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[DLMED] update monai and pytorch version
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+169
-175
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‎3d_image_transforms.ipynb

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"name": "stdout",
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"output_type": "stream",
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"text": [
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"MONAI version: 0.1.0+317.g031c133.dirty\n",
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"MONAI version: 0.2.0\n",
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"Python version: 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) [GCC 7.3.0]\n",
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"Numpy version: 1.18.1\n",
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"Pytorch version: 1.6.0\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: 0.3.0\n",
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"Nibabel version: 3.0.1\n",
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"Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Nibabel version: 3.1.1\n",
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"scikit-image version: 0.15.0\n",
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"Pillow version: 7.0.0\n",
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"Pillow version: 7.2.0\n",
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"Tensorboard version: 2.1.0\n",
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"\n",
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"For details about installing the optional dependencies, please visit:\n",

‎automatic_mixed_precision.ipynb

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"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Project-MONAI/MONAI/blob/master/examples/notebooks/automatic_mixed_precision.ipynb)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Copyright 2020 MONAI Consortium\n",
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"# Licensed under the Apache License, Version 2.0 (the \"License\");\n",
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"# you may not use this file except in compliance with the License.\n",
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"# You may obtain a copy of the License at\n",
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"# http://www.apache.org/licenses/LICENSE-2.0\n",
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"# Unless required by applicable law or agreed to in writing, software\n",
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"# distributed under the License is distributed on an \"AS IS\" BASIS,\n",
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"# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
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"# See the License for the specific language governing permissions and\n",
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"# limitations under the License.\n",
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"\n",
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"import os\n",
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"import glob\n",
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"import time\n",
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"import numpy as np\n",
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"import torch\n",
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"from torch.utils.data import DataLoader\n",
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"import matplotlib.pyplot as plt\n",
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"\n",
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"from monai.config import get_torch_version_tuple\n",
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"from monai.data import Dataset, CacheDataset, list_data_collate\n",
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"from monai.transforms import \\\n",
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" Compose, LoadNiftid, AddChanneld, ScaleIntensityRanged, CropForegroundd, \\\n",
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" RandCropByPosNegLabeld, RandAffined, Spacingd, Orientationd, ToTensord\n",
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"from monai.inferers import sliding_window_inference\n",
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"from monai.networks.layers import Norm\n",
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"from monai.networks.nets import UNet\n",
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"from monai.losses import DiceLoss\n",
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"from monai.metrics import compute_meandice\n",
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"from monai.utils import set_determinism\n",
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"\n",
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"if get_torch_version_tuple() < (1, 6):\n",
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" raise RuntimeError('AMP feature only exists in PyTorch version greater than v1.6.')"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"%matplotlib inline"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Setup imports"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"MONAI version: 0.2.0\n",
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"Python version: 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) [GCC 7.3.0]\n",
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"Numpy version: 1.18.1\n",
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"Pytorch version: 1.6.0\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Nibabel version: 3.1.1\n",
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"scikit-image version: 0.15.0\n",
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"Pillow version: 7.2.0\n",
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"Tensorboard version: 2.1.0\n",
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"\n",
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"For details about installing the optional dependencies, please visit:\n",
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" https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
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"\n"
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]
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}
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],
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"source": [
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"# Copyright 2020 MONAI Consortium\n",
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"# Licensed under the Apache License, Version 2.0 (the \"License\");\n",
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"# you may not use this file except in compliance with the License.\n",
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"# You may obtain a copy of the License at\n",
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"# http://www.apache.org/licenses/LICENSE-2.0\n",
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"# Unless required by applicable law or agreed to in writing, software\n",
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"# distributed under the License is distributed on an \"AS IS\" BASIS,\n",
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"# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
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"# See the License for the specific language governing permissions and\n",
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"# limitations under the License.\n",
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"\n",
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"import os\n",
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"import glob\n",
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"import time\n",
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"import numpy as np\n",
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"import torch\n",
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"from torch.utils.data import DataLoader\n",
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"import matplotlib.pyplot as plt\n",
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"\n",
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"from monai.config import get_torch_version_tuple\n",
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"from monai.data import Dataset, CacheDataset, list_data_collate\n",
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"from monai.transforms import \\\n",
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" Compose, LoadNiftid, AddChanneld, ScaleIntensityRanged, CropForegroundd, \\\n",
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" RandCropByPosNegLabeld, RandAffined, Spacingd, Orientationd, ToTensord\n",
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"from monai.inferers import sliding_window_inference\n",
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"from monai.networks.layers import Norm\n",
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"from monai.networks.nets import UNet\n",
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"from monai.losses import DiceLoss\n",
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"from monai.metrics import compute_meandice\n",
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"from monai.utils import set_determinism\n",
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"from monai.config import print_config\n",
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"\n",
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"print_config()\n",
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"\n",
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"if get_torch_version_tuple() < (1, 6):\n",
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" raise RuntimeError('AMP feature only exists in PyTorch version greater than v1.6.')"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},

‎brats_segmentation_3d.ipynb

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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": 1,
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"metadata": {
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"tags": []
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},
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"MONAI version: 0.1.0+318.ga2cd842\n",
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"MONAI version: 0.2.0\n",
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"Python version: 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) [GCC 7.3.0]\n",
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"Numpy version: 1.18.1\n",
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"Pytorch version: 1.6.0\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: 0.3.0\n",
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"Nibabel version: 3.0.1\n",
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"Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Nibabel version: 3.1.1\n",
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"scikit-image version: 0.15.0\n",
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"Pillow version: 7.0.0\n",
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"Pillow version: 7.2.0\n",
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"Tensorboard version: 2.1.0\n",
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"\n",
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"For details about installing the optional dependencies, please visit:\n",

‎cache_dataset_speed.ipynb

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"name": "stdout",
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"output_type": "stream",
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"text": [
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"MONAI version: 0.1.0+318.ga2cd842.dirty\n",
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"MONAI version: 0.2.0\n",
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"Python version: 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) [GCC 7.3.0]\n",
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"Numpy version: 1.18.1\n",
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"Pytorch version: 1.6.0\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: 0.3.0\n",
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"Nibabel version: 3.0.1\n",
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"Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Nibabel version: 3.1.1\n",
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"scikit-image version: 0.15.0\n",
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"Pillow version: 7.0.0\n",
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"Pillow version: 7.2.0\n",
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"Tensorboard version: 2.1.0\n",
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"\n",
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"For details about installing the optional dependencies, please visit:\n",

‎mednist_GAN_tutorial.ipynb

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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": 1,
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"metadata": {
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"tags": []
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},
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"output_type": "stream",
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"text": [
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"MONAI version: 0.2.0\n",
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"Python version: 3.7.5 (default, Nov 7 2019, 10:50:52) [GCC 8.3.0]\n",
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"Numpy version: 1.19.1\n",
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"Python version: 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) [GCC 7.3.0]\n",
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"Numpy version: 1.18.1\n",
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"Pytorch version: 1.6.0\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Nibabel version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"scikit-image version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Nibabel version: 3.1.1\n",
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"scikit-image version: 0.15.0\n",
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"Pillow version: 7.2.0\n",
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"Tensorboard version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Tensorboard version: 2.1.0\n",
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"\n",
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"For details about installing the optional dependencies, please visit:\n",
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" https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",

‎mednist_GAN_workflow.ipynb

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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": []
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Note: you may need to restart the kernel to use updated packages.\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"# temporarily need this, FIXME remove when d93c0a6 released\n",
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"# temporarily need this, FIXME: remove when d93c0a6 released\n",
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"%pip install -qU git+https://github.com/Project-MONAI/MONAI#egg=MONAI"
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]
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},
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},
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": []
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"outputs": [
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"MONAI version: 0.1.0+318.ga2cd842.dirty\n",
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"Python version: 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) [GCC 7.3.0]\n",
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"Numpy version: 1.18.1\n",
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"Pytorch version: 1.6.0\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: 0.3.0\n",
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"Nibabel version: 3.0.1\n",
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"scikit-image version: 0.15.0\n",
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"Pillow version: 7.0.0\n",
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"Tensorboard version: 2.1.0\n",
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"\n",
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"For details about installing the optional dependencies, please visit:\n",
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" https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
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"\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"import logging\n",
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"import os\n",

‎mednist_tutorial.ipynb

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"name": "stdout",
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"text": [
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"MONAI version: 0.1.0+318.ga2cd842.dirty\n",
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"MONAI version: 0.2.0\n",
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"Python version: 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) [GCC 7.3.0]\n",
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"Numpy version: 1.18.1\n",
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"Pytorch version: 1.6.0\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: 0.3.0\n",
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"Nibabel version: 3.0.1\n",
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"Pytorch Ignite version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Nibabel version: 3.1.1\n",
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"scikit-image version: 0.15.0\n",
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"Pillow version: 7.0.0\n",
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"Pillow version: 7.2.0\n",
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"Tensorboard version: 2.1.0\n",
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"\n",
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"For details about installing the optional dependencies, please visit:\n",

‎models_ensemble.ipynb

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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"tags": []
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"outputs": [
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"name": "stdout",
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"text": [
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"Note: you may need to restart the kernel to use updated packages.\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"# temporarily need this, FIXME remove when 7143b8b released\n",
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"%pip install -qU git+https://github.com/Project-MONAI/MONAI#egg=MONAI"
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},
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"cell_type": "code",
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"metadata": {
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"tags": []
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"MONAI version: 0.1.0+318.ga2cd842.dirty\n",
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"Python version: 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) [GCC 7.3.0]\n",
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"Numpy version: 1.18.1\n",
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"Pytorch version: 1.6.0\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: 0.3.0\n",
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"Nibabel version: 3.0.1\n",
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"scikit-image version: 0.15.0\n",
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"Pillow version: 7.0.0\n",
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"Tensorboard version: 2.1.0\n",
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"\n",
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"For details about installing the optional dependencies, please visit:\n",
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" https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
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"\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"# Copyright 2020 MONAI Consortium\n",
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"# Licensed under the Apache License, Version 2.0 (the \"License\");\n",

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