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2620 3595 Writer backend selector, deprecating nifti_saver/writer, png_saver/writer#3773

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wyli merged 11 commits intoProject-MONAI:devfrom
wyli:writer-backend-selector
Feb 10, 2022
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2620 3595 Writer backend selector, deprecating nifti_saver/writer, png_saver/writer#3773
wyli merged 11 commits intoProject-MONAI:devfrom
wyli:writer-backend-selector

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@wyli wyli commented Feb 5, 2022 •
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closes #3595
closes #2620

Description

this is to add a resolve_writer and register_writer,
update monai.transform.SaveImage to use the latest API.

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 wyli force-pushed the writer-backend-selector branch 2 times, most recently from c122c0e to a934a49 Compare February 7, 2022 16:02
@wyli wyli mentioned this pull request Feb 7, 2022
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@wyli wyli force-pushed the writer-backend-selector branch from 88b00c0 to c4e23df Compare February 8, 2022 14:26
@wyli wyli changed the title 3595 Writer backend selector, deprecating nifti_saver/writer, png_saver/writer 2620 3595 Writer backend selector, deprecating nifti_saver/writer, png_saver/writer Feb 8, 2022
@wyli wyli marked this pull request as ready for review February 9, 2022 11:09
@wyli wyli requested review from Nic-Ma, ericspod and rijobro February 9, 2022 11:10
ericspod
ericspod approved these changes Feb 9, 2022
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Looks good to me!

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Nic-Ma commented Feb 9, 2022

Hi @wyli ,

Thanks for the quick update.
I will try to review this PR tomorrow morning.

Thanks.

@wyli
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wyli commented Feb 9, 2022

/black

@wyli wyli mentioned this pull request Feb 9, 2022
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@wyli wyli force-pushed the writer-backend-selector branch from a4df129 to d55e922 Compare February 10, 2022 10:36
wyli added 7 commits February 10, 2022 10:39
@wyli
update saveimage and writer selector
33f0348 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
more tests
0df2424 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
more tests
677cb10 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
adds saving loading tests
05b94ad 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
fixes Project-MONAI#3783
aa7af63 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
enhance import checks
7439019 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
warn to exception; int check
f86ce2b 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli wyli force-pushed the writer-backend-selector branch from 6b2e6d8 to f86ce2b Compare February 10, 2022 10:39
@wyli
fixes tests
9292690 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Nic-Ma
Nic-Ma reviewed Feb 10, 2022
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Comment thread monai/data/image_writer.py Outdated
Comment thread monai/data/image_writer.py Outdated
Comment thread monai/data/image_writer.py
fmt = f"{ext_name}".lower()
existing = look_up_option(fmt, SUPPORTED_WRITERS, default=())
all_writers = im_writer + existing
SUPPORTED_WRITERS[fmt] = all_writers
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Hi @wyli ,

Here you use a global dictionary to store the supported format -> writers mapping, while in the image readers we store readers in LoadImage transform with its own supported formats, for example:
https://github.com/Project-MONAI/MONAI/blob/dev/monai/data/image_reader.py#L386

I am not very sure which way is better, the readers way is similar to the Chain of Responsibility design pattern, This global SUPPORTED_WRITERS may be not easy to maintain, especially in multi-threads cases, etc.
Maybe because I was Java / C++ developer before, I usually never use global variables even in python. I prefer to use class to implement complicated logic, because it can maintain self-contained local states. For example you implemented FolderLayout as a class instead of a function.
Glad to see your opinions.
@ericspod @rijobro What do you guys think?

Thanks in advance.

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@wyli wyli Feb 10, 2022 •
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SUPPORTED_WRITERS is a module-level variable, it's not a global one. it's a global dict accessed without global keyword.. I believe it's a
very common design, for example, scikit-image and PIL used it in a similar way

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OK, I am not sure whether it can work fine if calling SaveImage in multi-thread? I think all our non-random transforms are thread-safe now.

Thanks.

Comment thread monai/data/image_writer.py Outdated
Comment thread monai/data/image_writer.py Outdated
Comment thread monai/data/image_writer.py
Comment thread monai/data/image_writer.py Outdated
Comment thread monai/data/image_writer.py
Comment thread monai/transforms/io/array.py
Comment thread monai/transforms/io/array.py Outdated
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Nic-Ma commented Feb 10, 2022

Hi @wyli ,

Thanks for the quick implementation, put some comments inline, I will review the unit tests later.

Thanks.

Nic-Ma
Nic-Ma reviewed Feb 10, 2022
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Comment thread tests/min_tests.py
@wyli
update based on comments
01853a6 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli wyli force-pushed the writer-backend-selector branch from 67826e8 to 01853a6 Compare February 10, 2022 18:14
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wyli commented Feb 10, 2022 •
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/integration-test
/black

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wyli commented Feb 10, 2022

/build

@wyli wyli mentioned this pull request Feb 10, 2022
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@wyli
fixes Project-MONAI#3787
2c09f8e 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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wyli commented Feb 10, 2022

/build

@wyli
unit testing
0152543 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli wyli force-pushed the writer-backend-selector branch from 696c77e to 0152543 Compare February 10, 2022 22:36
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wyli commented Feb 10, 2022

/build

@wyli wyli enabled auto-merge (squash) February 10, 2022 22:39
@wyli wyli merged commit 127e823 into Project-MONAI:dev Feb 10, 2022
@wyli wyli deleted the writer-backend-selector branch April 27, 2022 22:35
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refactoring the image writer modules Image writer with itk backend to support more output image formats

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