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Merged
rijobro merged 27 commits into from
Mar 20, 2021
Merged

Batch inverse #1795

rijobro merged 27 commits into from
Mar 20, 2021

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@rijobro rijobro commented Mar 17, 2021 •
edited by wyli
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Batch inverse.

part of #1515

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.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

rijobro added 3 commits March 4, 2021 15:50
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batch inverse
6dfd7b6 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
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add batch_inverse tests
c4ff072 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
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Merge remote-tracking branch 'MONAI/master' into batch_inverse
81c9aa8
@rijobro rijobro requested review from Nic-Ma, ericspod and wyli March 17, 2021 16:46
@rijobro rijobro mentioned this pull request Mar 17, 2021
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rijobro added 6 commits March 17, 2021 17:07
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update
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autofix
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Merge remote-tracking branch 'MONAI/master' into batch_inverse
de51114 
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Merge remote-tracking branch 'MONAI/master' into batch_inverse
77ff3cd 
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cant pickle lambda
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No ID check for windows
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@rijobro rijobro added the enhancement New feature or request label Mar 18, 2021
rijobro added 6 commits March 18, 2021 12:17
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win32 change
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autofix
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code format
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more changes
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changes
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Merge remote-tracking branch 'MONAI/master' into batch_inverse
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rijobro commented Mar 19, 2021

Hi @Nic-Ma, @wyli, I know it takes a lot of time, but I would really appreciate reviews on this PR, #1793 and #1794 so that I can move onto something else! Thanks in advance

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wyli commented Mar 19, 2021

yes, I'm looking into these... @Nic-Ma is taking a few days off, I think he'll be back next Tuesday

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rijobro commented Mar 19, 2021

great, thanks!

wyli
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thanks! I put some comments inline, still need more time to think and test this. I'm not very familiar with the use cases, I'll look into #1794 to get a complete picture...

monai/data/inverse_batch_transform.py Outdated
transform: InvertibleTransform,
pad_collation_used: bool,
) -> None:
self.data = decollate_batch(data)
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@wyli wyli Mar 19, 2021 •
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could you help add some tests for random transforms in test_decollate with random prob=0.0?

also, not in this PR but came across an issue in monai.transforms.Decollated that missing a call to super().__init__

_BatchInverseDataset should call super() in its constructor as well

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Added tests and added call to super constructors

monai/data/inverse_batch_transform.py Outdated
for key in data.keys():
transform_key = str(key) + "_transforms"
transform = data[transform_key][-1]
if transform["class"] == "SpatialPadd":
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this is coupled with the pad_list_data_collate, could we make a special invertible transformPadListDataCollate, so that we could have the __call__ and inverse in one place...what do you think?

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@rijobro rijobro Mar 19, 2021 •
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Done and split into its own PR. Let's merge that first, which will simply the diff of this PR again.

rijobro added 4 commits March 19, 2021 18:29
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create PadListDataCollate transform
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rst
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change default collation of batch inversion
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Merge remote-tracking branch 'MONAI/master' into batch_inverse
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thanks, looks good to me now.

@rijobro
Merge remote-tracking branch 'MONAI/master' into batch_inverse
3f8c630 
Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro rijobro enabled auto-merge (squash) March 19, 2021 23:12
rijobro added 6 commits March 20, 2021 07:40
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Merge branch 'master' into batch_inverse
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Merge branch 'master' into batch_inverse
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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
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update docs
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Merge branch 'batch_inverse' of https://github.com/rijobro/MONAI into…
56d57c8 
… batch_inverse
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Merge branch 'batch_inverse' into rijobro/batch_inverse
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update docs
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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
@rijobro rijobro merged commit a2aeb40 into Project-MONAI:master Mar 20, 2021
@rijobro rijobro deleted the batch_inverse branch March 20, 2021 13:54
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@wyli wyli wyli approved these changes

@ericspod ericspod Awaiting requested review from ericspod

@Nic-Ma Nic-Ma Awaiting requested review from Nic-Ma

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