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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,221 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Install dependencies for this example\n", | ||
| "# Note: This does not include itkwidgets, itself\n", | ||
| "import sys\n", | ||
| "!{sys.executable} -m pip install itk-io scikit-image skan pandas numba" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from urllib.request import urlretrieve\n", | ||
| "import os\n", | ||
| "from skimage import data\n", | ||
| "\n", | ||
| "import itk\n", | ||
| "import skan\n", | ||
| "from skimage.util import img_as_float64, invert\n", | ||
| "from skimage.morphology import skeletonize\n", | ||
| "import numpy as np\n", | ||
| "\n", | ||
| "from itkwidgets import view, cm" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "application/vnd.jupyter.widget-view+json": { | ||
| "model_id": "80e1cd86fdb24327874163e5bca1148a", | ||
| "version_major": 2, | ||
| "version_minor": 0 | ||
| }, | ||
| "text/plain": [ | ||
| "Viewer(annotations=False, cmap='gray_Matlab', geometries=[], gradient_opacity=0.22, interpolation=False, point…" | ||
| ] | ||
| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "image = invert(data.horse())\n", | ||
| "view(image.astype(np.uint8),\n", | ||
| " ui_collapsed=True, annotations=False,\n", | ||
| " interpolation=False, cmap=cm.gray)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "skeleton = skeletonize(image)\n", | ||
| "skeleton_csr = skan.csr.Skeleton(skeleton)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "application/vnd.jupyter.widget-view+json": { | ||
| "model_id": "e7c2699edd604adbafd510a684292650", | ||
| "version_major": 2, | ||
| "version_minor": 0 | ||
| }, | ||
| "text/plain": [ | ||
| "Viewer(annotations=False, cmap='gray_Matlab', geometries=[{'vtkClass': 'vtkPolyData', 'points': {'vtkClass': '…" | ||
| ] | ||
| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "view(image.astype(np.uint8), geometries=skeleton_csr,\n", | ||
| " ui_collapsed=True, annotations=False,\n", | ||
| " interpolate=False, cmap=cm.gray)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Download 3D data\n", | ||
| "file_name = 'input.tiff'\n", | ||
| "if not os.path.exists(file_name):\n", | ||
| " url = 'https://data.kitware.com/api/v1/item/5e1ea82eaf2e2eed35033055/download'\n", | ||
| " urlretrieve(url, file_name)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 7, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "application/vnd.jupyter.widget-view+json": { | ||
| "model_id": "fda4764e751a4220b32c2dc1733a3aed", | ||
| "version_major": 2, | ||
| "version_minor": 0 | ||
| }, | ||
| "text/plain": [ | ||
| "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF3; proxy o…" | ||
| ] | ||
| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "image = itk.imread(file_name, itk.F)\n", | ||
| "view(image, ui_collapsed=True, shadow=False)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 8, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Normalize for skimage\n", | ||
| "image_arr = itk.array_from_image(image)\n", | ||
| "image_arr = img_as_float64(image_arr)\n", | ||
| "image_arr = image_arr / image_arr.max()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 17, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "skeleton = skeletonize(image_arr)\n", | ||
| "skeleton_csr = skan.csr.Skeleton(skeleton, spacing=list(itk.spacing(image))[::-1])" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 18, | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "application/vnd.jupyter.widget-view+json": { | ||
| "model_id": "72e4c8ab26e8498091b25d48286ed25d", | ||
| "version_major": 2, | ||
| "version_minor": 0 | ||
| }, | ||
| "text/plain": [ | ||
| "Viewer(annotations=False, camera=array([[ 4.6124218e+01, 9.3229523e+01, 2.7596173e+02],\n", | ||
| " [ 4.9500000e+…" | ||
| ] | ||
| }, | ||
| "metadata": {}, | ||
| "output_type": "display_data" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "view(image_arr, geometries=skeleton_csr,\n", | ||
| " ui_collapsed=True, shadow=False, annotations=False,\n", | ||
| " camera=[[ 4.6124218e+01, 9.3229523e+01, 2.7596173e+02],\n", | ||
| " [ 4.9500000e+01, 4.9500000e+01, 7.5000000e+00],\n", | ||
| " [-6.0824049e-01, 7.8217846e-01, -1.3505679e-01]])" | ||
| ] | ||
| } | ||
| ], | ||
| "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" | ||
| }, | ||
| "toc": { | ||
| "base_numbering": 1, | ||
| "nav_menu": {}, | ||
| "number_sections": false, | ||
| "sideBar": false, | ||
| "skip_h1_title": false, | ||
| "title_cell": "Table of Contents", | ||
| "title_sidebar": "Contents", | ||
| "toc_cell": false, | ||
| "toc_position": {}, | ||
| "toc_section_display": false, | ||
| "toc_window_display": false | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 4 | ||
| } |
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