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Merged
merged 7 commits into from
Jul 16, 2022
Merged

Update acceleration tutorials for MetaTensor #786

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ccf82bb
updated AMP tutorial for 0.9.1rc2
Jul 14, 2022
bc03716
updated for 0.9.1rc2 compatibility
Jul 15, 2022
8b7b312
modification done, pending final checks
Jul 15, 2022
5983bbb
tests run on 0.9.1rc3, ready for review
Jul 16, 2022
8b4d1ea
updated for 0.9.1rc3
Jul 16, 2022
0111871
Merge branch 'main' into 782-acceleration-metatensor
wyli Jul 16, 2022
56eae31
Merge branch 'main' into 782-acceleration-metatensor
wyli Jul 16, 2022
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91 changes: 21 additions & 70 deletions acceleration/automatic_mixed_precision.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -28,17 +28,9 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Note: you may need to restart the kernel to use updated packages.\n"
]
}
],
"outputs": [],
"source": [
"!python -c \"import monai\" || pip install -q \"monai-weekly[nibabel, tqdm]\"\n",
"!python -c \"import matplotlib\" || pip install -q matplotlib\n",
Expand All @@ -54,40 +46,9 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"MONAI version: 0.6.0rc1+15.gf3d436a0\n",
"Numpy version: 1.20.3\n",
"Pytorch version: 1.9.0a0+c3d40fd\n",
"MONAI flags: HAS_EXT = True, USE_COMPILED = False\n",
"MONAI rev id: f3d436a09deefcf905ece2faeec37f55ab030003\n",
"\n",
"Optional dependencies:\n",
"Pytorch Ignite version: 0.4.5\n",
"Nibabel version: 3.2.1\n",
"scikit-image version: 0.15.0\n",
"Pillow version: 8.2.0\n",
"Tensorboard version: 2.5.0\n",
"gdown version: 3.13.0\n",
"TorchVision version: 0.10.0a0\n",
"ITK version: 5.1.2\n",
"tqdm version: 4.53.0\n",
"lmdb version: 1.2.1\n",
"psutil version: 5.8.0\n",
"pandas version: 1.1.4\n",
"einops version: 0.3.0\n",
"\n",
"For details about installing the optional dependencies, please visit:\n",
" https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n",
"\n"
]
}
],
"outputs": [],
"source": [
"# Copyright 2020 MONAI Consortium\n",
"# Licensed under the Apache License, Version 2.0 (the \"License\");\n",
Expand All @@ -110,7 +71,7 @@
"import torch\n",
"from monai.apps import download_and_extract\n",
"from monai.config import print_config\n",
"from monai.data import CacheDataset, list_data_collate, decollate_batch\n",
"from monai.data import CacheDataset, DataLoader, decollate_batch\n",
"from monai.inferers import sliding_window_inference\n",
"from monai.losses import DiceLoss\n",
"from monai.metrics import DiceMetric\n",
Expand All @@ -127,11 +88,8 @@
" RandCropByPosNegLabeld,\n",
" ScaleIntensityRanged,\n",
" Spacingd,\n",
" EnsureTyped,\n",
" EnsureType,\n",
")\n",
"from monai.utils import get_torch_version_tuple, set_determinism\n",
"from torch.utils.data import DataLoader\n",
"\n",
"print_config()\n",
"\n",
Expand All @@ -154,17 +112,11 @@
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"root dir is: /workspace/data/medical\n"
]
}
],
"execution_count": null,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
"root_dir = tempfile.mkdtemp() if directory is None else directory\n",
Expand All @@ -182,7 +134,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -204,7 +156,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -230,7 +182,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -275,7 +227,6 @@
" fg_indices_key=\"label_fg\",\n",
" bg_indices_key=\"label_bg\",\n",
" ),\n",
" EnsureTyped(keys=[\"image\", \"label\"]),\n",
" ]\n",
" )\n",
" val_transforms = Compose(\n",
Expand All @@ -297,7 +248,6 @@
" clip=True,\n",
" ),\n",
" CropForegroundd(keys=[\"image\", \"label\"], source_key=\"image\"),\n",
" EnsureTyped(keys=[\"image\", \"label\"]),\n",
" ]\n",
" )\n",
" return train_transforms, val_transforms"
Expand All @@ -313,7 +263,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"metadata": {
"scrolled": true
},
Expand All @@ -335,7 +285,6 @@
" batch_size=2,\n",
" shuffle=True,\n",
" num_workers=1,\n",
" collate_fn=list_data_collate,\n",
" )\n",
" val_loader = DataLoader(val_ds, batch_size=1, num_workers=1)\n",
" device = torch.device(\"cuda:0\")\n",
Expand All @@ -352,8 +301,8 @@
" optimizer = torch.optim.Adam(model.parameters(), 1e-4)\n",
" scaler = torch.cuda.amp.GradScaler() if amp else None\n",
"\n",
" post_pred = Compose([EnsureType(), AsDiscrete(argmax=True, to_onehot=2)])\n",
" post_label = Compose([EnsureType(), AsDiscrete(to_onehot=2)])\n",
" post_pred = Compose([AsDiscrete(argmax=True, to_onehot=2)])\n",
" post_label = Compose([AsDiscrete(to_onehot=2)])\n",
"\n",
" dice_metric = DiceMetric(include_background=False, reduction=\"mean\", get_not_nans=False)\n",
"\n",
Expand Down Expand Up @@ -474,7 +423,9 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"set_determinism(seed=0)\n",
Expand Down Expand Up @@ -856,7 +807,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -870,7 +821,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.10"
"version": "3.8.13"
}
},
"nbformat": 4,
Expand Down
73 changes: 14 additions & 59 deletions acceleration/dataset_type_performance.ipynb
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23 changes: 9 additions & 14 deletions acceleration/fast_training_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {
"vscode": {
"languageId": "python"
Expand Down Expand Up @@ -126,8 +126,6 @@
" ScaleIntensityRanged,\n",
" Spacingd,\n",
" ToDeviced,\n",
" EnsureTyped,\n",
" EnsureType,\n",
")\n",
"from monai.utils import set_determinism\n",
"\n",
Expand Down Expand Up @@ -180,7 +178,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {
"vscode": {
"languageId": "python"
Expand Down Expand Up @@ -234,7 +232,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {
"vscode": {
"languageId": "python"
Expand Down Expand Up @@ -298,7 +296,7 @@
},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": null,
"metadata": {
"vscode": {
"languageId": "python"
Expand Down Expand Up @@ -328,7 +326,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"metadata": {
"vscode": {
"languageId": "python"
Expand Down Expand Up @@ -364,8 +362,6 @@
" bg_postfix=\"_bg\",\n",
" image_key=\"image\",\n",
" )),\n",
" # change to execute transforms with Tensor data\n",
" range_func(\"EnsureType\", EnsureTyped(keys=[\"image\", \"label\"])),\n",
" ]\n",
"\n",
" if fast:\n",
Expand Down Expand Up @@ -407,7 +403,6 @@
" clip=True,\n",
" ),\n",
" CropForegroundd(keys=[\"image\", \"label\"], source_key=\"image\"),\n",
" EnsureTyped(keys=[\"image\", \"label\"]),\n",
" ]\n",
" if fast:\n",
" # move the data to GPU and cache to avoid CPU -> GPU sync in every epoch\n",
Expand Down Expand Up @@ -438,7 +433,7 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": null,
"metadata": {
"vscode": {
"languageId": "python"
Expand Down Expand Up @@ -518,8 +513,8 @@
" norm=Norm.BATCH,\n",
" ).to(device)\n",
"\n",
" post_pred = Compose([EnsureType(), AsDiscrete(argmax=True, to_onehot=2)])\n",
" post_label = Compose([EnsureType(), AsDiscrete(to_onehot=2)])\n",
" post_pred = Compose([AsDiscrete(argmax=True, to_onehot=2)])\n",
" post_label = Compose([AsDiscrete(to_onehot=2)])\n",
"\n",
" dice_metric = DiceMetric(include_background=False, reduction=\"mean\", get_not_nans=False)\n",
"\n",
Expand Down Expand Up @@ -1020,7 +1015,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": null,
"metadata": {
"vscode": {
"languageId": "python"
Expand Down
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