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Add sample_std parameter to RandGaussianNoise. #7492

Merged
merged 4 commits into from
Feb 26, 2024
Merged

Add sample_std parameter to RandGaussianNoise. #7492

merged 4 commits into from
Feb 26, 2024

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bakert1
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@bakert1 bakert1 commented Feb 26, 2024 •
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Fixes issue #7425

Description

Add a sample_std parameter to RandGaussianNoise and RandGaussianNoised. When True, the Gaussian's standard deviation is sampled uniformly from 0 to std (i.e., what is currently done). When False, the noise's standard deviation is non-random and set to std. The default for sample_std would be True for backwards compatibility.

Changes were based on RandRicianNoise which already has a sample_std parameter and is similar to RandGaussianNoise in concept and implementation.

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

@bakert1
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bakert1 commented Feb 26, 2024

Question: I added the new sample_std parameter to the end of the RandGaussianNoise and RandGaussianNoised __init__ functions as to not break existing code that passed parameters by position. However, it seems weird that allow_missing_keys is not the last parameter of RandGaussianNoised. What is the correct trade-off between code consistency and backwards compatibility?

@bakert1
Fixed code formatting.
7574aa0
@bakert1
DCO Remediation Commit for Timothy Baker <bakertim@umich.edu>
86a646f 
I, Timothy Baker <bakertim@umich.edu>, hereby add my Signed-off-by to this commit: 420a2d1
I, Timothy Baker <bakertim@umich.edu>, hereby add my Signed-off-by to this commit: 7574aa0

Signed-off-by: Timothy Baker <bakertim@umich.edu>
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KumoLiu commented Feb 26, 2024

I added the new sample_std parameter to the end of the RandGaussianNoise and RandGaussianNoised init functions as to not break existing code that passed parameters by position

This way should be ok.

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bakert1 commented Feb 26, 2024 •
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Cool thanks. Also, I am running tests locally and the tests/test_integration_classification_2d.py test seems to be running slow. I think it's because I am running on Mac silicon (i.e., no CUDA device) - is there anyway around this?

Not sure the integration tests are necessary for such a small change, but I may work on other MONAI features in the future.

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KumoLiu commented Feb 26, 2024

Not sure the integration tests are necessary for such a small change, but I may work on other MONAI features in the future.

It would be great if the tests in the relevant part could be tested. Of course, I will do more tests before merging.

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bakert1 commented Feb 26, 2024

Not sure the integration tests are necessary for such a small change, but I may work on other MONAI features in the future.

It would be great if the tests in the relevant part could be tested. Of course, I will do more tests before merging.

Yeah I added a test for the new sample_std parameter and ran the tests related to RandGaussianNoise as well the quick tests. Everything passed locally.

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KumoLiu commented Feb 26, 2024

/build

@KumoLiu KumoLiu requested review from ericspod and Nic-Ma February 26, 2024 05:52
@bakert1 bakert1 marked this pull request as ready for review February 26, 2024 12:42
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ericspod approved these changes Feb 26, 2024
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Looks good to me, I don't think these changes will affect compatibility anywhere.

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KumoLiu commented Feb 26, 2024

/build

@KumoLiu KumoLiu enabled auto-merge (squash) February 26, 2024 15:40
@KumoLiu KumoLiu merged commit 7cfa2c9 into Project-MONAI:dev Feb 26, 2024
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juampatronics pushed a commit to juampatronics/MONAI that referenced this pull request Mar 25, 2024
@bakert1 @juampatronics
Add sample_std parameter to RandGaussianNoise. (Project-MONAI#7492)
b0c96d8 
Fixes issue Project-MONAI#7425

### Description

Add a `sample_std` parameter to `RandGaussianNoise` and
`RandGaussianNoised`. When True, the Gaussian's standard deviation is
sampled uniformly from 0 to std (i.e., what is currently done). When
False, the noise's standard deviation is non-random and set to std. The
default for sample_std would be True for backwards compatibility.

Changes were based on RandRicianNoise which already has a `sample_std`
parameter and is similar to RandGaussianNoise in concept and
implementation.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: Timothy Baker <bakertim@umich.edu>
Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>
Yu0610 pushed a commit to Yu0610/MONAI that referenced this pull request Apr 11, 2024
@bakert1 @Yu0610
Add sample_std parameter to RandGaussianNoise. (Project-MONAI#7492)
57e197c 
Fixes issue Project-MONAI#7425

### Description

Add a `sample_std` parameter to `RandGaussianNoise` and
`RandGaussianNoised`. When True, the Gaussian's standard deviation is
sampled uniformly from 0 to std (i.e., what is currently done). When
False, the noise's standard deviation is non-random and set to std. The
default for sample_std would be True for backwards compatibility.

Changes were based on RandRicianNoise which already has a `sample_std`
parameter and is similar to RandGaussianNoise in concept and
implementation.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [x] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [x] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: Timothy Baker <bakertim@umich.edu>
Signed-off-by: Yu0610 <612410030@alum.ccu.edu.tw>
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