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yuchen-xuYuchen Xu
yuchen-xu
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Yuchen Xu
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Update acceleration tutorials for MetaTensor (#786)
* updated AMP tutorial for 0.9.1rc2 * updated for 0.9.1rc2 compatibility * modification done, pending final checks * tests run on 0.9.1rc3, ready for review * updated for 0.9.1rc3 Co-authored-by: Yuchen Xu <[email protected]>
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‎acceleration/automatic_mixed_precision.ipynb

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},
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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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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"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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"!python -c \"import monai\" || pip install -q \"monai-weekly[nibabel, tqdm]\"\n",
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"!python -c \"import matplotlib\" || pip install -q matplotlib\n",
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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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"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: 0.6.0rc1+15.gf3d436a0\n",
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"Numpy version: 1.20.3\n",
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"Pytorch version: 1.9.0a0+c3d40fd\n",
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"MONAI flags: HAS_EXT = True, USE_COMPILED = False\n",
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"MONAI rev id: f3d436a09deefcf905ece2faeec37f55ab030003\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: 0.4.5\n",
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"Nibabel version: 3.2.1\n",
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"scikit-image version: 0.15.0\n",
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"Pillow version: 8.2.0\n",
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"Tensorboard version: 2.5.0\n",
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"gdown version: 3.13.0\n",
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"TorchVision version: 0.10.0a0\n",
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"ITK version: 5.1.2\n",
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"tqdm version: 4.53.0\n",
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"lmdb version: 1.2.1\n",
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"psutil version: 5.8.0\n",
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"pandas version: 1.1.4\n",
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"einops version: 0.3.0\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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"import torch\n",
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"from monai.apps import download_and_extract\n",
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"from monai.config import print_config\n",
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"from monai.data import CacheDataset, list_data_collate, decollate_batch\n",
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"from monai.data import CacheDataset, DataLoader, decollate_batch\n",
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"from monai.inferers import sliding_window_inference\n",
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"from monai.losses import DiceLoss\n",
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"from monai.metrics import DiceMetric\n",
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" RandCropByPosNegLabeld,\n",
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" ScaleIntensityRanged,\n",
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" Spacingd,\n",
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" EnsureTyped,\n",
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" EnsureType,\n",
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")\n",
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"from monai.utils import get_torch_version_tuple, set_determinism\n",
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"from torch.utils.data import DataLoader\n",
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"\n",
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"print_config()\n",
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"\n",
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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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"root dir is: /workspace/data/medical\n"
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]
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}
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],
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"execution_count": null,
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"metadata": {
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"scrolled": true
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},
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"outputs": [],
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"source": [
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"directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
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"root_dir = tempfile.mkdtemp() if directory is None else directory\n",
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},
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{
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"cell_type": "code",
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},
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},
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"cell_type": "code",
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" fg_indices_key=\"label_fg\",\n",
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" bg_indices_key=\"label_bg\",\n",
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" ),\n",
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" EnsureTyped(keys=[\"image\", \"label\"]),\n",
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" ]\n",
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" )\n",
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" val_transforms = Compose(\n",
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" clip=True,\n",
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" ),\n",
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" CropForegroundd(keys=[\"image\", \"label\"], source_key=\"image\"),\n",
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" EnsureTyped(keys=[\"image\", \"label\"]),\n",
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" ]\n",
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" )\n",
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" return train_transforms, val_transforms"
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},
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"cell_type": "code",
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"scrolled": true
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" batch_size=2,\n",
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" shuffle=True,\n",
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" num_workers=1,\n",
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" collate_fn=list_data_collate,\n",
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" )\n",
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" val_loader = DataLoader(val_ds, batch_size=1, num_workers=1)\n",
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" device = torch.device(\"cuda:0\")\n",
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" optimizer = torch.optim.Adam(model.parameters(), 1e-4)\n",
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" scaler = torch.cuda.amp.GradScaler() if amp else None\n",
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"\n",
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" post_pred = Compose([EnsureType(), AsDiscrete(argmax=True, to_onehot=2)])\n",
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" post_label = Compose([EnsureType(), AsDiscrete(to_onehot=2)])\n",
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" post_pred = Compose([AsDiscrete(argmax=True, to_onehot=2)])\n",
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" post_label = Compose([AsDiscrete(to_onehot=2)])\n",
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"\n",
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" dice_metric = DiceMetric(include_background=False, reduction=\"mean\", get_not_nans=False)\n",
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"execution_count": null,
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"metadata": {
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"scrolled": true
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},
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"set_determinism(seed=0)\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.10"
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"version": "3.8.13"
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}
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},
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"nbformat": 4,

‎acceleration/dataset_type_performance.ipynb

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‎acceleration/fast_training_tutorial.ipynb

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" ScaleIntensityRanged,\n",
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" Spacingd,\n",
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" ToDeviced,\n",
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" EnsureTyped,\n",
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" EnsureType,\n",
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"from monai.utils import set_determinism\n",
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" # change to execute transforms with Tensor data\n",
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" range_func(\"EnsureType\", EnsureTyped(keys=[\"image\", \"label\"])),\n",
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" post_pred = Compose([AsDiscrete(argmax=True, to_onehot=2)])\n",
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" post_label = Compose([AsDiscrete(to_onehot=2)])\n",
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