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Bump numpy >= 1.20 to avoid MKL error in conda env, and add --upgrade for pip install app sdk #211

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Nov 26, 2021
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Bump numpy >= 1.20 to avoid MKL error in conda env, and add --upgrade for pip install app sdk #211

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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>=1.17", "nibabel"])
@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.20", "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>=1.17", "nibabel"])
@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.20", "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>=1.17", "nibabel"])
@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.20", "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 @@ -31,7 +31,7 @@ Without using the MONAI Deploy App SDK Packager to automatically detect the depe
monai>=0.6.0
monai-deploy-app-sdk>=0.1.0
nibabel
numpy>=1.17
numpy>=1.20
pydicom>=1.4.2
torch>=1.5
```
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2 changes: 1 addition & 1 deletion monai/deploy/operators/monai_seg_inference_operator.py
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Expand Up @@ -41,7 +41,7 @@

@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>=1.17"])
@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.20"])
class MonaiSegInferenceOperator(InferenceOperator):
"""This segmentation operator uses MONAI transforms and Sliding Window Inference.

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8 changes: 4 additions & 4 deletions notebooks/tutorials/03_segmentation_app.ipynb
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Expand Up @@ -99,14 +99,14 @@
"# Install MONAI and other necessary image processing packages for the application\n",
"!python -c \"import monai\" || pip install -q \"monai\"\n",
"!python -c \"import torch\" || pip install -q \"torch>=1.5\"\n",
"!python -c \"import numpy\" || pip install -q \"numpy>=1.17\"\n",
"!python -c \"import numpy\" || pip install -q \"numpy>=1.20\"\n",
"!python -c \"import nibabel\" || pip install -q \"nibabel>=3.2.1\"\n",
"!python -c \"import pydicom\" || pip install -q \"pydicom>=1.4.2\"\n",
"!python -c \"import SimpleITK\" || pip install -q \"SimpleITK>=2.0.0\"\n",
"!python -c \"import typeguard\" || pip install -q \"typeguard>=2.12.1\"\n",
"\n",
"# Install MONAI Deploy App SDK package\n",
"!python -c \"import monai.deploy\" || pip install -q \"monai-deploy-app-sdk\""
"!python -c \"import monai.deploy\" || pip install --upgrade -q \"monai-deploy-app-sdk\""
]
},
{
Expand Down Expand Up @@ -747,7 +747,7 @@
"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>=1.17\", \"nibabel\"])\n",
"@md.env(pip_packages=[\"monai==0.6.0\", \"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 @@ -1025,7 +1025,7 @@
"\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>=1.17\", \"nibabel\", \"typeguard\"])\n",
"@md.env(pip_packages=[\"monai==0.6.0\", \"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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8 changes: 4 additions & 4 deletions notebooks/tutorials/05_full_tutorial.ipynb
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Expand Up @@ -89,15 +89,15 @@
"# Install MONAI and other necessary image processing packages for the application\n",
"!python -c \"import monai\" || pip install -q \"monai\"\n",
"!python -c \"import torch\" || pip install -q \"torch>=1.5\"\n",
"!python -c \"import numpy\" || pip install -q \"numpy>=1.17\"\n",
"!python -c \"import numpy\" || pip install -q \"numpy>=1.20\"\n",
"!python -c \"import nibabel\" || pip install -q \"nibabel>=3.2.1\"\n",
"!python -c \"import pydicom\" || pip install -q \"pydicom>=1.4.2\"\n",
"!python -c \"import SimpleITK\" || pip install -q \"SimpleITK>=2.0.0\"\n",
"!python -c \"import typeguard\" || pip install -q \"typeguard>=2.12.1\"\n",
"!python -c \"import nilearn\" || pip install -q \"nilearn>=0.8.1\"\n",
"\n",
"# Install MONAI Deploy App SDK package\n",
"!python -c \"import monai.deploy\" || pip install -q \"monai-deploy-app-sdk\""
"!python -c \"import monai.deploy\" || pip install --upgrade -q \"monai-deploy-app-sdk\""
]
},
{
Expand Down Expand Up @@ -738,7 +738,7 @@
"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>=1.17\", \"nibabel\"])\n",
"@md.env(pip_packages=[\"monai==0.6.0\", \"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 @@ -1016,7 +1016,7 @@
"\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>=1.17\", \"nibabel\", \"typeguard\"])\n",
"@md.env(pip_packages=[\"monai==0.6.0\", \"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",
Expand Down