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Merged
wyli merged 3 commits into from
Feb 15, 2022
Merged

545 orientation/spacing #546

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97b6633
fixes #545
wyli Feb 14, 2022
ccc2f7d
update 3d image transforms tutorial
wyli Feb 14, 2022
6444a44
Merge branch 'master' into 545-orientation
wyli Feb 15, 2022
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6 changes: 3 additions & 3 deletions 3d_segmentation/brats_segmentation_3d.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -266,12 +266,12 @@
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=\"image\"),\n",
" ConvertToMultiChannelBasedOnBratsClassesd(keys=\"label\"),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.0, 1.0, 1.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" RandSpatialCropd(keys=[\"image\", \"label\"], roi_size=[224, 224, 144], random_size=False),\n",
" RandFlipd(keys=[\"image\", \"label\"], prob=0.5, spatial_axis=0),\n",
" RandFlipd(keys=[\"image\", \"label\"], prob=0.5, spatial_axis=1),\n",
Expand All @@ -287,12 +287,12 @@
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=\"image\"),\n",
" ConvertToMultiChannelBasedOnBratsClassesd(keys=\"label\"),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.0, 1.0, 1.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" NormalizeIntensityd(keys=\"image\", nonzero=True, channel_wise=True),\n",
" EnsureTyped(keys=[\"image\", \"label\"]),\n",
" ]\n",
Expand Down Expand Up @@ -784,8 +784,8 @@
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=[\"image\"]),\n",
" ConvertToMultiChannelBasedOnBratsClassesd(keys=\"label\"),\n",
" Spacingd(keys=[\"image\"], pixdim=(1.0, 1.0, 1.0), mode=\"bilinear\"),\n",
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
" Spacingd(keys=[\"image\"], pixdim=(1.0, 1.0, 1.0), mode=\"bilinear\"),\n",
" NormalizeIntensityd(keys=\"image\", nonzero=True, channel_wise=True),\n",
" EnsureTyped(keys=[\"image\", \"label\"]),\n",
" ]\n",
Expand Down
12 changes: 6 additions & 6 deletions 3d_segmentation/spleen_segmentation_3d.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -259,8 +259,8 @@
"Here we use several transforms to augment the dataset:\n",
"1. `LoadImaged` loads the spleen CT images and labels from NIfTI format files.\n",
"1. `AddChanneld` as the original data doesn't have channel dim, add 1 dim to construct \"channel first\" shape.\n",
"1. `Spacingd` adjusts the spacing by `pixdim=(1.5, 1.5, 2.)` based on the affine matrix.\n",
"1. `Orientationd` unifies the data orientation based on the affine matrix.\n",
"1. `Spacingd` adjusts the spacing by `pixdim=(1.5, 1.5, 2.)` based on the affine matrix.\n",
"1. `ScaleIntensityRanged` extracts intensity range [-57, 164] and scales to [0, 1].\n",
"1. `CropForegroundd` removes all zero borders to focus on the valid body area of the images and labels.\n",
"1. `RandCropByPosNegLabeld` randomly crop patch samples from big image based on pos / neg ratio. \n",
Expand All @@ -279,9 +279,9 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(keys=[\"image\", \"label\"], pixdim=(\n",
" 1.5, 1.5, 2.0), mode=(\"bilinear\", \"nearest\")),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"], a_min=-57, a_max=164,\n",
" b_min=0.0, b_max=1.0, clip=True,\n",
Expand Down Expand Up @@ -311,9 +311,9 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(keys=[\"image\", \"label\"], pixdim=(\n",
" 1.5, 1.5, 2.0), mode=(\"bilinear\", \"nearest\")),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"], a_min=-57, a_max=164,\n",
" b_min=0.0, b_max=1.0, clip=True,\n",
Expand Down Expand Up @@ -692,9 +692,9 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" EnsureChannelFirstd(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
" Spacingd(keys=[\"image\"], pixdim=(\n",
" 1.5, 1.5, 2.0), mode=\"bilinear\"),\n",
" Orientationd(keys=[\"image\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"], a_min=-57, a_max=164,\n",
" b_min=0.0, b_max=1.0, clip=True,\n",
Expand Down Expand Up @@ -785,7 +785,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -799,7 +799,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.7.10"
}
},
"nbformat": 4,
Expand Down
8 changes: 4 additions & 4 deletions 3d_segmentation/spleen_segmentation_3d_lightning.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -270,12 +270,12 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"], a_min=-57, a_max=164,\n",
" b_min=0.0, b_max=1.0, clip=True,\n",
Expand Down Expand Up @@ -310,12 +310,12 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"], a_min=-57, a_max=164,\n",
" b_min=0.0, b_max=1.0, clip=True,\n",
Expand Down Expand Up @@ -691,7 +691,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -705,7 +705,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.7.10"
}
},
"nbformat": 4,
Expand Down
8 changes: 4 additions & 4 deletions 3d_segmentation/unetr_btcv_segmentation_3d.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -197,12 +197,12 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"],\n",
" a_min=-175,\n",
Expand Down Expand Up @@ -254,12 +254,12 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"], a_min=-175, a_max=250, b_min=0.0, b_max=1.0, clip=True\n",
" ),\n",
Expand Down Expand Up @@ -833,7 +833,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -847,7 +847,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.7.10"
}
},
"nbformat": 4,
Expand Down
8 changes: 4 additions & 4 deletions 3d_segmentation/unetr_btcv_segmentation_3d_lightning.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -444,12 +444,12 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"],\n",
" a_min=-175,\n",
Expand Down Expand Up @@ -501,12 +501,12 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"],\n",
" a_min=-175,\n",
Expand Down Expand Up @@ -771,7 +771,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -785,7 +785,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.7.10"
}
},
"nbformat": 4,
Expand Down
8 changes: 4 additions & 4 deletions acceleration/automatic_mixed_precision.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -239,12 +239,12 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"],\n",
" a_min=-57,\n",
Expand Down Expand Up @@ -282,12 +282,12 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"],\n",
" a_min=-57,\n",
Expand Down Expand Up @@ -856,7 +856,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -870,7 +870,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.7.10"
}
},
"nbformat": 4,
Expand Down
8 changes: 4 additions & 4 deletions acceleration/dataset_type_performance.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -398,12 +398,12 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"],\n",
" a_min=-57,\n",
Expand Down Expand Up @@ -437,12 +437,12 @@
" [\n",
" LoadImaged(keys=[\"image\", \"label\"]),\n",
" AddChanneld(keys=[\"image\", \"label\"]),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" Spacingd(\n",
" keys=[\"image\", \"label\"],\n",
" pixdim=(1.5, 1.5, 2.0),\n",
" mode=(\"bilinear\", \"nearest\"),\n",
" ),\n",
" Orientationd(keys=[\"image\", \"label\"], axcodes=\"RAS\"),\n",
" ScaleIntensityRanged(\n",
" keys=[\"image\"],\n",
" a_min=-57,\n",
Expand Down Expand Up @@ -739,7 +739,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -753,7 +753,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.7.10"
}
},
"nbformat": 4,
Expand Down
4 changes: 2 additions & 2 deletions acceleration/distributed_training/brats_training_ddp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,12 +189,12 @@ def main_worker(args):
LoadImaged(keys=["image", "label"]),
EnsureChannelFirstd(keys="image"),
ConvertToMultiChannelBasedOnBratsClassesd(keys="label"),
Orientationd(keys=["image", "label"], axcodes="RAS"),
Spacingd(
keys=["image", "label"],
pixdim=(1.0, 1.0, 1.0),
mode=("bilinear", "nearest"),
),
Orientationd(keys=["image", "label"], axcodes="RAS"),
EnsureTyped(keys=["image", "label"]),
ToDeviced(keys=["image", "label"], device=device),
RandSpatialCropd(keys=["image", "label"], roi_size=[224, 224, 144], random_size=False),
Expand Down Expand Up @@ -225,12 +225,12 @@ def main_worker(args):
LoadImaged(keys=["image", "label"]),
EnsureChannelFirstd(keys="image"),
ConvertToMultiChannelBasedOnBratsClassesd(keys="label"),
Orientationd(keys=["image", "label"], axcodes="RAS"),
Spacingd(
keys=["image", "label"],
pixdim=(1.0, 1.0, 1.0),
mode=("bilinear", "nearest"),
),
Orientationd(keys=["image", "label"], axcodes="RAS"),
NormalizeIntensityd(keys="image", nonzero=True, channel_wise=True),
EnsureTyped(keys=["image", "label"]),
ToDeviced(keys=["image", "label"], device=device),
Expand Down
2 changes: 1 addition & 1 deletion acceleration/fast_model_training_guide.md
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Original file line number Diff line number Diff line change
Expand Up @@ -260,8 +260,8 @@ For example:
train_transforms = [
LoadImaged(...),
AddChanneld(...),
Spacingd(...),
Orientationd(...),
Spacingd(...),
ScaleIntensityRanged(...),
CropForegroundd(...),
FgBgToIndicesd(...),
Expand Down
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