add anchor generators used for detection by Can-Zhao · Pull Request #4336 · Project-MONAI/MONAI

Can-Zhao · 2022-05-24T20:26:35Z

Signed-off-by: Can Zhao [email protected]

Fixes #3573 .

Description

add anchor generators used for detection

Status

Ready/Work in progress/Hold

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.

Signed-off-by: Can Zhao <[email protected]>

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wyli

could you please add some unit tests for this module?

monai/apps/detection/networks/utils/anchor_utils.py

Signed-off-by: Can Zhao <[email protected]>

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Can-Zhao · 2022-05-25T18:41:10Z

could you please add some unit tests for this module?

Thanks. Just added

Signed-off-by: Can Zhao <[email protected]>

wyli · 2022-05-29T19:29:27Z

/build

- torchvision compatibility - torchscript compatibility Signed-off-by: Wenqi Li <[email protected]>

wyli · 2022-05-30T08:12:10Z

fyi, some issues with torch 1.7/1.8 from tests:

Details

[2022-05-29T19:56:23.845Z] ======================================================================
[2022-05-29T19:56:23.845Z] ERROR: test_anchor_2d_0 (tests.test_anchor_box.TestAnchorGenerator)
[2022-05-29T19:56:23.845Z] ----------------------------------------------------------------------
[2022-05-29T19:56:23.845Z] Traceback (most recent call last):
[2022-05-29T19:56:23.845Z]   File "/usr/local/lib/python3.7/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
[2022-05-29T19:56:23.845Z]     return func(*(a + p.args), **p.kwargs)
[2022-05-29T19:56:23.845Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_anchor_box.py", line 53, in test_anchor_2d
[2022-05-29T19:56:23.845Z]     for a, a_f in zip(anchor.cell_anchors, anchor_ref.cell_anchors):
[2022-05-29T19:56:23.845Z] TypeError: zip argument #2 must support iteration
[2022-05-29T19:56:23.845Z] 
[2022-05-29T19:56:23.845Z] ======================================================================
[2022-05-29T19:56:23.845Z] ERROR: test_script_2d_0 (tests.test_anchor_box.TestAnchorGenerator)
[2022-05-29T19:56:23.845Z] ----------------------------------------------------------------------
[2022-05-29T19:56:23.845Z] Traceback (most recent call last):
[2022-05-29T19:56:23.845Z]   File "/usr/local/lib/python3.7/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
[2022-05-29T19:56:23.845Z]     return func(*(a + p.args), **p.kwargs)
[2022-05-29T19:56:23.845Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_anchor_box.py", line 76, in test_script_2d
[2022-05-29T19:56:23.845Z]     test_script_save(anchor, images, feature_maps)
[2022-05-29T19:56:23.845Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/utils.py", line 682, in test_script_save
[2022-05-29T19:56:23.845Z]     atol=atol,
[2022-05-29T19:56:23.845Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/networks/utils.py", line 539, in convert_to_torchscript
[2022-05-29T19:56:23.845Z]     script_module = torch.jit.script(model, **kwargs)
[2022-05-29T19:56:23.845Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_script.py", line 898, in script
[2022-05-29T19:56:23.845Z]     obj, torch.jit._recursive.infer_methods_to_compile
[2022-05-29T19:56:23.845Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_recursive.py", line 352, in create_script_module
[2022-05-29T19:56:23.845Z]     return create_script_module_impl(nn_module, concrete_type, stubs_fn)
[2022-05-29T19:56:23.845Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_recursive.py", line 410, in create_script_module_impl
[2022-05-29T19:56:23.845Z]     create_methods_and_properties_from_stubs(concrete_type, method_stubs, property_stubs)
[2022-05-29T19:56:23.845Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_recursive.py", line 304, in create_methods_and_properties_from_stubs
[2022-05-29T19:56:23.845Z]     concrete_type._create_methods_and_properties(property_defs, property_rcbs, method_defs, method_rcbs, method_defaults)
[2022-05-29T19:56:23.846Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_recursive.py", line 680, in compile_unbound_method
[2022-05-29T19:56:23.846Z]     create_methods_and_properties_from_stubs(concrete_type, (stub,), ())
[2022-05-29T19:56:23.846Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_recursive.py", line 304, in create_methods_and_properties_from_stubs
[2022-05-29T19:56:23.846Z]     concrete_type._create_methods_and_properties(property_defs, property_rcbs, method_defs, method_rcbs, method_defaults)
[2022-05-29T19:56:23.846Z] RuntimeError: 
[2022-05-29T19:56:23.846Z] 
[2022-05-29T19:56:23.846Z] aten::meshgrid(Tensor[] tensors) -> (Tensor[]):
[2022-05-29T19:56:23.846Z] Keyword argument indexing unknown.
[2022-05-29T19:56:23.846Z] :
[2022-05-29T19:56:23.846Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/detection/utils/anchor_utils.py", line 256
[2022-05-29T19:56:23.846Z]             if self.spatial_dims == 2:
[2022-05-29T19:56:23.846Z]                 shifts_centers = list(
[2022-05-29T19:56:23.846Z]                     torch.meshgrid([shifts_centers[0], shifts_centers[1]], indexing="ij")
[2022-05-29T19:56:23.846Z]                     ~~~~~~~~~~~~~~ <--- HERE
[2022-05-29T19:56:23.846Z]                 )  # indexing="ij"
[2022-05-29T19:56:23.846Z]             else:
[2022-05-29T19:56:23.846Z] 'AnchorGenerator.grid_anchors' is being compiled since it was called from 'AnchorGenerator.forward'
[2022-05-29T19:56:23.846Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/detection/utils/anchor_utils.py", line 318
[2022-05-29T19:56:23.846Z]         # Code below come from torchvision.models.detection.anchor_utils.AnchorGenerator.forward()
[2022-05-29T19:56:23.846Z]         self.set_cell_anchors(dtype, device)
[2022-05-29T19:56:23.846Z]         anchors_over_all_feature_maps = self.grid_anchors(grid_sizes, strides)
[2022-05-29T19:56:23.846Z]         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <--- HERE
[2022-05-29T19:56:23.846Z] 
[2022-05-29T19:56:23.846Z]         anchors: List[List[torch.Tensor]] = []
[2022-05-29T19:56:23.846Z] 
[2022-05-29T19:56:23.846Z] 
[2022-05-29T19:56:23.846Z] ======================================================================
[2022-05-29T19:56:23.846Z] ERROR: test_script_3d_0 (tests.test_anchor_box.TestAnchorGenerator)
[2022-05-29T19:56:23.846Z] ----------------------------------------------------------------------
[2022-05-29T19:56:23.846Z] Traceback (most recent call last):
[2022-05-29T19:56:23.846Z]   File "/usr/local/lib/python3.7/dist-packages/parameterized/parameterized.py", line 533, in standalone_func
[2022-05-29T19:56:23.846Z]     return func(*(a + p.args), **p.kwargs)
[2022-05-29T19:56:23.846Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/test_anchor_box.py", line 84, in test_script_3d
[2022-05-29T19:56:23.846Z]     test_script_save(anchor, images, feature_maps)
[2022-05-29T19:56:23.846Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/tests/utils.py", line 682, in test_script_save
[2022-05-29T19:56:23.846Z]     atol=atol,
[2022-05-29T19:56:23.846Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/networks/utils.py", line 539, in convert_to_torchscript
[2022-05-29T19:56:23.846Z]     script_module = torch.jit.script(model, **kwargs)
[2022-05-29T19:56:23.846Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_script.py", line 898, in script
[2022-05-29T19:56:23.846Z]     obj, torch.jit._recursive.infer_methods_to_compile
[2022-05-29T19:56:23.846Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_recursive.py", line 352, in create_script_module
[2022-05-29T19:56:23.846Z]     return create_script_module_impl(nn_module, concrete_type, stubs_fn)
[2022-05-29T19:56:23.846Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_recursive.py", line 410, in create_script_module_impl
[2022-05-29T19:56:23.846Z]     create_methods_and_properties_from_stubs(concrete_type, method_stubs, property_stubs)
[2022-05-29T19:56:23.846Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_recursive.py", line 304, in create_methods_and_properties_from_stubs
[2022-05-29T19:56:23.846Z]     concrete_type._create_methods_and_properties(property_defs, property_rcbs, method_defs, method_rcbs, method_defaults)
[2022-05-29T19:56:23.846Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_recursive.py", line 680, in compile_unbound_method
[2022-05-29T19:56:23.846Z]     create_methods_and_properties_from_stubs(concrete_type, (stub,), ())
[2022-05-29T19:56:23.846Z]   File "/usr/local/lib/python3.7/dist-packages/torch/jit/_recursive.py", line 304, in create_methods_and_properties_from_stubs
[2022-05-29T19:56:23.846Z]     concrete_type._create_methods_and_properties(property_defs, property_rcbs, method_defs, method_rcbs, method_defaults)
[2022-05-29T19:56:23.846Z] RuntimeError: 
[2022-05-29T19:56:23.846Z] 
[2022-05-29T19:56:23.846Z] aten::meshgrid(Tensor[] tensors) -> (Tensor[]):
[2022-05-29T19:56:23.846Z] Keyword argument indexing unknown.
[2022-05-29T19:56:23.846Z] :
[2022-05-29T19:56:23.846Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/detection/utils/anchor_utils.py", line 256
[2022-05-29T19:56:23.846Z]             if self.spatial_dims == 2:
[2022-05-29T19:56:23.846Z]                 shifts_centers = list(
[2022-05-29T19:56:23.846Z]                     torch.meshgrid([shifts_centers[0], shifts_centers[1]], indexing="ij")
[2022-05-29T19:56:23.846Z]                     ~~~~~~~~~~~~~~ <--- HERE
[2022-05-29T19:56:23.846Z]                 )  # indexing="ij"
[2022-05-29T19:56:23.846Z]             else:
[2022-05-29T19:56:23.846Z] 'AnchorGeneratorWithAnchorShape.grid_anchors' is being compiled since it was called from 'AnchorGeneratorWithAnchorShape.forward'
[2022-05-29T19:56:23.846Z]   File "/home/jenkins/agent/workspace/MONAI-premerge/monai/monai/apps/detection/utils/anchor_utils.py", line 318
[2022-05-29T19:56:23.846Z]         # Code below come from torchvision.models.detection.anchor_utils.AnchorGenerator.forward()
[2022-05-29T19:56:23.846Z]         self.set_cell_anchors(dtype, device)
[2022-05-29T19:56:23.846Z]         anchors_over_all_feature_maps = self.grid_anchors(grid_sizes, strides)
[2022-05-29T19:56:23.846Z]         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <--- HERE
[2022-05-29T19:56:23.846Z] 
[2022-05-29T19:56:23.846Z]         anchors: List[List[torch.Tensor]] = []
[2022-05-29T19:56:23.846Z] 
[2022-05-29T19:56:23.846Z] 
[2022-05-29T19:56:23.846Z] ----------------------------------------------------------------------

wyli · 2022-05-30T08:18:32Z

/build

Signed-off-by: Wenqi Li <[email protected]>

wyli · 2022-05-30T09:07:56Z

/build

Signed-off-by: Wenqi Li <[email protected]>

wyli · 2022-05-30T10:08:46Z

/build

Signed-off-by: Wenqi Li <[email protected]>

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.pre-commit-config.yaml

wyli · 2022-05-30T10:34:51Z

/build

Signed-off-by: Wenqi Li <[email protected]>

wyli · 2022-05-30T13:54:44Z

/build

mibaumgartner

Left some small notes, the rest looks good to me.

monai/apps/detection/utils/anchor_utils.py

Signed-off-by: Can Zhao <[email protected]>

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wyli · 2022-05-30T18:59:20Z

/build

Can-Zhao and others added 2 commits May 24, 2022 16:25

add anchor generators used for detection

8d453ca

Signed-off-by: Can Zhao <[email protected]>

Merge branch 'dev' into anchor

95e596c

Can-Zhao added this to the Detection module [P0] milestone May 24, 2022

Can-Zhao added the Feature request label May 24, 2022

Can-Zhao requested review from Nic-Ma, mibaumgartner and wyli May 24, 2022 20:31

Can-Zhao and others added 3 commits May 24, 2022 16:33

update comments

05a8cbc

Signed-off-by: Can Zhao <[email protected]>

consider a corner case

0aa4c85

Signed-off-by: Can Zhao <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

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Can-Zhao marked this pull request as ready for review May 24, 2022 21:02

Can-Zhao requested a review from dongyang0122 May 24, 2022 21:02

Merge branch 'dev' into anchor

7bf8a52

wyli reviewed May 25, 2022

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Can-Zhao and others added 3 commits May 25, 2022 14:38

add unit test, compare with results from torchvison

7a3b12f

Signed-off-by: Can Zhao <[email protected]>

Merge branch 'anchor' of github.com:Can-Zhao/MONAI into anchor

784493b

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Can-Zhao and others added 12 commits May 25, 2022 14:41

Merge branch 'dev' into anchor

e6dee7a

fix a few issues

1c96316

Signed-off-by: Can Zhao <[email protected]>

add torchvision license

504d83e

Signed-off-by: Can Zhao <[email protected]>

add indexing

bcfbe72

Signed-off-by: Can Zhao <[email protected]>

license

880dee2

Signed-off-by: Can Zhao <[email protected]>

docstring

44c96a6

Signed-off-by: Can Zhao <[email protected]>

init

b6a8050

Signed-off-by: Can Zhao <[email protected]>

Merge branch 'dev' into anchor

820a308

docstring typo

c7692f2

Signed-off-by: Can Zhao <[email protected]>

mv to detection/

d6464f5

Signed-off-by: Can Zhao <[email protected]>

doc

2cb779a

Signed-off-by: Can Zhao <[email protected]>

mv to detection/

b0214c3

Signed-off-by: Can Zhao <[email protected]>

Can-Zhao added 2 commits May 29, 2022 10:43

fix unit test

a306ba5

Signed-off-by: Can Zhao <[email protected]>

support torchscript

ccf8cbc

Signed-off-by: Can Zhao <[email protected]>

wyli enabled auto-merge (squash) May 29, 2022 19:29

fixes unit tests

54d8300

- torchvision compatibility - torchscript compatibility Signed-off-by: Wenqi Li <[email protected]>

update version req

55bda4d

Signed-off-by: Wenqi Li <[email protected]>

wyli added 2 commits May 30, 2022 10:48

unit tests

a7148b8

Signed-off-by: Wenqi Li <[email protected]>

fixes meshgrid_ij

fedc84f

Signed-off-by: Wenqi Li <[email protected]>

remove unused import

d34d9f6

Signed-off-by: Wenqi Li <[email protected]>

wyli force-pushed the anchor branch from d16b657 to d34d9f6 Compare May 30, 2022 10:29

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fixes meshgrid

675a058

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mibaumgartner reviewed May 30, 2022

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wyli disabled auto-merge May 30, 2022 14:34

Can-Zhao and others added 6 commits May 30, 2022 11:39

docstring

e4e3e92

Signed-off-by: Can Zhao <[email protected]>

docstring

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Signed-off-by: Can Zhao <[email protected]>

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Merge branch 'dev' into anchor

97782a2

Merge branch 'dev' into anchor

4c72bac

Merge branch 'dev' into anchor

94704d6

wyli merged commit d635339 into Project-MONAI:dev May 30, 2022

Can-Zhao deleted the anchor branch May 30, 2022 20:10

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Can-Zhao commented May 24, 2022

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