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Merged
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Apr 8, 2022
Merged

Update MONAI version after having validated compatibility. #288

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2 changes: 1 addition & 1 deletion examples/apps/ai_livertumor_seg_app/livertumor_seg_operator.py
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Expand Up @@ -34,7 +34,7 @@
@md.input("image", Image, IOType.IN_MEMORY)
@md.output("seg_image", Image, IOType.IN_MEMORY)
@md.output("saved_images_folder", DataPath, IOType.DISK)
@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.21", "nibabel"])
@md.env(pip_packages=["monai>=0.8.1", "torch>=1.5", "numpy>=1.21", "nibabel"])
class LiverTumorSegOperator(Operator):
"""Performs liver and tumor segmentation using a DL model with an image converted from a DICOM CT series.

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2 changes: 1 addition & 1 deletion examples/apps/ai_spleen_seg_app/spleen_seg_operator.py
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Expand Up @@ -34,7 +34,7 @@

@md.input("image", Image, IOType.IN_MEMORY)
@md.output("seg_image", Image, IOType.IN_MEMORY)
@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.21", "nibabel"])
@md.env(pip_packages=["monai>=0.8.1", "torch>=1.5", "numpy>=1.21", "nibabel"])
class SpleenSegOperator(Operator):
"""Performs Spleen segmentation with a 3D image converted from a DICOM CT series.

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2 changes: 1 addition & 1 deletion examples/apps/ai_unetr_seg_app/unetr_seg_operator.py
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Expand Up @@ -35,7 +35,7 @@
@md.input("image", Image, IOType.IN_MEMORY)
@md.output("seg_image", Image, IOType.IN_MEMORY)
@md.output("saved_images_folder", DataPath, IOType.DISK)
@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.21", "nibabel"])
@md.env(pip_packages=["monai>=0.8.1", "torch>=1.5", "numpy>=1.21", "nibabel"])
class UnetrSegOperator(Operator):
"""Performs multi-organ segmentation using UNETR model with an image converted from a DICOM CT series.

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2 changes: 1 addition & 1 deletion examples/apps/deply_app_on_aarch64_interim.md
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Expand Up @@ -28,7 +28,7 @@ In the following sections, the UNETR Multi-organ Segmentation application will b
### Create the requirements file
Without using the MONAI Deploy App SDK Packager to automatically detect the dependencies of an application, one has to explicitly create the `requierments.txt` file to be used in the `Dockerfile`. Create the `requirements.txt` file in the application's folder with the content shown below,
```bash
monai>=0.6.0
monai>=0.8.1
monai-deploy-app-sdk>=0.1.0
nibabel
numpy>=1.21
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Empty file modified monai/deploy/operators/dicom_data_loader_operator.py
100755 → 100644
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2 changes: 1 addition & 1 deletion monai/deploy/operators/monai_seg_inference_operator.py
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Expand Up @@ -43,7 +43,7 @@

@md.input("image", Image, IOType.IN_MEMORY)
@md.output("seg_image", Image, IOType.IN_MEMORY)
@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.21"])
@md.env(pip_packages=["monai>=0.8.1", "torch>=1.5", "numpy>=1.21"])
class MonaiSegInferenceOperator(InferenceOperator):
"""This segmentation operator uses MONAI transforms and Sliding Window Inference.

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4 changes: 2 additions & 2 deletions notebooks/tutorials/03_segmentation_app.ipynb
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Expand Up @@ -754,7 +754,7 @@
"source": [
"@md.input(\"image\", Image, IOType.IN_MEMORY)\n",
"@md.output(\"seg_image\", Image, IOType.IN_MEMORY)\n",
"@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\"])\n",
"@md.env(pip_packages=[\"monai>=0.8.1\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\"])\n",
"class SpleenSegOperator(Operator):\n",
" \"\"\"Performs Spleen segmentation with a 3D image converted from a DICOM CT series.\n",
" \"\"\"\n",
Expand Down Expand Up @@ -1076,7 +1076,7 @@
"\n",
"@md.input(\"image\", Image, IOType.IN_MEMORY)\n",
"@md.output(\"seg_image\", Image, IOType.IN_MEMORY)\n",
"@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\", \"typeguard\"])\n",
"@md.env(pip_packages=[\"monai>=0.8.1\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\", \"typeguard\"])\n",
"class SpleenSegOperator(Operator):\n",
" \"\"\"Performs Spleen segmentation with a 3D image converted from a DICOM CT series.\n",
" \"\"\"\n",
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4 changes: 2 additions & 2 deletions notebooks/tutorials/03_segmentation_viz_app.ipynb
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Expand Up @@ -753,7 +753,7 @@
"source": [
"@md.input(\"image\", Image, IOType.IN_MEMORY)\n",
"@md.output(\"seg_image\", Image, IOType.IN_MEMORY)\n",
"@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.20\", \"nibabel\"])\n",
"@md.env(pip_packages=[\"monai>=0.8.1\", \"torch>=1.5\", \"numpy>=1.20\", \"nibabel\"])\n",
"class SpleenSegOperator(Operator):\n",
" \"\"\"Performs Spleen segmentation with a 3D image converted from a DICOM CT series.\n",
" \"\"\"\n",
Expand Down Expand Up @@ -1103,7 +1103,7 @@
"\n",
"@md.input(\"image\", Image, IOType.IN_MEMORY)\n",
"@md.output(\"seg_image\", Image, IOType.IN_MEMORY)\n",
"@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.20\", \"nibabel\", \"typeguard\"])\n",
"@md.env(pip_packages=[\"monai>=0.8.1\", \"torch>=1.5\", \"numpy>=1.20\", \"nibabel\", \"typeguard\"])\n",
"class SpleenSegOperator(Operator):\n",
" \"\"\"Performs Spleen segmentation with a 3D image converted from a DICOM CT series.\n",
" \"\"\"\n",
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4 changes: 2 additions & 2 deletions notebooks/tutorials/05_full_tutorial.ipynb
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Expand Up @@ -746,7 +746,7 @@
"source": [
"@md.input(\"image\", Image, IOType.IN_MEMORY)\n",
"@md.output(\"seg_image\", Image, IOType.IN_MEMORY)\n",
"@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\"])\n",
"@md.env(pip_packages=[\"monai>=0.8.1\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\"])\n",
"class SpleenSegOperator(Operator):\n",
" \"\"\"Performs Spleen segmentation with a 3D image converted from a DICOM CT series.\n",
" \"\"\"\n",
Expand Down Expand Up @@ -1024,7 +1024,7 @@
"\n",
"@md.input(\"image\", Image, IOType.IN_MEMORY)\n",
"@md.output(\"seg_image\", Image, IOType.IN_MEMORY)\n",
"@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\", \"typeguard\"])\n",
"@md.env(pip_packages=[\"monai>=0.8.1\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\", \"typeguard\"])\n",
"class SpleenSegOperator(Operator):\n",
" \"\"\"Performs Spleen segmentation with a 3D image converted from a DICOM CT series.\n",
" \"\"\"\n",
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2 changes: 1 addition & 1 deletion requirements-dev.txt
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Expand Up @@ -23,7 +23,7 @@ pytest==6.2.4
pytest-cov==2.12.1
pytest-lazy-fixture==0.6.3
cucim~=21.06; platform_system == "Linux"
monai
monai>=0.8.1
docker>=5.0.0
pydicom>=1.4.2
SimpleITK>=2.0.0
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