, 4, 2)

First differing element 2:
2
4

- torch.Size([1, 3, 2, 4])
+ (1, 3, 4, 2)

======================================================================
FAIL: test_shape_8 (tests.test_as_channel_last.TestAsChannelLast)
----------------------------------------------------------------------

tests finished, printing completed times >10.0s in ascending order...

test_cpu_precise_backwards_7_3_dimension_1_channel_high_spatial_sigma_high_color_sigma (tests.test_bilateral_precise.BilateralFilterTestCaseCpuPrecise) (10.8s)
test_script (tests.test_highresnet.TestHighResNet) (11.4s)
test_script_0 (tests.test_senet.TestSENET) (11.5s)
test_shape_0 (tests.test_efficientnet.TestExtractFeatures) (11.7s)
test_cuda_3_1_batches_3_dimensions_1_channels_2_classes_1_mixtures (tests.test_gmm.GMMTestCase) (12.1s)
test_cuda_2_1_batches_2_dimensions_2_channels_4_classes_4_mixtures (tests.test_gmm.GMMTestCase) (12.2s)
test_cuda_1_1_batches_1_dimensions_5_channels_2_classes_1_mixtures (tests.test_gmm.GMMTestCase) (12.3s)
test_cuda_0_2_batches_1_dimensions_1_channels_2_classes_2_mixtures (tests.test_gmm.GMMTestCase) (13.0s)
test_lr_finder (tests.test_lr_finder.TestLRFinder) (28.9s)
test_senet_shape_0 (tests.test_senet.TestPretrainedSENET) (3.18e+02s)
test discovery time: 4.24s
total testing time: 4.42e+02s
Remember to check above times for any errors!

Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_as_channel_last.py", line 32, in test_shape
    self.assertTupleEqual(result.shape, expected_shape)
AssertionError: Tuples differ: torch.Size([1, 2, 4, 3]) != (1, 2, 3, 4)

First differing element 2:
4
3

- torch.Size([1, 2, 4, 3])
+ (1, 2, 3, 4)

----------------------------------------------------------------------
Ran 4411 tests in 992.790s

FAILED (failures=12, skipped=408)

version:

================================
Printing MONAI config...
================================
MONAI version: 0+unknown
Numpy version: 1.19.5
Pytorch version: 1.7.1
MONAI flags: HAS_EXT = True, USE_COMPILED = True
MONAI rev id: None

Optional dependencies:
Pytorch Ignite version: 0.4.5
Nibabel version: 3.2.1
scikit-image version: 0.17.2
Pillow version: 8.3.1
Tensorboard version: 2.6.0
gdown version: 3.13.0
TorchVision version: 0.8.2
tqdm version: 4.62.2
lmdb version: 1.2.1
psutil version: 5.8.0
pandas version: 1.1.5
einops version: 0.3.0

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies

Signed-off-by: Richard Brown <[email protected]>

madil90 · 2021-08-27T06:00:55Z

/build

Signed-off-by: Richard Brown <[email protected]>

rijobro · 2021-08-27T13:28:35Z

@wyli @Nic-Ma tests are green, would you be able to review when possible? Thanks.

wyli

looks good to me

…ty, RepeatChannel (Project-MONAI#2840)

rijobro added 4 commits August 25, 2021 11:04

backends -> backend

beab17d

Signed-off-by: Richard Brown <[email protected]>

code format

c3192ba

Signed-off-by: Richard Brown <[email protected]>

code format2

f790ad7

Signed-off-by: Richard Brown <[email protected]>

AddChannel, AsChannelFirst, AsChannelLast, EnsureChannelFirst, Identi…

1d28704

…ty, RepeatChannel Signed-off-by: Richard Brown <[email protected]>

rijobro requested review from Nic-Ma and wyli August 25, 2021 10:56

Merge remote-tracking branch 'MONAI/dev' into utility_transforms

fe0c787

Nic-Ma reviewed Aug 25, 2021

View reviewed changes

monai/transforms/utility/array.py Outdated Show resolved Hide resolved

monai/transforms/utility/array.py Outdated Show resolved Hide resolved

rijobro and others added 3 commits August 25, 2021 15:59

moveaxis backwards compatible

be7eac2

Signed-off-by: Richard Brown <[email protected]>

code format

0d27527

Signed-off-by: Richard Brown <[email protected]>

Merge branch 'dev' into utility_transforms

69ff653

Merge branch 'dev' into utility_transforms

95622bc

rijobro mentioned this pull request Aug 26, 2021

EnsureType, RemoveRepeatedChannel, SplitChannel, ToCupy, ToNumpy, ToPil, ToTensor, Transpose #2850

Merged

6 tasks

trigger ci/cd

754a684

Signed-off-by: Richard Brown <[email protected]>

rijobro force-pushed the utility_transforms branch from 956a557 to 754a684 Compare August 26, 2021 13:02

rijobro and others added 2 commits August 26, 2021 15:42

permute requires positive indices

e38e7a3

Signed-off-by: Richard Brown <[email protected]>

Merge branch 'dev' into utility_transforms

24c136d

rijobro added 2 commits August 27, 2021 10:30

Merge branch 'dev' into utility_transforms

2971cdb

correct permute

b1e476d

Signed-off-by: Richard Brown <[email protected]>

Merge branch 'dev' into utility_transforms

baecdf8

rijobro enabled auto-merge (squash) August 27, 2021 13:28

wyli approved these changes Aug 27, 2021

View reviewed changes

Merge branch 'dev' into utility_transforms

845aa03

rijobro merged commit fe6ac0a into Project-MONAI:dev Aug 27, 2021

rijobro deleted the utility_transforms branch August 27, 2021 15:50

wyli pushed a commit to Borda/MONAI that referenced this pull request Aug 27, 2021

AddChannel, AsChannelFirst, AsChannelLast, EnsureChannelFirst, Identi…

9bbe2b2

…ty, RepeatChannel (Project-MONAI#2840)

wyli pushed a commit to Borda/MONAI that referenced this pull request Aug 27, 2021

AddChannel, AsChannelFirst, AsChannelLast, EnsureChannelFirst, Identi…

e3b325f

…ty, RepeatChannel (Project-MONAI#2840)

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rijobro merged 16 commits intoProject-MONAI:devfrom
rijobro:utility_transforms

rijobro commented Aug 25, 2021

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rijobro commented Aug 25, 2021

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