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Add support for Google Colab
Adding the option to launch notebooks using Google Colab. Unlike Binder, colab launches each of the notebooks in an independent environment. To set up the notebook dependencies, the first cell clones the git repository and installs the dependencies from the requirements.txt file. The working directory is changed to the Python directory so that the notebook has access to modules, .py files, used by more than one notebook.
1 parent ae4595a commit d21f1a9

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‎Python/01_Image_Basics.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# SimpleITK Image Basics <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/master?filepath=Python%2F01_Image_Basics.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\"></a>\n",
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"<table align=\"right\">\n",
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" <tr>\n",
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" <td>\n",
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" <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/main?filepath=Python%2F01_Image_Basics.ipynb\"><img src=\"https://mybinder.org/badge_logo.svg\" alt=\"Binder\"></a> \n",
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" </td>\n",
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" <td>\n",
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" <a href=\"https://colab.research.google.com/github/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/main/Python/01_Image_Basics.ipynb\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Colab\"/>\n",
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" </td>\n",
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" </tr>\n",
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"</table>"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"# Setup to enable running the notebook in the Google Colab environment\n",
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"import os\n",
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"\n",
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"if \"COLAB_NOTEBOOK_ID\" in os.environ:\n",
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" !git clone https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks\n",
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" %cd SimpleITK-Notebooks/Python\n",
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" !pip install -q -r requirements.txt"
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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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"source": [
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"# SimpleITK Image Basics \n",
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"\n",
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"This document will give a brief orientation to the SimpleITK Image class.\n",
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"\n",
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"metadata": {
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"anaconda-cloud": {},
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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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},
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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": "3.8.5"
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"version": "3.12.11"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 1
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"nbformat_minor": 4
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}

‎Python/02_Pythonic_Image.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Pythonic Syntactic Sugar <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/master?filepath=Python%2F02_Pythonic_Image.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\"></a>\n",
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"<table align=\"right\">\n",
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" <tr>\n",
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" <td>\n",
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" <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/main?filepath=Python%2F02_Pythonic_Image.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\" alt=\"Binder\"></a> \n",
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" </td>\n",
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" <td>\n",
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" <a href=\"https://colab.research.google.com/github/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/main/Python/02_Pythonic_Image.ipynb\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Colab\"/>\n",
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" </td>\n",
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" </tr>\n",
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"</table>"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"# Setup to enable running the notebook in the Google Colab environment\n",
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"import os\n",
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"\n",
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"if \"COLAB_NOTEBOOK_ID\" in os.environ:\n",
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" !git clone https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks\n",
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" %cd SimpleITK-Notebooks/Python\n",
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" !pip install -q -r requirements.txt"
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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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"source": [
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"# Pythonic Syntactic Sugar\n",
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"\n",
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"The Image Basics Notebook was straight forward and closely follows ITK's C++ interface.\n",
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"\n",
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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": "3.10.11"
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"version": "3.12.11"
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}
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},
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"nbformat": 4,

‎Python/03_Image_Details.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# SimpleITK Images, They're Physical Objects <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/master?filepath=Python%2F03_Image_Details.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\"></a>\n",
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"<table align=\"right\">\n",
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" <tr>\n",
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" <td>\n",
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" <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/main?filepath=Python%2F03_Image_Details.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\" alt=\"Binder\"></a>\n",
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" </td>\n",
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" <td>\n",
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" <a href=\"https://colab.research.google.com/github/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/main/Python/03_Image_Details.ipynb\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Colab\"/>\n",
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" </td>\n",
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" </tr>\n",
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"</table>"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"# Setup to enable running the notebook in the Google Colab environment\n",
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"import os\n",
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"\n",
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"if \"COLAB_NOTEBOOK_ID\" in os.environ:\n",
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" !git clone https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks\n",
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" %cd SimpleITK-Notebooks/Python\n",
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" !pip install -q -r requirements.txt"
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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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"source": [
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"# SimpleITK Images, They're Physical Objects\n",
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"\n",
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"**SimpleITK conventions**:\n",
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"* Image access is in x,y,z order, image.GetPixel(x,y,z) or image[x,y,z], with zero based indexing.\n",
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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": "3.11.10"
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"version": "3.12.11"
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}
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},
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"nbformat": 4,

‎Python/04_Image_Display.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Image Display <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/master?filepath=Python%2F04_Image_Display.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\"></a>\n",
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"<table align=\"right\">\n",
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" <tr>\n",
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" <td>\n",
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" <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/main?filepath=Python%2F04_Image_Display.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\" alt=\"Binder\"></a>\n",
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" </td>\n",
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" <td>\n",
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" <a href=\"https://colab.research.google.com/github/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/main/Python/04_Image_Display.ipynb\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Colab\"/>\n",
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" </td>\n",
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" </tr>\n",
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"</table>"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"# Setup to enable running the notebook in the Google Colab environment\n",
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"import os\n",
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"\n",
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"if \"COLAB_NOTEBOOK_ID\" in os.environ:\n",
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" !git clone https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks\n",
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" %cd SimpleITK-Notebooks/Python\n",
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" !pip install -q -r requirements.txt"
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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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"source": [
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"# Image Display\n",
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"\n",
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"The native SimpleITK approach to displaying images is to use an external viewing program. In the notebook environment it is convenient to use matplotlib to display inline images and if the need arises we can implement some reasonably rich inline graphical user interfaces, combining control components from the ipywidgets package and matplotlib based display.\n",
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"\n",
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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": "3.12.11"
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}
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},
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"nbformat": 4,

‎Python/05_Results_Visualization.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of Segmentation and Registration Results <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/master?filepath=Python%2F05_Results_Visualization.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\"></a>\n",
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"<table align=\"right\">\n",
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" <tr>\n",
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" <td>\n",
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" <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/main?filepath=Python%2F05_Results_Visualization.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\" alt=\"Binder\"></a>\n",
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" </td>\n",
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" <td>\n",
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" <a href=\"https://colab.research.google.com/github/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/main/Python/05_Results_Visualization.ipynb\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Colab\"/>\n",
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" </td>\n",
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" </tr>\n",
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"</table>"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"# Setup to enable running the notebook in the Google Colab environment\n",
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"import os\n",
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"\n",
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"if \"COLAB_NOTEBOOK_ID\" in os.environ:\n",
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" !git clone https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks\n",
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" %cd SimpleITK-Notebooks/Python\n",
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" !pip install -q -r requirements.txt"
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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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"source": [
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"# Visualization of Segmentation and Registration Results\n",
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"\n",
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"In this notebook we illustrate various ways one can display the results of segmentation and registration algorithms so that they can be easily incorporated into a manuscript or presentation. For interactive data exploration we recommend using dedicated programs (e.g. 3D slicer). \n",
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"\n",
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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": "3.12.11"
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}
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},
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"nbformat": 4,

‎Python/10_matplotlibs_imshow.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Using `matplotlib` to display inline images <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/master?filepath=Python%2F10_matplotlib's_imshow.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\"></a>\n",
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"<table align=\"right\">\n",
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" <tr>\n",
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" <td>\n",
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" <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/main?filepath=Python%2F10_matplotlibs_imshow.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\" alt=\"Binder\"></a>\n",
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" </td>\n",
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" <td>\n",
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" <a href=\"https://colab.research.google.com/github/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/main/Python/10_matplotlibs_imshow.ipynb\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Colab\"/>\n",
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" </td>\n",
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" </tr>\n",
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"</table>"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"# Setup to enable running the notebook in the Google Colab environment\n",
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"import os\n",
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"\n",
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"if \"COLAB_NOTEBOOK_ID\" in os.environ:\n",
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" !git clone https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks\n",
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" %cd SimpleITK-Notebooks/Python\n",
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" !pip install -q -r requirements.txt"
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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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"source": [
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"# Using `matplotlib` to display inline images\n",
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"\n",
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"In this notebook we will explore using `matplotlib` to display images in our notebooks, and work towards developing a reusable function to display 2D,3D, color, and label overlays for SimpleITK images.\n",
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"\n",
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"metadata": {
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"collapsed": true,
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"metadata": {
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"collapsed": true,
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"name": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.12"
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"version": "3.12.11"
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}
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},
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"nbformat": 4,

‎Python/11_Progress.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Progress Reporting and Command Observers <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/master?filepath=Python%2F11_Progress.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\"></a>\n",
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"<table align=\"right\">\n",
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" <tr>\n",
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" <td>\n",
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" <a href=\"https://mybinder.org/v2/gh/InsightSoftwareConsortium/SimpleITK-Notebooks/main?filepath=Python%2F11_Progress.ipynb\"><img style=\"float: right;\" src=\"https://mybinder.org/badge_logo.svg\" alt=\"Binder\"></a>\n",
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" </td>\n",
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" <td>\n",
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" <a href=\"https://colab.research.google.com/github/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/main/Python/11_Progress.ipynb\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Colab\"/>\n",
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" </td>\n",
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" </tr>\n",
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"</table>"
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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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"metadata": {},
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"outputs": [],
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"source": [
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"# Setup to enable running the notebook in the Google Colab environment\n",
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"import os\n",
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"\n",
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"if \"COLAB_NOTEBOOK_ID\" in os.environ:\n",
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" !git clone https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks\n",
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" %cd SimpleITK-Notebooks/Python\n",
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" !pip install -q -r requirements.txt"
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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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"source": [
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"# Progress Reporting and Command Observers\n",
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"\n",
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"SimpleITK `Filter`s and other classes derived from `ProcessObject`s have the ability for user code to be executed when certain events occur. This is known as the Command and Observer design patters to implement user callbacks. This allows for the monitoring and abortion of processes as they are being executed.\n",
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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": "3.12.11"
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}
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},
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"nbformat": 4,

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