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3322 Optimize performance of the astype usage in arrays #3338

Merged
merged 16 commits into from
Nov 18, 2021
Merged

3322 Optimize performance of the astype usage in arrays #3338

merged 16 commits into from
Nov 18, 2021

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Nic-Ma
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@Nic-Ma Nic-Ma commented Nov 15, 2021 •
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Fixes #3322 .

Description

This PR optimized many np.astype() operations to avoid copy.

Status

Ready

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

@Nic-Ma Nic-Ma mentioned this pull request Nov 15, 2021
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Nic-Ma and others added 3 commits November 17, 2021 18:01
@Nic-Ma
Merge pull request #290 from Project-MONAI/dev
09dc7cf 
merge master
@Nic-Ma
[DLMED] improve astype
0550d77 
Signed-off-by: Nic Ma <nma@nvidia.com>
@Nic-Ma
[DLMED] fix flake8
f2ba306 
Signed-off-by: Nic Ma <nma@nvidia.com>
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Nic-Ma commented Nov 17, 2021

/black

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Nic-Ma commented Nov 17, 2021

/build

@Nic-Ma Nic-Ma changed the title [WIP] 3322 Optimize performance of the astype usage in arrays 3322 Optimize performance of the astype usage in arrays Nov 17, 2021
@Nic-Ma Nic-Ma marked this pull request as ready for review November 17, 2021 11:20
@Nic-Ma Nic-Ma requested a review from wyli November 17, 2021 23:51
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Nic-Ma commented Nov 18, 2021

/build

@Nic-Ma
[DLMED] update according to comments
268a3f8 
Signed-off-by: Nic Ma <nma@nvidia.com>
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Nic-Ma commented Nov 18, 2021

/black

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Nic-Ma commented Nov 18, 2021

/build

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Nic-Ma commented Nov 18, 2021

/black

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Nic-Ma commented Nov 18, 2021

/build

@Nic-Ma
[DLMED] update according to comments
be4dd9d 
Signed-off-by: Nic Ma <nma@nvidia.com>
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Nic-Ma commented Nov 18, 2021

/build

wyli
wyli approved these changes Nov 18, 2021
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monai/transforms/utility/array.py Outdated Show resolved Hide resolved
monai/apps/deepedit/transforms.py Show resolved Hide resolved
@Nic-Ma
[DLMED] update according to comments
7ed2a28 
Signed-off-by: Nic Ma <nma@nvidia.com>
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Nic-Ma commented Nov 18, 2021

/black

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Nic-Ma commented Nov 18, 2021

/build

@Nic-Ma Nic-Ma enabled auto-merge (squash) November 18, 2021 13:45
SachidanandAlle
SachidanandAlle reviewed Nov 18, 2021
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LGTM for deepxx Transforms..

These ones are done over click points.. size of the array typically less than 20.. you might not notice big boost wrt optimization unless something similar done on full 3D label/image

@Nic-Ma
[DLMED] fix flake8
ec9e835 
Signed-off-by: Nic Ma <nma@nvidia.com>
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Nic-Ma commented Nov 18, 2021

/black

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Nic-Ma commented Nov 18, 2021

/build

@Nic-Ma Nic-Ma merged commit bf55246 into Project-MONAI:dev Nov 18, 2021
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@SachidanandAlle SachidanandAlle SachidanandAlle left review comments

@wyli wyli wyli approved these changes

@rijobro rijobro Awaiting requested review from rijobro

@ericspod ericspod Awaiting requested review from ericspod

@yiheng-wang-nv yiheng-wang-nv Awaiting requested review from yiheng-wang-nv

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LoadImageD performance
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@Nic-Ma @wyli @SachidanandAlle