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Replace deprecated monai transforms #430

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marksgraham merged 6 commits into from
Oct 31, 2023
Merged

Replace deprecated monai transforms #430

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cdf5bc2
updates 3d_vqvae_tutorial.py
marksgraham Oct 31, 2023
da91c89
updates 3d_vqvae_tutorial.ipynb
marksgraham Oct 31, 2023
be3d060
updates 3d_ddpm_tutorial.py
marksgraham Oct 31, 2023
5c5f908
Replace addchannel from pyton tutorials
marksgraham Oct 31, 2023
ebdd1d9
Removes aschannelfirst
marksgraham Oct 31, 2023
bcdae94
Updates notebooks
marksgraham Oct 31, 2023
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4 changes: 2 additions & 2 deletions tests/test_integration_workflows_adversarial.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
from monai.data import create_test_image_2d
from monai.handlers import CheckpointSaver, StatsHandler, TensorBoardStatsHandler
from monai.networks.nets import AutoEncoder, Discriminator
from monai.transforms import AsChannelFirstd, Compose, LoadImaged, RandFlipd, ScaleIntensityd
from monai.transforms import Compose, EnsureChannelFirstd, LoadImaged, RandFlipd, ScaleIntensityd
from monai.utils import CommonKeys, set_determinism

from generative.engines import AdversarialTrainer
Expand All @@ -44,7 +44,7 @@ def run_training_test(root_dir, device="cuda:0"):
train_transforms = Compose(
[
LoadImaged(keys=[CommonKeys.IMAGE, CommonKeys.LABEL]),
AsChannelFirstd(keys=[CommonKeys.IMAGE, CommonKeys.LABEL]),
EnsureChannelFirstd(keys=[CommonKeys.IMAGE, CommonKeys.LABEL], channel_dim=2),
ScaleIntensityd(keys=[CommonKeys.IMAGE]),
RandFlipd(keys=[CommonKeys.IMAGE, CommonKeys.LABEL], prob=0.5),
]
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2,839 changes: 1,419 additions & 1,420 deletions tutorials/generative/2d_controlnet/2d_controlnet.ipynb
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3 changes: 1 addition & 2 deletions tutorials/generative/2d_controlnet/2d_controlnet.py
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Expand Up @@ -105,7 +105,7 @@
transforms.LoadImaged(keys=["image"]),
transforms.EnsureChannelFirstd(keys=["image"]),
transforms.Lambdad(keys=["image"], func=lambda x: x[channel, :, :, :]),
transforms.AddChanneld(keys=["image"]),
transforms.EnsureChannelFirstd(keys=["image"], channel_dim="no_channel"),
transforms.EnsureTyped(keys=["image"]),
transforms.Orientationd(keys=["image"], axcodes="RAS"),
transforms.Spacingd(keys=["image"], pixdim=(3.0, 3.0, 2.0), mode="bilinear"),
Expand Down Expand Up @@ -339,7 +339,6 @@
optimizer.zero_grad(set_to_none=True)

with autocast(enabled=True):

# Generate random noise
noise = torch.randn_like(images).to(device)

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1,958 changes: 979 additions & 979 deletions tutorials/generative/3d_autoencoderkl/3d_autoencoderkl_tutorial.ipynb
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6 changes: 3 additions & 3 deletions tutorials/generative/3d_autoencoderkl/3d_autoencoderkl_tutorial.py
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Expand Up @@ -6,7 +6,7 @@
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.14.4
# jupytext_version: 1.14.1
# kernelspec:
# display_name: Python 3 (ipykernel)
# language: python
Expand Down Expand Up @@ -91,7 +91,7 @@
transforms.LoadImaged(keys=["image"]),
transforms.EnsureChannelFirstd(keys=["image"]),
transforms.Lambdad(keys="image", func=lambda x: x[channel, :, :, :]),
transforms.AddChanneld(keys=["image"]),
transforms.EnsureChannelFirstd(keys=["image"], channel_dim="no_channel"),
transforms.EnsureTyped(keys=["image"]),
transforms.Orientationd(keys=["image"], axcodes="RAS"),
transforms.Spacingd(keys=["image"], pixdim=(2.4, 2.4, 2.2), mode=("bilinear")),
Expand Down Expand Up @@ -138,7 +138,7 @@
transforms.LoadImaged(keys=["image"]),
transforms.EnsureChannelFirstd(keys=["image"]),
transforms.Lambdad(keys="image", func=lambda x: x[channel, :, :, :]),
transforms.AddChanneld(keys=["image"]),
transforms.EnsureChannelFirstd(keys=["image"], channel_dim="no_channel"),
transforms.EnsureTyped(keys=["image"]),
transforms.Orientationd(keys=["image"], axcodes="RAS"),
transforms.Spacingd(keys=["image"], pixdim=(2.4, 2.4, 2.2), mode=("bilinear")),
Expand Down
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