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ImageFilterd removes applied_operations #7394

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vlaminckaxel opened this issue Jan 16, 2024 · 0 comments · Fixed by #7395
Closed

ImageFilterd removes applied_operations #7394

vlaminckaxel opened this issue Jan 16, 2024 · 0 comments · Fixed by #7395

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@vlaminckaxel
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Describe the bug
When ImageFilterd is in the transformation sequence it removes all the applied_operations from the history.
Now we cant inverse the transformation sequence!

To Reproduce

    LoadImaged,
    Spacingd,
    ImageFilterd,
    Compose,
)
import numpy as np

# applied operations are present in the output of the transform
image = np.random.rand(10, 10, 10)
transforms = Compose(
    [
        Spacingd(keys=["image"], pixdim=(1.0, 1.0, 1.0), mode=("bilinear")),
    ]
)
print(transforms({"image": image})['image'].applied_operations)

# applied operations are not present in the output of the transform when using ImageFilterd
image = np.random.rand(10, 10, 10)
transforms = Compose(
    [
        Spacingd(keys=["image"], pixdim=(1.0, 1.0, 1.0), mode=("bilinear")),
        ImageFilterd(keys=["image"], kernel="mean", kernel_size=3)
    ]
)

print(transforms({"image": image})['image'].applied_operations)

Output:

[]
[{class: 'SpatialResample', id: 140011668257424, tracing: True, do_transforms: True, orig_size: (10, 10), lazy: False, extra_info: {'dtype': 'float64', 'mode': 'bilinear', 'padding_mode': 'border', 'align_corners': False, 'src_affine': tensor([[1., 0., 0.],
        [0., 1., 0.],
        [0., 0., 1.]], dtype=torch.float64)}}]

Environment

================================
Printing MONAI config...
================================
MONAI version: 1.3.0
Numpy version: 1.26.3
Pytorch version: 2.1.2+cu121
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 865972f7a791bf7b42efbcd87c8402bd865b329e
MONAI __file__: /home/<username>/protocept/rheumafinder_poc/.venv/lib/python3.11/site-packages/monai/__init__.py

Optional dependencies:
Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.
ITK version: NOT INSTALLED or UNKNOWN VERSION.
Nibabel version: 5.2.0
scikit-image version: NOT INSTALLED or UNKNOWN VERSION.
scipy version: 1.11.4
Pillow version: 10.2.0
Tensorboard version: 2.15.1
gdown version: NOT INSTALLED or UNKNOWN VERSION.
TorchVision version: NOT INSTALLED or UNKNOWN VERSION.
tqdm version: 4.66.1
lmdb version: NOT INSTALLED or UNKNOWN VERSION.
psutil version: 5.9.7
pandas version: NOT INSTALLED or UNKNOWN VERSION.
einops version: 0.7.0
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: NOT INSTALLED or UNKNOWN VERSION.
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: Linux
Linux version: Ubuntu 22.04.3 LTS
Platform: Linux-6.5.0-14-generic-x86_64-with-glibc2.35
Processor: x86_64
Machine: x86_64
Python version: 3.11.3
Process name: python
Command: ['python', '-c', 'import monai; monai.config.print_debug_info()']
Open files: [popenfile(path='/home/avlaminck/.vscode-server/data/logs/20240116T230111/ptyhost.log', fd=19, position=4331, mode='a', flags=33793), popenfile(path='/home/avlaminck/.vscode-server/data/logs/20240116T230111/network.log', fd=20, position=0, mode='a', flags=33793), popenfile(path='/home/avlaminck/.vscode-server/data/logs/20240116T230111/remoteagent.log', fd=22, position=5021, mode='a', flags=33793), popenfile(path='/home/avlaminck/.vscode-server/bin/0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2/vscode-remote-lock.avlaminck.0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2', fd=99, position=0, mode='w', flags=32769)]
Num physical CPUs: 24
Num logical CPUs: 32
Num usable CPUs: 32
CPU usage (%): [13.0, 14.5, 13.2, 13.0, 11.8, 11.9, 13.0, 13.2, 98.5, 13.2, 14.5, 13.2, 13.2, 13.2, 13.2, 13.2, 13.2, 11.9, 13.2, 14.5, 11.9, 13.2, 11.9, 13.2, 13.0, 13.2, 11.9, 14.5, 13.2, 11.8, 13.2, 11.9]
CPU freq. (MHz): 1871
Load avg. in last 1, 5, 15 mins (%): [0.1, 0.5, 4.5]
Disk usage (%): 96.3
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 125.6
Available memory (GB): 111.6
Used memory (GB): 12.5

================================
Printing GPU config...
================================
Num GPUs: 1
Has CUDA: True
CUDA version: 12.1
cuDNN enabled: True
NVIDIA_TF32_OVERRIDE: None
TORCH_ALLOW_TF32_CUBLAS_OVERRIDE: None
cuDNN version: 8902
Current device: 0
Library compiled for CUDA architectures: ['sm_50', 'sm_60', 'sm_70', 'sm_75', 'sm_80', 'sm_86', 'sm_90']
GPU 0 Name: NVIDIA GeForce RTX 4090
GPU 0 Is integrated: False
GPU 0 Is multi GPU board: False
GPU 0 Multi processor count: 128
GPU 0 Total memory (GB): 23.6
GPU 0 CUDA capability (maj.min): 8.9
@vlaminckaxel vlaminckaxel changed the title ImageFilterd clears applied_operations ImageFilterd removes applied_operations Jan 16, 2024
KumoLiu pushed a commit that referenced this issue Jan 18, 2024
Fixes #7394 

### Description

When ImageFilter is in the transformation sequence it didn't pass the
applied_operations.
Now it is passed when present.

### 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).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] 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.

---------

Signed-off-by: axel.vlaminck <axel.vlaminck@gmail.com>
marksgraham pushed a commit to marksgraham/MONAI that referenced this issue Jan 30, 2024
Fixes Project-MONAI#7394

### Description

When ImageFilter is in the transformation sequence it didn't pass the
applied_operations.
Now it is passed when present.

### 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).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] 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.

---------

Signed-off-by: axel.vlaminck <axel.vlaminck@gmail.com>
Signed-off-by: Mark Graham <markgraham539@gmail.com>
juampatronics pushed a commit to juampatronics/MONAI that referenced this issue Mar 25, 2024
Fixes Project-MONAI#7394

### Description

When ImageFilter is in the transformation sequence it didn't pass the
applied_operations.
Now it is passed when present.

### 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).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] 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.

---------

Signed-off-by: axel.vlaminck <axel.vlaminck@gmail.com>
Signed-off-by: Juan Pablo de la Cruz Gutiérrez <juampatronics@gmail.com>
Yu0610 pushed a commit to Yu0610/MONAI that referenced this issue Apr 11, 2024
Fixes Project-MONAI#7394

### Description

When ImageFilter is in the transformation sequence it didn't pass the
applied_operations.
Now it is passed when present.

### 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).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [x] 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.

---------

Signed-off-by: axel.vlaminck <axel.vlaminck@gmail.com>
Signed-off-by: Yu0610 <612410030@alum.ccu.edu.tw>
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