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@thewtex
Created June 10, 2020 02:28
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itk.ContourExtractor2DImageFilter example
Display the source blob
Display the rendered blob
Raw
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Ensure dependencies are installed. If itkwidgets was not installed, reload the browser tab after installation.\n",
"import sys\n",
"!{sys.executable} -m pip install itk itkwidgets"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [],
"source": [
"from urllib.request import urlretrieve\n",
"import os\n",
"import itk\n",
"import numpy as np\n",
"\n",
"from itkwidgets import view, cm"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"file_name = 'cthead1.png'\n",
"if not os.path.exists(file_name):\n",
" url = 'https://data.kitware.com/api/v1/file/57b5d9ef8d777f10f269538f/download'\n",
" urlretrieve(url, file_name)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "e606d650b4024ca5b85dec72d862ed72",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itk.itkImagePython.itkImageUC2; pr…"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"cthead1 = itk.imread(file_name)\n",
"view(cthead1, vmax=150)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"paths = itk.contour_extractor2_d_image_filter(cthead1, contour_value=150)"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "3a40809e39fc45a38d9a48d2842c8c2a",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Viewer(cmap='gray_Matlab', geometries=[{'vtkClass': 'vtkPolyData', 'points': {'vtkClass': 'vtkPoints', 'name':…"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"p0 = paths[0]\n",
"view(cthead1, geometries=p0, cmap=cm.gray, ui_collapsed=True)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.6"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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