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January 25, 2019 16:57
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itk-phasesymmetry on 3D ultrasoun
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 1, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "Collecting itk-phasesymmetry\n", | |
| " Using cached https://files.pythonhosted.org/packages/c3/17/998b66d78289fd83a6a4db77b56f0088312bfc7dd00c61fe7ae4ac2b640e/itk_phasesymmetry-1.0.2-cp36-cp36m-manylinux1_x86_64.whl\n", | |
| "Collecting itk-anisotropicdiffusionlbr\n", | |
| " Using cached https://files.pythonhosted.org/packages/cb/6a/5006bbfb97a4b122c47cb244aa9d0ea22d30f1c4a446c341f2396f6d8ea4/itk_anisotropicdiffusionlbr-1.0.1-cp36-cp36m-manylinux1_x86_64.whl\n", | |
| "Collecting plotly\n", | |
| "\u001b[?25l Downloading https://files.pythonhosted.org/packages/3e/77/905effe9361395d3e094ffd2b54b4085d339a7b7de9c2c91fa55ec257422/plotly-3.5.0-py2.py3-none-any.whl (38.3MB)\n", | |
| "\u001b[K 100% |████████████████████████████████| 38.4MB 891kB/s ta 0:00:011\n", | |
| "\u001b[?25hCollecting itk>=5.0b01 (from itk-phasesymmetry)\n", | |
| " Using cached https://files.pythonhosted.org/packages/d3/9d/ff1f2bed6c07f7a54cc9b8baff4b1098a32350b2258a6fd58b43c9119e5e/itk-5.0b3-cp36-cp36m-manylinux1_x86_64.whl\n", | |
| "Collecting requests (from plotly)\n", | |
| " Using cached https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl\n", | |
| "Requirement already satisfied: six in ./lib/python3.6/site-packages (from plotly) (1.12.0)\n", | |
| "Requirement already satisfied: nbformat>=4.2 in ./lib/python3.6/site-packages (from plotly) (4.4.0)\n", | |
| "Collecting retrying>=1.3.3 (from plotly)\n", | |
| "Requirement already satisfied: decorator>=4.0.6 in ./lib/python3.6/site-packages (from plotly) (4.3.2)\n", | |
| "Collecting pytz (from plotly)\n", | |
| "\u001b[?25l Downloading https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl (510kB)\n", | |
| "\u001b[K 100% |████████████████████████████████| 512kB 3.6MB/s ta 0:00:01\n", | |
| "\u001b[?25hCollecting itk-segmentation>=5.0b3 (from itk>=5.0b01->itk-phasesymmetry)\n", | |
| " Using cached https://files.pythonhosted.org/packages/e0/25/2986f9cc438f4ed51e9b438e195802c45ba5bafeaf69d1e8949da6ac6f8f/itk_segmentation-5.0b3-cp36-cp36m-manylinux1_x86_64.whl\n", | |
| "Requirement already satisfied: numpy in ./lib/python3.6/site-packages (from itk>=5.0b01->itk-phasesymmetry) (1.16.0)\n", | |
| "Collecting itk-io>=5.0b3 (from itk>=5.0b01->itk-phasesymmetry)\n", | |
| " Using cached https://files.pythonhosted.org/packages/05/42/f045e39af147e7b6a1d033aaaad4d3f7e67380a8a22a67c0be15e4e75512/itk_io-5.0b3-cp36-cp36m-manylinux1_x86_64.whl\n", | |
| "Collecting itk-core>=5.0b3 (from itk>=5.0b01->itk-phasesymmetry)\n", | |
| " Using cached https://files.pythonhosted.org/packages/bd/0e/88a28d841895c56e9941d6ea5a10de702199902399f49e508aa51e806863/itk_core-5.0b3-cp36-cp36m-manylinux1_x86_64.whl\n", | |
| "Collecting itk-filtering>=5.0b3 (from itk>=5.0b01->itk-phasesymmetry)\n", | |
| " Using cached https://files.pythonhosted.org/packages/e4/2a/274d186d7d501d435226052005d5993ad7be0ed431c74f2c3fb0e7eab533/itk_filtering-5.0b3-cp36-cp36m-manylinux1_x86_64.whl\n", | |
| "Collecting itk-numerics>=5.0b3 (from itk>=5.0b01->itk-phasesymmetry)\n", | |
| " Using cached https://files.pythonhosted.org/packages/dc/1d/a60e341fd9624feddfbedbe7787a5f2c18b1e2fe3d68119ebe4a53dff455/itk_numerics-5.0b3-cp36-cp36m-manylinux1_x86_64.whl\n", | |
| "Collecting itk-registration>=5.0b3 (from itk>=5.0b01->itk-phasesymmetry)\n", | |
| " Using cached https://files.pythonhosted.org/packages/93/f3/b20041964c1652213f5b1e9d621b4818d9fe5cb38b448d1ac379b2080fc8/itk_registration-5.0b3-cp36-cp36m-manylinux1_x86_64.whl\n", | |
| "Collecting certifi>=2017.4.17 (from requests->plotly)\n", | |
| " Using cached https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl\n", | |
| "Collecting urllib3<1.25,>=1.21.1 (from requests->plotly)\n", | |
| " Using cached https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl\n", | |
| "Collecting chardet<3.1.0,>=3.0.2 (from requests->plotly)\n", | |
| " Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl\n", | |
| "Collecting idna<2.9,>=2.5 (from requests->plotly)\n", | |
| " Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl\n", | |
| "Requirement already satisfied: ipython-genutils in ./lib/python3.6/site-packages (from nbformat>=4.2->plotly) (0.2.0)\n", | |
| "Requirement already satisfied: jupyter-core in ./lib/python3.6/site-packages (from nbformat>=4.2->plotly) (4.4.0)\n", | |
| "Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in ./lib/python3.6/site-packages (from nbformat>=4.2->plotly) (2.6.0)\n", | |
| "Requirement already satisfied: traitlets>=4.1 in ./lib/python3.6/site-packages (from nbformat>=4.2->plotly) (4.3.2)\n", | |
| "Installing collected packages: itk-core, itk-numerics, itk-filtering, itk-segmentation, itk-io, itk-registration, itk, itk-phasesymmetry, itk-anisotropicdiffusionlbr, certifi, urllib3, chardet, idna, requests, retrying, pytz, plotly\n", | |
| " Found existing installation: itk-core 4.13.1.post1\n", | |
| " Uninstalling itk-core-4.13.1.post1:\n", | |
| " Successfully uninstalled itk-core-4.13.1.post1\n", | |
| " Found existing installation: itk-numerics 4.13.1.post1\n", | |
| " Uninstalling itk-numerics-4.13.1.post1:\n", | |
| " Successfully uninstalled itk-numerics-4.13.1.post1\n", | |
| " Found existing installation: itk-filtering 4.13.1.post1\n", | |
| " Uninstalling itk-filtering-4.13.1.post1:\n", | |
| " Successfully uninstalled itk-filtering-4.13.1.post1\n", | |
| "Successfully installed certifi-2018.11.29 chardet-3.0.4 idna-2.8 itk-5.0b3 itk-anisotropicdiffusionlbr-1.0.1 itk-core-5.0b3 itk-filtering-5.0b3 itk-io-5.0b3 itk-numerics-5.0b3 itk-phasesymmetry-1.0.2 itk-registration-5.0b3 itk-segmentation-5.0b3 plotly-3.5.0 pytz-2018.9 requests-2.21.0 retrying-1.3.3 urllib3-1.24.1\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "# Note: `pip install itkwidgets` before starting the notebook\n", | |
| "import sys\n", | |
| "!{sys.executable} -m pip install itk-phasesymmetry itk-anisotropicdiffusionlbr plotly" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 3, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "import itk\n", | |
| "from itkwidgets import view, line_profile\n", | |
| "import numpy as np" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 4, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "image = itk.imread('./input.nrrd', itk.ctype('float'))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 5, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "application/vnd.jupyter.widget-view+json": { | |
| "model_id": "2bc91ca18a4d45ed8f392721aa8819ad", | |
| "version_major": 2, | |
| "version_minor": 0 | |
| }, | |
| "text/plain": [ | |
| "Viewer(gradient_opacity=0.22, rendered_image=<itkImagePython.itkImageF3; proxy of <Swig Object of type 'itkIma…" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "viewer = view(image, ui_collapsed=True)\n", | |
| "viewer" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 6, | |
| "metadata": { | |
| "scrolled": true | |
| }, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "application/vnd.jupyter.widget-view+json": { | |
| "model_id": "b7ad13bcee18452cb9460c423c5f664a", | |
| "version_major": 2, | |
| "version_minor": 0 | |
| }, | |
| "text/plain": [ | |
| "VBox(children=(LineProfiler(interpolation=False, mode='z', rendered_image=<itkImagePython.itkImageF3; proxy of…" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "diffusion_filter = itk.CoherenceEnhancingDiffusionImageFilter.New(image)\n", | |
| "diffusion_filter.SetEnhancement(3)\n", | |
| "diffusion_filter.SetDiffusionTime(5.0)\n", | |
| "diffusion_filter.SetLambda(0.5)\n", | |
| "diffusion_filter.SetNoiseScale(1.5)\n", | |
| "diffusion_filter.SetFeatureScale(3.0)\n", | |
| "diffusion_filter.Update()\n", | |
| "\n", | |
| "line_profile(diffusion_filter.GetOutput(), interpolation=False)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 7, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "dimension = image.GetImageDimension()\n", | |
| "\n", | |
| "phase_symmetry_filter = itk.PhaseSymmetryImageFilter.New(diffusion_filter.GetOutput())\n", | |
| "#phase_symmetry_filter = itk.PhaseSymmetryImageFilter.New(image)\n", | |
| "\n", | |
| "phase_symmetry_filter.SetSigma(0.45)\n", | |
| "phase_symmetry_filter.SetPolarity(1)\n", | |
| "phase_symmetry_filter.SetNoiseThreshold(5.0)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 8, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "application/vnd.jupyter.widget-view+json": { | |
| "model_id": "f6b76533a3174e6ca4afae4cf410bbb3", | |
| "version_major": 2, | |
| "version_minor": 0 | |
| }, | |
| "text/plain": [ | |
| "Viewer(gradient_opacity=0.22, rendered_image=<itkImagePython.itkImageF3; proxy of <Swig Object of type 'itkIma…" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "wavelengths = [4, 4, 4, 8, 8, 8, 12, 12, 12]\n", | |
| "#wavelengths = [2, 2, 4, 4, 6, 6]\n", | |
| "dimension = image.GetImageDimension()\n", | |
| "\n", | |
| "scales = len(wavelengths) / dimension\n", | |
| "wavelength_matrix = itk.Array2D[itk.D](int(scales), dimension)\n", | |
| "np_array = np.array(wavelengths, dtype=np.float64)\n", | |
| "vnl_vector = itk.GetVnlVectorFromArray(np_array)\n", | |
| "wavelength_matrix.copy_in(vnl_vector.data_block())\n", | |
| "phase_symmetry_filter.SetWavelengths(wavelength_matrix)\n", | |
| "\n", | |
| "phase_symmetry_filter.Initialize()\n", | |
| "phase_symmetry_filter.Update()\n", | |
| "view(phase_symmetry_filter, 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": "3.6.5" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 2 | |
| } |
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