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Merged
merged 11 commits into from
Apr 13, 2023
Merged

semantic updates for Auto3dseg #1288

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e29c343
semantic updates for Auto3dseg
myron Apr 6, 2023
a0e1d21
small
myron Apr 6, 2023
e1041a7
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 6, 2023
d815cad
fixes
wyli Apr 13, 2023
5228860
fixes
wyli Apr 13, 2023
ad85fec
update
wyli Apr 13, 2023
9e38267
update
wyli Apr 13, 2023
8a21305
update markdonw
mingxin-zheng Apr 13, 2023
6fef68d
update notebooks
mingxin-zheng Apr 13, 2023
11bcfac
Merge branch 'main' into update_algo_id
mingxin-zheng Apr 13, 2023
77fefef
fix test taking too long
mingxin-zheng Apr 13, 2023
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4 changes: 2 additions & 2 deletions auto3dseg/docs/ensemble.md
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ from monai.apps.auto3dseg import (
AlgoEnsembleBuilder,
import_bundle_algo_history,
)
from monai.utils.enums import AlgoEnsembleKeys
from monai.utils.enums import AlgoKeys

# Assuming you have already trained the models

Expand All @@ -33,7 +33,7 @@ ensemble = builder.get_ensemble()
pred = ensemble()
print("ensemble picked the following best {0:d}:".format(n_best))
for algo in ensemble.get_algo_ensemble():
print(algo[AlgoEnsembleKeys.ID])
print(algo[AlgoKeys.ID])
```

### Customization
Expand Down
20 changes: 9 additions & 11 deletions auto3dseg/notebooks/auto3dseg_autorunner_ref_api.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -66,12 +66,12 @@
"from monai.auto3dseg import algo_to_pickle\n",
"from monai.bundle.config_parser import ConfigParser\n",
"from monai.config import print_config\n",
"from monai.utils.enums import AlgoKeys\n",
"\n",
"print_config()"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -224,7 +224,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand All @@ -246,7 +245,6 @@
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -308,11 +306,11 @@
"outputs": [],
"source": [
"history = import_bundle_algo_history(work_dir, only_trained=False)\n",
"for task in history:\n",
" for _, algo in task.items():\n",
" algo.train(train_param) # can use default params by `algo.train()`\n",
" acc = algo.get_score()\n",
" algo_to_pickle(algo, template_path=algo.template_path, best_metrics=acc)"
"for algo_dict in history:\n",
" algo = algo_dict[AlgoKeys.ALGO]\n",
" algo.train(train_param) # can use default params by `algo.train()`\n",
" acc = algo.get_score()\n",
" algo_to_pickle(algo, template_path=algo.template_path, best_metric=acc)"
]
},
{
Expand Down Expand Up @@ -355,7 +353,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "monai-0",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -369,11 +367,11 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.13 (default, Mar 28 2022, 06:59:08) [MSC v.1916 64 bit (AMD64)]"
"version": "3.8.13"
},
"vscode": {
"interpreter": {
"hash": "85754776c861f3ba5898fde994bfc400ed208cd401a6036e85fdc16c4f506eaf"
"hash": "adad466f3ae0207e0597f6bf999e86a6601b04f4db83734c81b06a9e73a01812"
}
}
},
Expand Down
20 changes: 10 additions & 10 deletions auto3dseg/notebooks/ensemble_byoc.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -70,7 +70,7 @@
"from monai.bundle.config_parser import ConfigParser\n",
"from monai.config import print_config\n",
"from monai.data import create_test_image_3d\n",
"from monai.utils.enums import AlgoEnsembleKeys\n",
"from monai.utils.enums import AlgoKeys\n",
"\n",
"print_config()"
]
Expand All @@ -91,7 +91,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -130,7 +130,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -165,7 +165,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -239,9 +239,9 @@
" \"num_warmup_epochs\": 1,\n",
"}\n",
"\n",
"for h in history:\n",
" for _, algo in h.items():\n",
" algo.train(train_param)"
"for algo_dict in history:\n",
" algo = algo_dict[AlgoKeys.ALGO]\n",
" algo.train(train_param)"
]
},
{
Expand All @@ -266,7 +266,7 @@
"\n",
"print(\"The ensemble randomly picks the following models:\")\n",
"for algo in ensemble.get_algo_ensemble():\n",
" print(algo[AlgoEnsembleKeys.ID])"
" print(algo[AlgoKeys.ID])"
]
}
],
Expand All @@ -286,7 +286,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.13"
"version": "3.8.10"
},
"vscode": {
"interpreter": {
Expand Down
44 changes: 12 additions & 32 deletions auto3dseg/notebooks/hpo_nni.ipynb
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -76,12 +76,12 @@
"from monai.apps.auto3dseg.utils import export_bundle_algo_history, import_bundle_algo_history\n",
"from monai.bundle.config_parser import ConfigParser\n",
"from monai.config import print_config\n",
"from monai.utils.enums import AlgoKeys\n",
"\n",
"print_config()"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -202,19 +202,7 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"algorithms imported from the history:\n",
"0: segresnet2d_0\n",
"1: dints_0\n",
"2: swinunetr_0\n",
"3: segresnet_0\n"
]
}
],
"outputs": [],
"source": [
"try:\n",
" history = bundle_generator.get_history()\n",
Expand All @@ -223,8 +211,9 @@
" history = import_bundle_algo_history(work_dir, only_trained=False)\n",
"\n",
"print(\"algorithms imported from the history:\")\n",
"\n",
"for i, algo_dict in enumerate(history):\n",
" print(f\"{i}: \", list(algo_dict.keys())[0])"
" print(f\"{i}: \", algo_dict[AlgoKeys.ID])"
]
},
{
Expand All @@ -239,23 +228,14 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"User selected algorithm: \n",
"segresnet2d_0\n"
]
}
],
"outputs": [],
"source": [
"selected_algorithm_index = 0\n",
"algo_dict = history[selected_algorithm_index]\n",
"algo_name = list(algo_dict.keys())[0]\n",
"algo = algo_dict[algo_name]\n",
"print(\"User selected algorithm: \")\n",
"print(algo_name)"
"for algo_dict in history:\n",
" if algo_dict[AlgoKeys.ID].split(\"_\")[0] == \"segresnet\":\n",
" break\n",
"algo_name = algo_dict[AlgoKeys.ID]\n",
"algo = algo_dict[AlgoKeys.ALGO]\n",
"print(f\"{algo_name} is selected. \")"
]
},
{
Expand Down Expand Up @@ -382,7 +362,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.13"
"version": "3.8.10"
},
"vscode": {
"interpreter": {
Expand Down
18 changes: 9 additions & 9 deletions auto3dseg/notebooks/hpo_optuna.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,7 @@
"from monai.apps.auto3dseg.utils import export_bundle_algo_history, import_bundle_algo_history\n",
"from monai.bundle.config_parser import ConfigParser\n",
"from monai.config import print_config\n",
"from monai.utils.enums import AlgoKeys\n",
"\n",
"print_config()"
]
Expand Down Expand Up @@ -211,7 +212,7 @@
"\n",
"print(\"algorithms imported from the history:\")\n",
"for i, algo_dict in enumerate(history):\n",
" print(f\"{i}: \", list(algo_dict.keys())[0])"
" print(f\"{i}: \", algo_dict[AlgoKeys.ID])"
]
},
{
Expand All @@ -228,16 +229,15 @@
"metadata": {},
"outputs": [],
"source": [
"selected_algorithm_index = 0\n",
"algo_dict = history[selected_algorithm_index]\n",
"algo_name = list(algo_dict.keys())[0]\n",
"algo = algo_dict[algo_name]\n",
"print(\"User selected algorithm: \")\n",
"print(algo_name)"
"for algo_dict in history:\n",
" if algo_dict[AlgoKeys.ID].split(\"_\")[0] == \"segresnet\":\n",
" break\n",
"algo_name = algo_dict[AlgoKeys.ID]\n",
"algo = algo_dict[AlgoKeys.ALGO]\n",
"print(f\"{algo_name} is selected. \")"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
Expand Down Expand Up @@ -333,7 +333,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.13"
"version": "3.8.10"
},
"vscode": {
"interpreter": {
Expand Down