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Merged
merged 14 commits into from
Jan 16, 2023
Merged

Update modules notebooks to match format requirements #1156

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99b6979
[DLMED] update notebook format
Nic-Ma Jan 11, 2023
24fe7b2
[DLMED] update all notebooks
Nic-Ma Jan 11, 2023
172e0ab
Merge branch 'main' into update-modules-toolkit
Nic-Ma Jan 11, 2023
b4809a5
[DLMED] fix typo
Nic-Ma Jan 11, 2023
5a4518b
Merge branch 'main' into update-modules-toolkit
Nic-Ma Jan 12, 2023
6e1488e
[DLMED] update copyright
Nic-Ma Jan 12, 2023
786e0cc
[DLMED] update RSNA Bone Age Challenge link
Nic-Ma Jan 12, 2023
d0ce13c
[DLMED] update according to comments
Nic-Ma Jan 12, 2023
59b9eb3
Merge branch 'main' into update-modules-toolkit
Nic-Ma Jan 12, 2023
a568f57
Merge branch 'main' into update-modules-toolkit
Nic-Ma Jan 13, 2023
aa5f5f8
[DLMED] fix typo in the notebooks
Nic-Ma Jan 13, 2023
06af24d
Merge branch 'main' into update-modules-toolkit
Nic-Ma Jan 13, 2023
0c41b8c
Merge branch 'main' into update-modules-toolkit
Nic-Ma Jan 16, 2023
1fd610c
[DLMED] remove imports
Nic-Ma Jan 16, 2023
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88 changes: 27 additions & 61 deletions modules/decollate_batch.ipynb
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Original file line number Diff line number Diff line change
@@ -1,5 +1,21 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Copyright (c) MONAI Consortium \n",
"Licensed under the Apache License, Version 2.0 (the \"License\"); \n",
"you may not use this file except in compliance with the License. \n",
"You may obtain a copy of the License at \n",
"    http://www.apache.org/licenses/LICENSE-2.0 \n",
"Unless required by applicable law or agreed to in writing, software \n",
"distributed under the License is distributed on an \"AS IS\" BASIS, \n",
"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. \n",
"See the License for the specific language governing permissions and \n",
"limitations under the License."
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -49,7 +65,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {
"tags": []
},
Expand All @@ -67,54 +83,12 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"MONAI version: 0.4.0+544.g5e7345d\n",
"Numpy version: 1.21.0\n",
"Pytorch version: 1.9.0+cu102\n",
"MONAI flags: HAS_EXT = False, USE_COMPILED = False\n",
"MONAI rev id: 5e7345d384ae08011b0e250b93f615d6d5190258\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: 7.0.0\n",
"Tensorboard version: 1.15.0+nv\n",
"gdown version: 3.13.0\n",
"TorchVision version: 0.9.0a0\n",
"ITK version: 5.1.2\n",
"tqdm version: 4.53.0\n",
"lmdb version: 1.1.1\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",
"# you may not use this file except in compliance with the License.\n",
"# You may obtain a copy of the License at\n",
"# http://www.apache.org/licenses/LICENSE-2.0\n",
"# Unless required by applicable law or agreed to in writing, software\n",
"# distributed under the License is distributed on an \"AS IS\" BASIS,\n",
"# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
"# See the License for the specific language governing permissions and\n",
"# limitations under the License.\n",
"\n",
"import logging\n",
"import os\n",
"import sys\n",
Expand Down Expand Up @@ -162,19 +136,11 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/workspace/data/medical\n"
]
}
],
"outputs": [],
"source": [
"directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
"root_dir = tempfile.mkdtemp() if directory is None else directory\n",
Expand All @@ -190,7 +156,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -210,7 +176,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -237,7 +203,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -267,7 +233,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"metadata": {
"tags": []
},
Expand Down Expand Up @@ -353,7 +319,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"metadata": {
"pycharm": {
"is_executing": true
Expand Down Expand Up @@ -382,7 +348,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.8.10"
}
},
"nbformat": 4,
Expand Down
48 changes: 47 additions & 1 deletion modules/dice_loss_metric_notes.ipynb
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Original file line number Diff line number Diff line change
@@ -1,5 +1,22 @@
{
"cells": [
{
"cell_type": "markdown",
"id": "6459ddb8",
"metadata": {},
"source": [
"Copyright (c) MONAI Consortium \n",
"Licensed under the Apache License, Version 2.0 (the \"License\"); \n",
"you may not use this file except in compliance with the License. \n",
"You may obtain a copy of the License at \n",
"    http://www.apache.org/licenses/LICENSE-2.0 \n",
"Unless required by applicable law or agreed to in writing, software \n",
"distributed under the License is distributed on an \"AS IS\" BASIS, \n",
"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. \n",
"See the License for the specific language governing permissions and \n",
"limitations under the License."
]
},
{
"cell_type": "markdown",
"id": "0c5bf94b-4f1d-4e94-a6e6-94644095e910",
Expand All @@ -10,6 +27,32 @@
"This notebook summarises some of the details relating to the `DiceLoss` and `DiceMetric` classes and their behaviour."
]
},
{
"cell_type": "markdown",
"id": "952771b9",
"metadata": {},
"source": [
"## Setup environment"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7b7eb650",
"metadata": {},
"outputs": [],
"source": [
"!python -c \"import monai\" || pip install -q \"monai-weekly\""
]
},
{
"cell_type": "markdown",
"id": "55f81921",
"metadata": {},
"source": [
"## Setup imports"
]
},
{
"cell_type": "code",
"execution_count": 1,
Expand All @@ -18,10 +61,13 @@
"outputs": [],
"source": [
"import torch\n",
"from monai.config import print_config\n",
"from monai.losses import DiceLoss\n",
"from monai.metrics import DiceMetric\n",
"from monai.transforms import AsDiscrete, Compose\n",
"\n",
"print_config()\n",
"\n",
"\n",
"def print_tensor(name, t):\n",
" print(f\"{name}: {t.numpy().tolist()} shape: {tuple(t.shape)}\")"
Expand Down Expand Up @@ -412,7 +458,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
"version": "3.8.10"
}
},
"nbformat": 4,
Expand Down
79 changes: 20 additions & 59 deletions modules/image_dataset.ipynb
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,21 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Copyright (c) MONAI Consortium \n",
"Licensed under the Apache License, Version 2.0 (the \"License\"); \n",
"you may not use this file except in compliance with the License. \n",
"You may obtain a copy of the License at \n",
"    http://www.apache.org/licenses/LICENSE-2.0 \n",
"Unless required by applicable law or agreed to in writing, software \n",
"distributed under the License is distributed on an \"AS IS\" BASIS, \n",
"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. \n",
"See the License for the specific language governing permissions and \n",
"limitations under the License."
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -44,7 +60,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {
"execution": {
"iopub.execute_input": "2021-01-14T12:34:04.909819Z",
Expand All @@ -54,63 +70,8 @@
},
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"MONAI version: 1.1.0+16.gd990ff5e\n",
"Numpy version: 1.23.5\n",
"Pytorch version: 1.13.1\n",
"MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False\n",
"MONAI rev id: d990ff5e6acab8655d507aeac934defd4f7a5fdc\n",
"MONAI __file__: /Users/Documents/MONAI/monai/__init__.py\n",
"\n",
"Optional dependencies:\n",
"Pytorch Ignite version: 0.4.10\n",
"Nibabel version: 5.0.0\n",
"scikit-image version: NOT INSTALLED or UNKNOWN VERSION.\n",
"Pillow version: 9.4.0\n",
"Tensorboard version: 2.11.0\n",
"gdown version: 4.6.0\n",
"TorchVision version: 0.14.1\n",
"tqdm version: 4.64.1\n",
"lmdb version: 1.4.0\n",
"psutil version: 5.9.4\n",
"pandas version: 1.5.2\n",
"einops version: 0.6.0\n",
"transformers version: 4.21.3\n",
"mlflow version: 2.1.1\n",
"pynrrd version: 1.0.0\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 - 2021 MONAI Consortium\n",
"# Licensed under the Apache License, Version 2.0 (the \"License\");\n",
"# you may not use this file except in compliance with the License.\n",
"# You may obtain a copy of the License at\n",
"# http://www.apache.org/licenses/LICENSE-2.0\n",
"# Unless required by applicable law or agreed to in writing, software\n",
"# distributed under the License is distributed on an \"AS IS\" BASIS,\n",
"# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
"# See the License for the specific language governing permissions and\n",
"# limitations under the License.\n",
"\n",
"# Copyright 2020 MONAI Consortium\n",
"# Licensed under the Apache License, Version 2.0 (the \"License\");\n",
"# you may not use this file except in compliance with the License.\n",
"# You may obtain a copy of the License at\n",
"# http://www.apache.org/licenses/LICENSE-2.0\n",
"# Unless required by applicable law or agreed to in writing, software\n",
"# distributed under the License is distributed on an \"AS IS\" BASIS,\n",
"# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
"# See the License for the specific language governing permissions and\n",
"# limitations under the License.\n",
"import os\n",
"import tempfile\n",
"import shutil\n",
Expand Down Expand Up @@ -195,7 +156,7 @@
" transform_with_metadata=True,\n",
")\n",
"print(\"image shape:\", img_dataset[0][0].shape)\n",
"print(\"seg. shape:\", img_dataset[0][1].shape)"
"print(\"seg shape:\", img_dataset[0][1].shape)"
]
},
{
Expand Down Expand Up @@ -231,7 +192,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.13"
"version": "3.8.10"
}
},
"nbformat": 4,
Expand Down
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