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3595 Adds nibabel/pil writers#3772

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wyli merged 44 commits intoProject-MONAI:devfrom
wyli:adds-nibabel-pil-writer
Feb 8, 2022
Merged

3595 Adds nibabel/pil writers#3772
wyli merged 44 commits intoProject-MONAI:devfrom
wyli:adds-nibabel-pil-writer

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@wyli wyli commented Feb 5, 2022 •
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part of #3595

Description

adds a Nibabelwriter, PILWriter

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

wyli and others added 30 commits January 25, 2022 18:20
@wyli
temp spatial_resample
dad9365 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes resampling
0f07fc9 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes precisions
b09e568 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
update dict version
0b4bc52 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes unit tests
996dacf 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
adds docs
2790ca4 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
copy grid for resampling
4ef11bf 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes unit tests
f65605e 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
remove normalize coordinates
b3011a7 
Signed-off-by: Wenqi Li <[email protected]>
@monai-bot @wyli
[MONAI] python code formatting
a1200dc 
Signed-off-by: monai-bot <[email protected]>
@wyli
try to fix Project-MONAI#3621 (Project-MONAI#3673)
7b91be4 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes typing
ec9aaf3 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes grid_sample, interpolate URLs
0ac197f 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
Merge branch 'fixes-url' into add-spatial-resample
87ff30b 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
Merge remote-tracking branch 'upstream/dev' into add-spatial-resample
080f803 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
simplify norm_coords
aee76ee 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
update docstring
0dc88af 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
update moveaxis
d044188 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
spatial sample tests
7a42452 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
additional tests spatial resample
5ec96a4 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
test invert saptial resample
6509070 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
adds a base writer and an itk writer
0705aa7 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
update docstrings
df2631a 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
remove return self
4419803 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
adds reorient_spatial_axes
4f27d0d 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
update based on comments
9f2d311 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
update based on comments
f2a2ea9 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
fixes unit tests
bc9c705 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
Merge remote-tracking branch 'upstream/dev' into add-spatial-resample
47bf3e2 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
Merge branch 'add-spatial-resample' into adds-base-writer-itk-writer
0d93935 
Signed-off-by: Wenqi Li <[email protected]>
wyli and others added 10 commits January 27, 2022 22:11
@wyli
sync 3701
f96614b 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
Merge branch 'dev' into adds-base-writer-itk-writer
bac0b1a 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
Merge branch 'dev' into adds-base-writer-itk-writer
5ddcd90
@wyli
try to fix Project-MONAI#3766
b32336e 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
Merge branch 'dev' into adds-base-writer-itk-writer
14b9bda 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
revise docstring to be concise
dbf44ae 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
update based on comments
1f23c04 
Signed-off-by: Wenqi Li <[email protected]>
@Nic-Ma @wyli
3765 Enhance create_multigpu_supervised_XXX for distributed (Projec…
f49a092 
…t-MONAI#3768)

* [DLMED] add check for devices

Signed-off-by: Nic Ma <[email protected]>

* [DLMED] update according to comments

Signed-off-by: Nic Ma <[email protected]>
@wyli
update to support dynamic spatial_size
4fe1b12 
Signed-off-by: Wenqi Li <[email protected]>
@wyli
adds nibabel pil writers
73ceb4f 
Signed-off-by: Wenqi Li <[email protected]>
@wyli wyli mentioned this pull request Feb 5, 2022
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7 tasks
@wyli wyli requested review from Nic-Ma, ericspod and rijobro February 7, 2022 13:00
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wyli commented Feb 7, 2022

@Nic-Ma this is ready, mainly replaces write_nifti and write_png.

@wyli
remove unused ignore
100faf1 
Signed-off-by: Wenqi Li <[email protected]>
Nic-Ma
Nic-Ma approved these changes Feb 8, 2022
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The overall design looks good to me.
Could you please help also add the numpy writer to be consistent with readers?
And I think need to double confirm the data shape when reading and writing with mixed ITK / Nibabel Reader / Writer.

Thanks.

@wyli wyli force-pushed the adds-nibabel-pil-writer branch from 93d6296 to d4319be Compare February 8, 2022 10:47
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wyli commented Feb 8, 2022

/build

@wyli wyli enabled auto-merge (squash) February 8, 2022 12:59
@wyli wyli merged commit 4d0baa0 into Project-MONAI:dev Feb 8, 2022
@wyli wyli deleted the adds-nibabel-pil-writer branch April 27, 2022 22:35
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@Nic-Ma Nic-Ma Nic-Ma approved these changes

@rijobro rijobro Awaiting requested review from rijobro

@ericspod ericspod Awaiting requested review from ericspod ericspod is a code owner

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@wyli @Nic-Ma @monai-bot