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Update modules notebooks to match format requirements (#1156)
### Description This PR updated several modules tutorials to match the format requirements of contribution guideline. CC @mingxin-zheng . ### Checks <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Avoid including large-size files in the PR. - [x] Clean up long text outputs from code cells in the notebook. - [x] For security purposes, please check the contents and remove any sensitive info such as user names and private key. - [x] Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the `./figure` folder - [x] Notebook runs automatically `./runner.sh -t <path to .ipynb file>` Signed-off-by: Nic Ma <[email protected]>
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‎modules/decollate_batch.ipynb

Lines changed: 27 additions & 61 deletions
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{
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"cells": [
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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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"Copyright (c) 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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"&nbsp;&nbsp;&nbsp;&nbsp;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."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
@@ -49,7 +65,7 @@
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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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"execution_count": null,
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"metadata": {
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"tags": []
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},
@@ -67,54 +83,12 @@
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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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"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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"MONAI version: 0.4.0+544.g5e7345d\n",
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"Numpy version: 1.21.0\n",
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"Pytorch version: 1.9.0+cu102\n",
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"MONAI flags: HAS_EXT = False, USE_COMPILED = False\n",
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"MONAI rev id: 5e7345d384ae08011b0e250b93f615d6d5190258\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: 7.0.0\n",
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"Tensorboard version: 1.15.0+nv\n",
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"gdown version: 3.13.0\n",
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"TorchVision version: 0.9.0a0\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: 1.1.1\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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"# 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 logging\n",
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"import os\n",
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"import sys\n",
@@ -162,19 +136,11 @@
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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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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"/workspace/data/medical\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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"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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"execution_count": 3,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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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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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": null,
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"metadata": {
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"pycharm": {
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"is_executing": true
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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": "3.8.12"
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"version": "3.8.10"
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}
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},
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"nbformat": 4,

‎modules/dice_loss_metric_notes.ipynb

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Original file line numberDiff line numberDiff line change
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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "6459ddb8",
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"metadata": {},
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"source": [
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"Copyright (c) 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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"&nbsp;&nbsp;&nbsp;&nbsp;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."
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]
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},
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{
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"cell_type": "markdown",
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"id": "0c5bf94b-4f1d-4e94-a6e6-94644095e910",
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"This notebook summarises some of the details relating to the `DiceLoss` and `DiceMetric` classes and their behaviour."
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]
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},
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{
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"cell_type": "markdown",
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"id": "952771b9",
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"metadata": {},
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"source": [
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"## Setup environment"
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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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"id": "7b7eb650",
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"metadata": {},
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"outputs": [],
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"source": [
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"!python -c \"import monai\" || pip install -q \"monai-weekly\""
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]
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},
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{
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"cell_type": "markdown",
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"id": "55f81921",
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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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"cell_type": "code",
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"execution_count": 1,
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"outputs": [],
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"source": [
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"import torch\n",
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"from monai.config import print_config\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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"from monai.transforms import AsDiscrete, Compose\n",
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"\n",
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"print_config()\n",
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"\n",
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"\n",
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"def print_tensor(name, t):\n",
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" print(f\"{name}: {t.numpy().tolist()} shape: {tuple(t.shape)}\")"
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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": "3.8.12"
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"version": "3.8.10"
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}
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},
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"nbformat": 4,

‎modules/image_dataset.ipynb

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{
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"cells": [
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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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"Copyright (c) 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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"&nbsp;&nbsp;&nbsp;&nbsp;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."
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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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},
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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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"execution": {
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"iopub.execute_input": "2021-01-14T12:34:04.909819Z",
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},
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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: 1.1.0+16.gd990ff5e\n",
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"Numpy version: 1.23.5\n",
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"Pytorch version: 1.13.1\n",
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"MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False\n",
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"MONAI rev id: d990ff5e6acab8655d507aeac934defd4f7a5fdc\n",
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"MONAI __file__: /Users/Documents/MONAI/monai/__init__.py\n",
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"\n",
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"Optional dependencies:\n",
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"Pytorch Ignite version: 0.4.10\n",
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"Nibabel version: 5.0.0\n",
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"scikit-image version: NOT INSTALLED or UNKNOWN VERSION.\n",
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"Pillow version: 9.4.0\n",
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"Tensorboard version: 2.11.0\n",
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"gdown version: 4.6.0\n",
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"TorchVision version: 0.14.1\n",
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"tqdm version: 4.64.1\n",
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"lmdb version: 1.4.0\n",
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"psutil version: 5.9.4\n",
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"pandas version: 1.5.2\n",
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"einops version: 0.6.0\n",
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"transformers version: 4.21.3\n",
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"mlflow version: 2.1.1\n",
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"pynrrd version: 1.0.0\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 - 2021 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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"# 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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"import os\n",
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"import tempfile\n",
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"import shutil\n",
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" transform_with_metadata=True,\n",
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")\n",
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"print(\"image shape:\", img_dataset[0][0].shape)\n",
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"print(\"seg. shape:\", img_dataset[0][1].shape)"
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"print(\"seg shape:\", img_dataset[0][1].shape)"
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{
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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": "3.8.13"
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"version": "3.8.10"
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}
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},
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"nbformat": 4,

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