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ImageFilter's filter_size arg #8127

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oseymour opened this issue Oct 3, 2024 · 0 comments · May be fixed by #8189
Open

ImageFilter's filter_size arg #8127

oseymour opened this issue Oct 3, 2024 · 0 comments · May be fixed by #8189

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@oseymour
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oseymour commented Oct 3, 2024

Describe the bug
The docs say that NotImplementedError will be raised "when filter is a string and not in self.supported_filters". When I try to initialize a Gaussian filter with no filter_size arg, I get "ValueError: filter_size must be specified when specifying filters by string.". When I print out the support filters for ImageFilter, I get ['elliptical', 'gauss', 'laplace', 'mean', 'median', 'savitzky_golay', 'sharpen', 'sobel'].

To Reproduce
Steps to reproduce the behavior:

from monai.transforms import ImageFilter
import torch

x = torch.rand((1,10,10))
trans = ImageFilter(filter="gauss", sigma=2)
y = trans(x)

Expected behavior
When initializing a Gaussian filter, I shouldn't need to pass the filter_size arg.

Screenshots
n/a

Environment
Python 3.12.3

Ensuring you use the relevant python executable, please paste the output of:

================================
Printing MONAI config...
================================
MONAI version: 1.3.2
Numpy version: 1.25.2
Pytorch version: 2.4.0+cpu
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 59a7211070538586369afd4a01eca0a7fe2e742e
MONAI __file__: C:\Apps\Anaconda3\v3_9_7_x64\Local\lib\site-packages\monai\__init__.py

Optional dependencies:
Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.
ITK version: NOT INSTALLED or UNKNOWN VERSION.
Nibabel version: 5.2.1
scikit-image version: 0.19.2
scipy version: 1.9.3
Pillow version: 9.2.0
Tensorboard version: 2.8.0
gdown version: NOT INSTALLED or UNKNOWN VERSION.
TorchVision version: 0.19.0+cpu
tqdm version: 4.64.1
lmdb version: NOT INSTALLED or UNKNOWN VERSION.
psutil version: 5.9.0
pandas version: 1.5.1
einops version: NOT INSTALLED or UNKNOWN VERSION.
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: 2.12.1
pynrrd version: NOT INSTALLED or UNKNOWN VERSION.
clearml version: NOT INSTALLED or UNKNOWN VERSION.

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies


================================
Printing system config...
================================
System: Windows
Win32 version: ('10', '10.0.19045', 'SP0', 'Multiprocessor Free')
Win32 edition: Enterprise
Platform: Windows-10-10.0.19045-SP0
Processor: Intel64 Family 6 Model 186 Stepping 3, GenuineIntel
Machine: AMD64
Python version: 3.9.7
Process name: python.exe
Command: ['C:\\Apps\\Anaconda3\\v3_9_7_x64\\Local\\python.exe', '-c', 'import monai; monai.config.print_debug_info()']
Open files: [popenfile(path='C:\\Windows\\System32\\en-US\\KernelBase.dll.mui', fd=-1), popenfile(path='C:\\Windows\\System32\\en-US\\tzres.dll.mui', fd=-1), popenfile(path='C:\\Windows\\System32\\en-US\\kernel32.dll.mui', fd=-1)]
Num physical CPUs: 10
Num logical CPUs: 12
Num usable CPUs: 12
CPU usage (%): [37.8, 14.6, 45.1, 4.7, 7.3, 7.5, 4.4, 8.1, 14.5, 12.4, 8.0, 4.0]
CPU freq. (MHz): 1800
Load avg. in last 1, 5, 15 mins (%): [0.0, 0.0, 0.0]
Disk usage (%): 67.7
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 31.4
Available memory (GB): 18.7
Used memory (GB): 12.6

================================
Printing GPU config...
================================
Num GPUs: 0
Has CUDA: False
cuDNN enabled: False
NVIDIA_TF32_OVERRIDE: None
TORCH_ALLOW_TF32_CUBLAS_OVERRIDE: None

Additional context
Add any other context about the problem here.
EloiNavet added a commit to EloiNavet/MONAI that referenced this issue Nov 4, 2024
@EloiNavet
Fix ImageFilter to allow Gaussian filter without filter_size
79e8aa0 
Fixes Project-MONAI#8127

Update `ImageFilter` to handle Gaussian filter without requiring `filter_size`.

* Modify `monai/transforms/utility/array.py` to allow Gaussian filter without `filter_size`.
  - Adjust `_check_filter_format` method to skip `filter_size` check for Gaussian filter. Indeed Gauss filter is the only one in the list that doesn't require a filter_size.
* Add unit test in `tests/test_image_filter.py` for Gaussian filter without `filter_size`.
  - Verify output shape matches input shape.

Note that this method is compliant with the dictionnary version since this one load the fixed version.
@EloiNavet EloiNavet linked a pull request Nov 4, 2024 that will close this issue
Open
EloiNavet added a commit to EloiNavet/MONAI that referenced this issue Nov 6, 2024
@EloiNavet
Fix ImageFilter to allow Gaussian filter without filter_size
137892a 
Fixes Project-MONAI#8127

Update `ImageFilter` to handle Gaussian filter without requiring `filter_size`.

* Modify `monai/transforms/utility/array.py` to allow Gaussian filter without `filter_size`.
  - Adjust `_check_filter_format` method to skip `filter_size` check for Gaussian filter. Indeed Gauss filter is the only one in the list that doesn't require a filter_size.
* Add unit test in `tests/test_image_filter.py` for Gaussian filter without `filter_size`.
  - Verify output shape matches input shape.

Note that this method is compliant with the dictionnary version since this one load the fixed version.

Signed-off-by: Eloi Navet <[email protected]>
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Fix ImageFilter to allow Gaussian filter without filter_size EloiNavet/MONAI
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@oseymour