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Merge pull request #70 from thewtex/example
Python Example
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‎.gitignore‎

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*~
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build/
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.ipynb_checkpoints
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examples/.ipynb_checkpoints

‎examples/DigitalSubtractionAngiographyVesselPath.ipynb‎

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{
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"cells": [
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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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"# Install dependencies for this example\n",
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"# Note: This does not include itkwidgets, itself\n",
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"import sys\n",
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"!{sys.executable} -m pip install --upgrade itk-minimalpathextraction"
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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": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"from pathlib import Path\n",
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"\n",
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"import itk\n",
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"import numpy as np\n",
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"\n",
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"from itkwidgets import view"
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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": 2,
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"metadata": {},
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"outputs": [],
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"source": [
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"DATA_DIR = Path('../test/Input')"
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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": 3,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "0072c3bbb27a4bd4b35a965458611254",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageUC2; proxy …"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"dsa = itk.imread(str(DATA_DIR / 'Real-DSA-01.jpg'))\n",
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"view(dsa, ui_collapsed=True)"
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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": 4,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "6e9289c05fec4f19b77ebab14a5267e4",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF2; proxy o…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"dsa_speed = itk.imread(str(DATA_DIR / 'Real-DSA-01-Speed-02.mhd'))\n",
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"view(dsa_speed, ui_collapsed=True)"
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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": 5,
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"metadata": {},
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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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"Path: [394.00, 203.00] [388.00, 229.00] [356.00, 217.00] [289.00, 252.00] [194.00, 309.00] [162.00, 318.00] [232.00, 490.00]\r\n"
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]
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}
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],
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"source": [
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"path_file = str(DATA_DIR / 'Real-DSA-01.path')\n",
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"!cat {path_file}"
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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": 6,
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"metadata": {},
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"outputs": [],
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"source": [
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"PointType = itk.Point[itk.D,2]\n",
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"PathInformationType = itk.SpeedFunctionPathInformation[PointType]"
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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": 7,
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"metadata": {},
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"outputs": [],
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"source": [
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"path_information = PathInformationType.New()\n",
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"with open(path_file, 'r') as fp:\n",
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" for line in fp:\n",
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" line = line.replace(\"Path: \", \"\")\n",
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" line = line.replace(\"[\", \"\").strip()\n",
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" points = line.split(']')[:-1]\n",
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" way_points = np.empty((0, 2))\n",
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" for index, point in enumerate(points):\n",
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" point_float = PointType()\n",
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" point_float[0] = float(point.split(',')[0])\n",
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" point_float[1] = float(point.split(',')[1])\n",
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" if index == 0:\n",
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" start_point = np.array(point_float).reshape(1,2)\n",
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" path_information.SetStartPoint(point_float)\n",
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" elif index == len(points)-1:\n",
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" end_point = np.array(point_float).reshape(1,2)\n",
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" path_information.SetEndPoint(point_float)\n",
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" else:\n",
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" way_points = np.vstack((way_points, np.array(point_float).reshape(1,2)))\n",
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" path_information.AddWayPoint(point_float)"
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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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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "d907dae42c9243cf862bbb75e3f2ba77",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[], gradient_opacity=0.22, point_set_colors=array([[1. , 0. , 0. ],\n",
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" [1. , 0. , 0.5],\n",
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"…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"view(dsa_speed,\n",
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" point_sets=[start_point, way_points, end_point],\n",
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" point_set_colors=[(1.0,0.0,0.0), (1.0,0.0,0.5), (1.0,0.0,0.8)],\n",
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" ui_collapsed=True)"
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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": 9,
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"metadata": {},
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"outputs": [],
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"source": [
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"interpolator = itk.LinearInterpolateImageFunction.New(dsa_speed)\n",
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"interpolator.SetInputImage(dsa_speed)"
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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": 10,
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"metadata": {},
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"outputs": [],
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"source": [
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"cost_function = itk.SingleImageCostFunction[type(dsa_speed)].New(interpolator=interpolator)\n",
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"cost_function.SetInterpolator(interpolator)"
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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": 11,
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"metadata": {},
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"outputs": [],
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"source": [
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"spacing = list(dsa_speed.GetSpacing())\n",
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"min_spacing = min(spacing)\n",
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"step_length_factor = 0.25\n",
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"step_length_relax = 0.5\n",
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"number_of_iterations = 4000\n",
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"\n",
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"optimizer = itk.RegularStepGradientDescentOptimizer.New(\n",
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" number_of_iterations=number_of_iterations,\n",
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" maximum_step_length=1.0*step_length_factor*min_spacing,\n",
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" minimum_step_length=0.5*step_length_factor*min_spacing,\n",
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" relaxation_factor=step_length_relax)"
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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": 12,
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"metadata": {},
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"outputs": [],
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"source": [
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"termination_value = 3.0\n",
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"path_filter = itk.SpeedFunctionToPathFilter.New(dsa_speed,\n",
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" cost_function=cost_function,\n",
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" optimizer=optimizer,\n",
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" termination_value=termination_value)\n",
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"path_filter.SetInput(dsa_speed)"
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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": 13,
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"metadata": {},
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"outputs": [],
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"source": [
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"path_filter.AddPathInformation(path_information)"
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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": 14,
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"metadata": {},
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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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"CPU times: user 64.8 ms, sys: 0 ns, total: 64.8 ms\n",
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"Wall time: 64.2 ms\n"
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]
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}
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],
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"source": [
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"%time path_filter.Update()"
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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": 15,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"2232"
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]
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},
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"execution_count": 15,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"path = path_filter.GetOutput(0)\n",
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"path.GetVertexList().Size()"
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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": 16,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "6ed292f79b4647408ba500afa897af1a",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(geometries=[{'vtkClass': 'vtkPolyData', 'points': {'vtkClass': 'vtkPoints', 'name': '_points', 'numberO…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"view(dsa, geometries=path, ui_collapsed=True)"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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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": "3.6.8"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

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