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144 loadnifti transform common dataset #145

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Merged
madil90 merged 13 commits into from
Mar 9, 2020
Merged

144 loadnifti transform common dataset #145

madil90 merged 13 commits into from
Mar 9, 2020

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@Nic-Ma
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@Nic-Ma Nic-Ma commented Mar 5, 2020 •
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Fixes #144 #146 .

Description

This PR implemented:

  1. Vanilla level and dictionary level transforms of LoadNifti.
  2. Common Dataset for dictionary format input data.
  3. Updated 3D segmentation example to the latest dictionary-based APIs.
  4. Added ChangeToChannelFirst transform.
  5. Fixed bug in Dice loss.

Status

Ready

Types of changes

  • Bug fix (non-breaking change which fixes an issue)
  • Breaking change (fix or new feature that would cause existing functionality to change)
  • New tests added to cover the changes
  • Docstrings/Documentation updated

wyli
wyli reviewed Mar 5, 2020
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wyli
wyli reviewed Mar 5, 2020
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wyli
wyli reviewed Mar 5, 2020
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wyli
wyli reviewed Mar 5, 2020
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wyli
wyli reviewed Mar 5, 2020
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@Nic-Ma
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Nic-Ma commented Mar 5, 2020

Hi @wyli @ericspod @atbenmurray ,

I updated code according to the comments.
Could you please help review it again?
Thanks.

madil90
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madil90
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@Nic-Ma Left comments inline.

madil90
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Nic-Ma commented Mar 6, 2020

Hi @wyli @madil90 @ericspod @atbenmurray ,

I updated the code according to the comments.
And also added below features to this PR:

  1. Added ChangeToChannelFirst transform.
  2. Updated 3D segmentation example to the latest dictionary-based APIs.
    Used ChangeToChannelFirstd, RandCropByPosNegLabeld, RandRotate90d transforms.
  3. Fixed bug in Dice loss: remove smooth from top, otherwise it may generate negative loss value.

I think we need another separate PR to update inference related logic.
Could you please help review it again?
Thanks.

@Nic-Ma Nic-Ma linked an issue Mar 6, 2020 that may be closed by this pull request
update train example with transforms #146
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wyli
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madil90
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@madil90 madil90 merged commit 39b2cb2 into master Mar 9, 2020
@wyli wyli deleted the 144-loadnifti-transform-common-dataset branch May 21, 2020 13:31
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@wyli wyli wyli approved these changes

@ericspod ericspod Awaiting requested review from ericspod

@atbenmurray atbenmurray Awaiting requested review from atbenmurray

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@madil90 madil90 madil90 approved these changes

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update train example with transforms loadnifti transform and common dataset

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@Nic-Ma @wyli @madil90