{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "py2jemris_demo.ipynb",
      "provenance": [],
      "collapsed_sections": [],
      "toc_visible": true,
      "authorship_tag": "ABX9TyNiTDzq3M+MDicy0GDiNO3F",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/imr-framework/py2jemris/blob/master/py2jemris_demo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "f1OHVVKCZATg"
      },
      "source": [
        "# py2jemris demo \n",
        "This notebook demonstrates usage of py2jemris functions. In the end, we test-simulate a Pulseq file using JEMRIS on the command line.\n",
        "Run the cells in order to ensure that subsequent tests work. \n",
        "Look to the left for Table of Contents to access each part of the demo.\n",
        "Email questions to gt2407@columbia.edu. Thanks for trying this out!"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "5MUISdrvZJj-"
      },
      "source": [
        "## Install JEMRIS for simulation\n",
        "\n",
        "1. Download JEMRIS 2.8.3 from the official website"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "VWx-T1uVZBwx",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 213
        },
        "outputId": "2c33c4fa-e85a-4986-cdca-a12d930028f9"
      },
      "source": [
        "!wget http://www.jemris.org/get/jemris-2.8.3-Linux.deb --no-check-certificate"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2020-08-27 17:27:05--  http://www.jemris.org/get/jemris-2.8.3-Linux.deb\n",
            "Resolving www.jemris.org (www.jemris.org)... 193.175.154.2\n",
            "Connecting to www.jemris.org (www.jemris.org)|193.175.154.2|:80... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 8655898 (8.3M) [application/x-debian-package]\n",
            "Saving to: ‘jemris-2.8.3-Linux.deb’\n",
            "\n",
            "jemris-2.8.3-Linux. 100%[===================>]   8.25M  1.98MB/s    in 4.4s    \n",
            "\n",
            "2020-08-27 17:27:10 (1.89 MB/s) - ‘jemris-2.8.3-Linux.deb’ saved [8655898/8655898]\n",
            "\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "cZgjy_LA-UOS"
      },
      "source": [
        "Then we install JEMRIS dependencies. "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "M9g02RK6QL-W",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "outputId": "cf909aba-645e-4572-ba89-773c13ef75a8"
      },
      "source": [
        "# Install requirements for jemris \n",
        "!sudo apt-get update -y\n",
        "!sudo apt-get install -y libcln6 \n",
        "!sudo apt-get install -y libginac6\n",
        "!sudo apt-get install -y ginac-tools \n",
        "!sudo apt-get install -y libsundials-nvecserial2\n",
        "!sudo apt-get install -y libsundials-cvode2"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "\r0% [Working]\r            \rGet:1 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease [3,626 B]\n",
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            "dpkg-preconfigure: unable to re-open stdin: \n",
            "Selecting previously unselected package libcln6.\n",
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            "/sbin/ldconfig.real: /usr/local/lib/python3.6/dist-packages/ideep4py/lib/libmkldnn.so.0 is not a symbolic link\n",
            "\n",
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            "Building dependency tree       \n",
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            "The following package was automatically installed and is no longer required:\n",
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            "Use 'sudo apt autoremove' to remove it.\n",
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            "/sbin/ldconfig.real: /usr/local/lib/python3.6/dist-packages/ideep4py/lib/libmkldnn.so.0 is not a symbolic link\n",
            "\n",
            "Reading package lists... Done\n",
            "Building dependency tree       \n",
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            "The following package was automatically installed and is no longer required:\n",
            "  libnvidia-common-440\n",
            "Use 'sudo apt autoremove' to remove it.\n",
            "The following additional packages will be installed:\n",
            "  doc-base libuuid-perl libyaml-tiny-perl\n",
            "Suggested packages:\n",
            "  dhelp | dwww | doc-central | yelp | khelpcenter rarian-compat\n",
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            "Registering 18 doc-base files...\n",
            "Error in `/usr/share/doc-base/users-and-groups', line 13: all `Format' sections are invalid.\n",
            "Note: `install-docs --verbose --check file_name' may give more details about the above error.\n",
            "Processing triggers for man-db (2.8.3-2ubuntu0.1) ...\n",
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            "Setting up libsundials-nvecserial2:amd64 (2.7.0+dfsg-2build1) ...\n",
            "Processing triggers for libc-bin (2.27-3ubuntu1) ...\n",
            "/sbin/ldconfig.real: /usr/local/lib/python3.6/dist-packages/ideep4py/lib/libmkldnn.so.0 is not a symbolic link\n",
            "\n",
            "Reading package lists... Done\n",
            "Building dependency tree       \n",
            "Reading state information... Done\n",
            "The following package was automatically installed and is no longer required:\n",
            "  libnvidia-common-440\n",
            "Use 'sudo apt autoremove' to remove it.\n",
            "The following additional packages will be installed:\n",
            "  libamd2 libbtf1 libcolamd2 libklu1 libsuitesparseconfig5\n",
            "The following NEW packages will be installed:\n",
            "  libamd2 libbtf1 libcolamd2 libklu1 libsuitesparseconfig5 libsundials-cvode2\n",
            "0 upgraded, 6 newly installed, 0 to remove and 62 not upgraded.\n",
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            "Get:5 http://archive.ubuntu.com/ubuntu bionic/main amd64 libklu1 amd64 1:5.1.2-2 [69.3 kB]\n",
            "Get:6 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libsundials-cvode2 amd64 2.7.0+dfsg-2build1 [57.3 kB]\n",
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            "debconf: unable to initialize frontend: Dialog\n",
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            "debconf: unable to initialize frontend: Readline\n",
            "debconf: (This frontend requires a controlling tty.)\n",
            "debconf: falling back to frontend: Teletype\n",
            "dpkg-preconfigure: unable to re-open stdin: \n",
            "Selecting previously unselected package libsuitesparseconfig5:amd64.\n",
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            "Preparing to unpack .../0-libsuitesparseconfig5_1%3a5.1.2-2_amd64.deb ...\n",
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            "Selecting previously unselected package libamd2:amd64.\n",
            "Preparing to unpack .../1-libamd2_1%3a5.1.2-2_amd64.deb ...\n",
            "Unpacking libamd2:amd64 (1:5.1.2-2) ...\n",
            "Selecting previously unselected package libbtf1:amd64.\n",
            "Preparing to unpack .../2-libbtf1_1%3a5.1.2-2_amd64.deb ...\n",
            "Unpacking libbtf1:amd64 (1:5.1.2-2) ...\n",
            "Selecting previously unselected package libcolamd2:amd64.\n",
            "Preparing to unpack .../3-libcolamd2_1%3a5.1.2-2_amd64.deb ...\n",
            "Unpacking libcolamd2:amd64 (1:5.1.2-2) ...\n",
            "Selecting previously unselected package libklu1:amd64.\n",
            "Preparing to unpack .../4-libklu1_1%3a5.1.2-2_amd64.deb ...\n",
            "Unpacking libklu1:amd64 (1:5.1.2-2) ...\n",
            "Selecting previously unselected package libsundials-cvode2:amd64.\n",
            "Preparing to unpack .../5-libsundials-cvode2_2.7.0+dfsg-2build1_amd64.deb ...\n",
            "Unpacking libsundials-cvode2:amd64 (2.7.0+dfsg-2build1) ...\n",
            "Setting up libbtf1:amd64 (1:5.1.2-2) ...\n",
            "Setting up libsuitesparseconfig5:amd64 (1:5.1.2-2) ...\n",
            "Setting up libcolamd2:amd64 (1:5.1.2-2) ...\n",
            "Setting up libamd2:amd64 (1:5.1.2-2) ...\n",
            "Setting up libklu1:amd64 (1:5.1.2-2) ...\n",
            "Setting up libsundials-cvode2:amd64 (2.7.0+dfsg-2build1) ...\n",
            "Processing triggers for libc-bin (2.27-3ubuntu1) ...\n",
            "/sbin/ldconfig.real: /usr/local/lib/python3.6/dist-packages/ideep4py/lib/libmkldnn.so.0 is not a symbolic link\n",
            "\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "cu9jR78B-3GI"
      },
      "source": [
        "Link library names (?) so JEMRIS can find one specific CVODE package "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "6RsOnFBuQ1HG",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "outputId": "2c387422-2665-40b1-fe85-1fd0da266d89"
      },
      "source": [
        " !sudo /sbin/ldconfig -v"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/sbin/ldconfig.real: Path `/usr/local/lib' given more than once\n",
            "/sbin/ldconfig.real: Can't stat /usr/local/nvidia/lib: No such file or directory\n",
            "/sbin/ldconfig.real: Can't stat /usr/local/nvidia/lib64: No such file or directory\n",
            "/sbin/ldconfig.real: Can't stat /usr/local/lib/x86_64-linux-gnu: No such file or directory\n",
            "/sbin/ldconfig.real: Path `/lib/x86_64-linux-gnu' given more than once\n",
            "/sbin/ldconfig.real: Path `/usr/lib/x86_64-linux-gnu' given more than once\n",
            "/usr/local/cuda-10.1/extras/CUPTI/lib64:\n",
            "\tlibcupti.so.10.1 -> libcupti.so.10.1.208\n",
            "\tlibnvperf_host.so -> libnvperf_host.so\n",
            "\tlibnvperf_target.so -> libnvperf_target.so\n",
            "/usr/local/lib:\n",
            "\tlibmkl_avx.so -> libmkl_avx.so\n",
            "\tlibmkl_blacs_openmpi_ilp64.so -> libmkl_blacs_openmpi_ilp64.so\n",
            "\tlibmkl_vml_mc2.so -> libmkl_vml_mc2.so\n",
            "\tlibmkl_avx512_mic.so -> libmkl_avx512_mic.so\n",
            "\tlibmkl_mc3.so -> libmkl_mc3.so\n",
            "\tlibmkl_blacs_intelmpi_lp64.so -> libmkl_blacs_intelmpi_lp64.so\n",
            "\tlibmkl_vml_avx512.so -> libmkl_vml_avx512.so\n",
            "\tlibmkl_core.so -> libmkl_core.so\n",
            "\tlibmkl_intel_ilp64.so -> libmkl_intel_ilp64.so\n",
            "\tlibmkl_gf_lp64.so -> libmkl_gf_lp64.so\n",
            "\tlibiomp5.so -> libiomp5.so\n",
            "\tlibmkl_def.so -> libmkl_def.so\n",
            "\tlibiomp5_db.so -> libiomp5_db.so\n",
            "\tlibmkl_mc.so -> libmkl_mc.so\n",
            "\tlibmkl_blacs_sgimpt_ilp64.so -> libmkl_blacs_sgimpt_ilp64.so\n",
            "\tlibmkl_tbb_thread.so -> libmkl_tbb_thread.so\n",
            "\tlibmkl_pgi_thread.so -> libmkl_pgi_thread.so\n",
            "\tlibmkl_vml_def.so -> libmkl_vml_def.so\n",
            "\tlibmkl_vml_cmpt.so -> libmkl_vml_cmpt.so\n",
            "\tlibmkl_scalapack_lp64.so -> libmkl_scalapack_lp64.so\n",
            "\tlibmkl_gnu_thread.so -> libmkl_gnu_thread.so\n",
            "\tlibmkl_blacs_sgimpt_lp64.so -> libmkl_blacs_sgimpt_lp64.so\n",
            "\tlibmkl_avx2.so -> libmkl_avx2.so\n",
            "\tlibmkl_vml_avx2.so -> libmkl_vml_avx2.so\n",
            "\tlibmkl_avx512.so -> libmkl_avx512.so\n",
            "\tlibiompstubs5.so -> libiompstubs5.so\n",
            "\tlibmkl_intel_thread.so -> libmkl_intel_thread.so\n",
            "\tlibmkl_scalapack_ilp64.so -> libmkl_scalapack_ilp64.so\n",
            "\tlibmkl_vml_mc.so -> libmkl_vml_mc.so\n",
            "\tlibmkl_intel_lp64.so -> libmkl_intel_lp64.so\n",
            "\tlibmkl_blacs_openmpi_lp64.so -> libmkl_blacs_openmpi_lp64.so\n",
            "\tlibmkl_blacs_intelmpi_ilp64.so -> libmkl_blacs_intelmpi_ilp64.so\n",
            "\tlibmkl_vml_mc3.so -> libmkl_vml_mc3.so\n",
            "\tlibmkl_vml_avx512_mic.so -> libmkl_vml_avx512_mic.so\n",
            "\tlibmkl_rt.so -> libmkl_rt.so\n",
            "\tlibmkl_sequential.so -> libmkl_sequential.so\n",
            "\tlibmkl_cdft_core.so -> libmkl_cdft_core.so\n",
            "\tlibmkl_vml_avx.so -> libmkl_vml_avx.so\n",
            "\tlibmkl_gf_ilp64.so -> libmkl_gf_ilp64.so\n",
            "/usr/local/lib/python3.6/dist-packages/ideep4py/lib:\n",
            "\tlibiomp5.so -> libiomp5.so\n",
            "\tlibmklml_intel.so -> libmklml_intel.so\n",
            "/sbin/ldconfig.real: /usr/local/lib/python3.6/dist-packages/ideep4py/lib/libmkldnn.so.0 is not a symbolic link\n",
            "\n",
            "\tlibmkldnn.so.0 -> libmkldnn.so.0.14.0\n",
            "/usr/local/cuda-10.0/targets/x86_64-linux/lib:\n",
            "\tlibnppicc.so.10.0 -> libnppicc.so.10.0.130\n",
            "\tlibnvgraph.so.10.0 -> libnvgraph.so.10.0.130\n",
            "\tlibnppist.so.10.0 -> libnppist.so.10.0.130\n",
            "\tlibcudart.so.10.0 -> libcudart.so.10.0.130\n",
            "\tlibcufftw.so.10.0 -> libcufftw.so.10.0.145\n",
            "\tlibnppial.so.10.0 -> libnppial.so.10.0.130\n",
            "\tlibnppidei.so.10.0 -> libnppidei.so.10.0.130\n",
            "\tlibcuinj64.so.10.0 -> libcuinj64.so.10.0.130\n",
            "\tlibcusolver.so.10.0 -> libcusolver.so.10.0.130\n",
            "\tlibcusparse.so.10.0 -> libcusparse.so.10.0.130\n",
            "\tlibnppisu.so.10.0 -> libnppisu.so.10.0.130\n",
            "\tlibaccinj64.so.10.0 -> libaccinj64.so.10.0.130\n",
            "\tlibcufft.so.10.0 -> libcufft.so.10.0.145\n",
            "\tlibnvrtc.so.10.0 -> libnvrtc.so.10.0.130\n",
            "\tlibnppc.so.10.0 -> libnppc.so.10.0.130\n",
            "\tlibnvjpeg.so.10.0 -> libnvjpeg.so.10.0.318\n",
            "\tlibcurand.so.10.0 -> libcurand.so.10.0.130\n",
            "\tlibnvToolsExt.so.1 -> libnvToolsExt.so.1.0.0\n",
            "\tlibnppicom.so.10.0 -> libnppicom.so.10.0.130\n",
            "\tlibnpps.so.10.0 -> libnpps.so.10.0.130\n",
            "\tlibnppig.so.10.0 -> libnppig.so.10.0.130\n",
            "\tlibnppim.so.10.0 -> libnppim.so.10.0.130\n",
            "\tlibnvrtc-builtins.so.10.0 -> libnvrtc-builtins.so.10.0.130\n",
            "\tlibcublas.so.10.0 -> libcublas.so.10.0.130\n",
            "\tlibnvblas.so.10.0 -> libnvblas.so.10.0.130\n",
            "\tlibnppitc.so.10.0 -> libnppitc.so.10.0.130\n",
            "\tlibnppif.so.10.0 -> libnppif.so.10.0.130\n",
            "\tlibOpenCL.so.1 -> libOpenCL.so.1.1\n",
            "/usr/local/cuda-10.1/targets/x86_64-linux/lib:\n",
            "\tlibcusparse.so.10 -> libcusparse.so.10.3.0.243\n",
            "\tlibnppial.so.10 -> libnppial.so.10.2.0.243\n",
            "\tlibnppisu.so.10 -> libnppisu.so.10.2.0.243\n",
            "\tlibnvrtc-builtins.so.10.1 -> libnvrtc-builtins.so.10.1.243\n",
            "\tlibcusolver.so.10 -> libcusolver.so.10.2.0.243\n",
            "\tlibnppicom.so.10 -> libnppicom.so.10.2.0.243\n",
            "\tlibnvgraph.so.10 -> libnvgraph.so.10.1.243\n",
            "\tlibnvrtc.so.10.1 -> libnvrtc.so.10.1.243\n",
            "\tlibnpps.so.10 -> libnpps.so.10.2.0.243\n",
            "\tlibnppig.so.10 -> libnppig.so.10.2.0.243\n",
            "\tlibnppist.so.10 -> libnppist.so.10.2.0.243\n",
            "\tlibnppc.so.10 -> libnppc.so.10.2.0.243\n",
            "\tlibnppif.so.10 -> libnppif.so.10.2.0.243\n",
            "\tlibnvjpeg.so.10 -> libnvjpeg.so.10.3.0.243\n",
            "\tlibnvToolsExt.so.1 -> libnvToolsExt.so.1.0.0\n",
            "\tlibnppicc.so.10 -> libnppicc.so.10.2.0.243\n",
            "\tlibcurand.so.10 -> libcurand.so.10.1.1.243\n",
            "\tlibcusolverMg.so.10 -> libcusolverMg.so.10.2.0.243\n",
            "\tlibcufft.so.10 -> libcufft.so.10.1.1.243\n",
            "\tlibnppitc.so.10 -> libnppitc.so.10.2.0.243\n",
            "\tlibcufftw.so.10 -> libcufftw.so.10.1.1.243\n",
            "\tlibnppim.so.10 -> libnppim.so.10.2.0.243\n",
            "\tlibnppidei.so.10 -> libnppidei.so.10.2.0.243\n",
            "\tlibcuinj64.so.10.1 -> libcuinj64.so.10.1.243\n",
            "\tlibaccinj64.so.10.1 -> libaccinj64.so.10.1.243\n",
            "\tlibOpenCL.so.1 -> libOpenCL.so.1.1\n",
            "\tlibcudart.so.10.1 -> libcudart.so.10.1.243\n",
            "/lib/x86_64-linux-gnu:\n",
            "\tlibreadline.so.7 -> libreadline.so.7.0\n",
            "\tlibhistory.so.7 -> libhistory.so.7.0\n",
            "\tlibdbus-1.so.3 -> libdbus-1.so.3.19.4\n",
            "\tlibslang.so.2 -> libslang.so.2.3.1\n",
            "\tlibfuse.so.2 -> libfuse.so.2.9.7\n",
            "\tlibdevmapper.so.1.02.1 -> libdevmapper.so.1.02.1\n",
            "\tlibnl-3.so.200 -> libnl-3.so.200.24.0\n",
            "\tlibkmod.so.2 -> libkmod.so.2.3.2\n",
            "\tlibkeyutils.so.1 -> libkeyutils.so.1.5\n",
            "\tlibjson-c.so.3 -> libjson-c.so.3.0.1\n",
            "\tlibusb-1.0.so.0 -> libusb-1.0.so.0.1.0\n",
            "\tlibcryptsetup.so.12 -> libcryptsetup.so.12.2.0\n",
            "\tlibaio.so.1 -> libaio.so.1.0.1\n",
            "\tlibulockmgr.so.1 -> libulockmgr.so.1.0.1\n",
            "\tlibidn.so.11 -> libidn.so.11.6.16\n",
            "\tlibexpat.so.1 -> libexpat.so.1.6.7\n",
            "\tliblzo2.so.2 -> liblzo2.so.2.0.0\n",
            "\tlibbsd.so.0 -> libbsd.so.0.8.7\n",
            "\tlibapparmor.so.1 -> libapparmor.so.1.4.2\n",
            "\tlibcap.so.2 -> libcap.so.2.25\n",
            "\tlibwrap.so.0 -> libwrap.so.0.7.6\n",
            "\tlibnss_nisplus.so.2 -> libnss_nisplus-2.27.so\n",
            "\tlibblkid.so.1 -> libblkid.so.1.1.0\n",
            "\tlibcrypt.so.1 -> libcrypt-2.27.so\n",
            "\tlibext2fs.so.2 -> libext2fs.so.2.4\n",
            "\tlibudev.so.1 -> libudev.so.1.6.9\n",
            "\tlibbz2.so.1.0 -> libbz2.so.1.0.4\n",
            "\tlibdl.so.2 -> libdl-2.27.so\n",
            "/sbin/ldconfig.real: /lib/x86_64-linux-gnu/ld-2.27.so is the dynamic linker, ignoring\n",
            "\n",
            "\tld-linux-x86-64.so.2 -> ld-2.27.so\n",
            "\tlibcidn.so.1 -> libcidn-2.27.so\n",
            "\tlibmount.so.1 -> libmount.so.1.1.0\n",
            "\tlibsepol.so.1 -> libsepol.so.1\n",
            "\tlibpthread.so.0 -> libpthread-2.27.so\n",
            "\tlibseccomp.so.2 -> libseccomp.so.2.4.1\n",
            "\tlibnss_hesiod.so.2 -> libnss_hesiod-2.27.so\n",
            "\tlibpcprofile.so -> libpcprofile.so\n",
            "\tlibutil.so.1 -> libutil-2.27.so\n",
            "\tlibsystemd.so.0 -> libsystemd.so.0.21.0\n",
            "\tlibsmartcols.so.1 -> libsmartcols.so.1.1.0\n",
            "\tlibz.so.1 -> libz.so.1.2.11\n",
            "\tlibnss_compat.so.2 -> libnss_compat-2.27.so\n",
            "\tlibnss_nis.so.2 -> libnss_nis-2.27.so\n",
            "\tlibanl.so.1 -> libanl-2.27.so\n",
            "\tlibcom_err.so.2 -> libcom_err.so.2.1\n",
            "\tlibcap-ng.so.0 -> libcap-ng.so.0.0.0\n",
            "\tlibaudit.so.1 -> libaudit.so.1.0.0\n",
            "\tlibprocps.so.6 -> libprocps.so.6.0.0\n",
            "\tlibncurses.so.5 -> libncurses.so.5.9\n",
            "\tlibc.so.6 -> libc-2.27.so\n",
            "\tlibnsl.so.1 -> libnsl-2.27.so\n",
            "\tlibnss_dns.so.2 -> libnss_dns-2.27.so\n",
            "\tlibmvec.so.1 -> libmvec-2.27.so\n",
            "\tlibncursesw.so.5 -> libncursesw.so.5.9\n",
            "\tlibfdisk.so.1 -> libfdisk.so.1.1.0\n",
            "\tlibpcre.so.3 -> libpcre.so.3.13.3\n",
            "\tlibrt.so.1 -> librt-2.27.so\n",
            "\tlibmemusage.so -> libmemusage.so\n",
            "\tlibnss_files.so.2 -> libnss_files-2.27.so\n",
            "\tliblzma.so.5 -> liblzma.so.5.2.2\n",
            "\tlibss.so.2 -> libss.so.2.0\n",
            "\tlibselinux.so.1 -> libselinux.so.1\n",
            "\tlibuuid.so.1 -> libuuid.so.1.3.0\n",
            "\tlibpamc.so.0 -> libpamc.so.0.82.1\n",
            "\tlibgcrypt.so.20 -> libgcrypt.so.20.2.1\n",
            "\tlibpam.so.0 -> libpam.so.0.83.1\n",
            "\tlibattr.so.1 -> libattr.so.1.1.0\n",
            "\tlibpam_misc.so.0 -> libpam_misc.so.0.82.0\n",
            "\tlibm.so.6 -> libm-2.27.so\n",
            "\tlibe2p.so.2 -> libe2p.so.2.3\n",
            "\tlibBrokenLocale.so.1 -> libBrokenLocale-2.27.so\n",
            "\tlibSegFault.so -> libSegFault.so\n",
            "\tlibacl.so.1 -> libacl.so.1.1.0\n",
            "\tlibgpg-error.so.0 -> libgpg-error.so.0.22.0\n",
            "\tlibgcc_s.so.1 -> libgcc_s.so.1\n",
            "\tlibthread_db.so.1 -> libthread_db-1.0.so\n",
            "\tlibresolv.so.2 -> libresolv-2.27.so\n",
            "\tlibtinfo.so.5 -> libtinfo.so.5.9\n",
            "/usr/lib/x86_64-linux-gnu:\n",
            "\tlibsqlite3.so.0 -> libsqlite3.so.0.8.6\n",
            "\tlibgssapi.so.3 -> libgssapi.so.3.0.0\n",
            "\tlibhx509.so.5 -> libhx509.so.5.0.0\n",
            "\tlibhcrypto.so.4 -> libhcrypto.so.4.1.0\n",
            "\tlibksba.so.8 -> libksba.so.8.11.6\n",
            "\tlibkrb5.so.26 -> libkrb5.so.26.0.0\n",
            "\tlibldap_r-2.4.so.2 -> libldap_r-2.4.so.2.10.8\n",
            "\tlibnpth.so.0 -> libnpth.so.0.1.1\n",
            "\tlibheimbase.so.1 -> libheimbase.so.1.0.0\n",
            "\tlibsasl2.so.2 -> libsasl2.so.2.0.25\n",
            "\tlibheimntlm.so.0 -> libheimntlm.so.0.1.0\n",
            "\tlibasn1.so.8 -> libasn1.so.8.0.0\n",
            "\tlibassuan.so.0 -> libassuan.so.0.8.1\n",
            "\tliblber-2.4.so.2 -> liblber-2.4.so.2.10.8\n",
            "\tlibroken.so.18 -> libroken.so.18.1.0\n",
            "\tlibwind.so.0 -> libwind.so.0.0.0\n",
            "\tlibcublasLt.so.10 -> libcublasLt.so.10.2.1.243\n",
            "\tlibnccl.so.2 -> libnccl.so.2.4.8\n",
            "\tlibnvblas.so.10 -> libnvblas.so.10.2.1.243\n",
            "\tlibcublas.so.10 -> libcublas.so.10.2.1.243\n",
            "\tlibmpfr.so.6 -> libmpfr.so.6.0.1\n",
            "\tlibopcodes-2.30-system.so -> libopcodes-2.30-system.so\n",
            "\tlibisl.so.19 -> libisl.so.19.0.0\n",
            "\tlibperl.so.5.26 -> libperl.so.5.26.1\n",
            "\tlibgdbm.so.5 -> libgdbm.so.5.0.0\n",
            "\tlibbfd-2.30-system.so -> libbfd-2.30-system.so\n",
            "\tlibmpc.so.3 -> libmpc.so.3.1.0\n",
            "\tlibgdbm_compat.so.4 -> libgdbm_compat.so.4.0.0\n",
            "\tlibcudnn.so.7 -> libcudnn.so.7.6.5\n",
            "\tlibboost_container.so.1.65.1 -> libboost_container.so.1.65.1\n",
            "\tlibboost_chrono.so.1.65.1 -> libboost_chrono.so.1.65.1\n",
            "\tlibargon2.so.0 -> libargon2.so.0\n",
            "\tlibnss3.so -> libnss3.so\n",
            "\tlibvtkCommonExecutionModelPython27D-6.3.so.6.3 -> libvtkCommonExecutionModelPython27D-6.3.so.6.3.0\n",
            "\tlibcups.so.2 -> libcups.so.2\n",
            "\tlibcdio_paranoia.so.2 -> libcdio_paranoia.so.2.0.0\n",
            "\tlibvtkIOSQLPython27D-6.3.so.6.3 -> libvtkIOSQLPython27D-6.3.so.6.3.0\n",
            "\tlibtbbmalloc.so.2 -> libtbbmalloc.so.2\n",
            "\tlibvtkIOMINCPython27D-6.3.so.6.3 -> libvtkIOMINCPython27D-6.3.so.6.3.0\n",
            "\tlibboost_filesystem.so.1.65.1 -> libboost_filesystem.so.1.65.1\n",
            "\tlibboost_log_setup.so.1.65.1 -> libboost_log_setup.so.1.65.1\n",
            "\tlibopencv_ximgproc.so.3.2 -> libopencv_ximgproc.so.3.2.0\n",
            "\tlibvtkImagingMathTCL-6.3.so.6.3 -> libvtkImagingMathTCL-6.3.so.6.3.0\n",
            "\tlibclang-6.0.so.1 -> libclang-6.0.so.1\n",
            "\tlibboost_log.so.1.65.1 -> libboost_log.so.1.65.1\n",
            "\tlibvtkInfovisLayoutPython27D-6.3.so.6.3 -> libvtkInfovisLayoutPython27D-6.3.so.6.3.0\n",
            "\tlibssl3.so -> libssl3.so\n",
            "\tlibnvidia-glvkspirv.so.450.57 -> libnvidia-glvkspirv.so.450.57\n",
            "\tlibnvidia-tls.so.450.57 -> libnvidia-tls.so.450.57\n",
            "\tlibvtkImagingGeneralPython27D-6.3.so.6.3 -> libvtkImagingGeneralPython27D-6.3.so.6.3.0\n",
            "\tlibboost_stacktrace_noop.so.1.65.1 -> libboost_stacktrace_noop.so.1.65.1\n",
            "\tlibgdk_pixbuf_xlib-2.0.so.0 -> libgdk_pixbuf_xlib-2.0.so.0.3611.0\n",
            "\tlibexif.so.12 -> libexif.so.12.3.3\n",
            "\tlibvtkCommonTransforms-6.3.so.6.3 -> libvtkCommonTransforms-6.3.so.6.3.0\n",
            "\tlibLLVM-10.so.1 -> libLLVM-10.so.1\n",
            "\tlibjansson.so.4 -> libjansson.so.4.11.0\n",
            "\tlibvtkRenderingLICPython27D-6.3.so.6.3 -> libvtkRenderingLICPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOMPIImage-6.3.so.6.3 -> libvtkIOMPIImage-6.3.so.6.3.0\n",
            "\tlibvtkFiltersHybridPython27D-6.3.so.6.3 -> libvtkFiltersHybridPython27D-6.3.so.6.3.0\n",
            "\tlibboost_timer.so.1.65.1 -> libboost_timer.so.1.65.1\n",
            "\tlibvtkFiltersGeometry-6.3.so.6.3 -> libvtkFiltersGeometry-6.3.so.6.3.0\n",
            "\tlibboost_date_time.so.1.65.1 -> libboost_date_time.so.1.65.1\n",
            "\tlibboost_math_c99.so.1.65.1 -> libboost_math_c99.so.1.65.1\n",
            "\tlibboost_prg_exec_monitor.so.1.65.1 -> libboost_prg_exec_monitor.so.1.65.1\n",
            "\tlibrtmp.so.1 -> librtmp.so.1\n",
            "\tlibnvidia-cbl.so.450.57 -> libnvidia-cbl.so.450.57\n",
            "\tlibboost_serialization.so.1.65.1 -> libboost_serialization.so.1.65.1\n",
            "\tlibopencv_features2d.so.3.2 -> libopencv_features2d.so.3.2.0\n",
            "\tlibpathplan.so.4 -> libpathplan.so.4.0.0\n",
            "\tlibpcre2-8.so.0 -> libpcre2-8.so.0.7.0\n",
            "\tlibvtkFiltersGeneralPython27D-6.3.so.6.3 -> libvtkFiltersGeneralPython27D-6.3.so.6.3.0\n",
            "\tlibXt.so.6 -> libXt.so.6.0.0\n",
            "\tlibopencv_text.so.3.2 -> libopencv_text.so.3.2.0\n",
            "\tlibboost_program_options.so.1.65.1 -> libboost_program_options.so.1.65.1\n",
            "\tlibwayland-egl.so.1 -> libwayland-egl.so.1.0.0\n",
            "\tlibnvcuvid.so.1 -> libnvcuvid.so.450.57\n",
            "\tlibavcodec.so.57 -> libavcodec.so.57.107.100\n",
            "\tliblept.so.5 -> liblept.so.5.0.2\n",
            "\tlibvtkFiltersExtractionTCL-6.3.so.6.3 -> libvtkFiltersExtractionTCL-6.3.so.6.3.0\n",
            "\tlibhdf5_cpp.so.100 -> libhdf5_cpp.so.100.0.0\n",
            "\tlibhdf5_serial.so.100 -> libhdf5_serial.so.100.0.1\n",
            "\tlibtiff.so.5 -> libtiff.so.5.3.0\n",
            "\tlibboost_locale.so.1.65.1 -> libboost_locale.so.1.65.1\n",
            "\tlibopencv_dpm.so.3.2 -> libopencv_dpm.so.3.2.0\n",
            "\tlibvtkImagingGeneral-6.3.so.6.3 -> libvtkImagingGeneral-6.3.so.6.3.0\n",
            "\tlibLLVM-6.0.so.1 -> libLLVM-6.0.so.1\n",
            "\tlibsoxr.so.0 -> libsoxr.so.0.1.1\n",
            "\tlibopenmpt.so.0 -> libopenmpt.so.0.1.1\n",
            "\tlibboost_math_tr1l.so.1.65.1 -> libboost_math_tr1l.so.1.65.1\n",
            "\tlibvtkRenderingContextOpenGL-6.3.so.6.3 -> libvtkRenderingContextOpenGL-6.3.so.6.3.0\n",
            "\tlibmpxwrappers.so.2 -> libmpxwrappers.so.2.0.1\n",
            "\tlibvtkRenderingMatplotlibPython27D-6.3.so.6.3 -> libvtkRenderingMatplotlibPython27D-6.3.so.6.3.0\n",
            "\tlibtbbmalloc_proxy.so.2 -> libtbbmalloc_proxy.so.2\n",
            "\tlibvtkInfovisBoostGraphAlgorithmsPython27D-6.3.so.6.3 -> libvtkInfovisBoostGraphAlgorithmsPython27D-6.3.so.6.3.0\n",
            "\tlibjack.so.0 -> libjack.so.0.0.28\n",
            "\tlibvtkIOSQLTCL-6.3.so.6.3 -> libvtkIOSQLTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOParallelExodusPython27D-6.3.so.6.3 -> libvtkIOParallelExodusPython27D-6.3.so.6.3.0\n",
            "\tlibvtkInfovisLayout-6.3.so.6.3 -> libvtkInfovisLayout-6.3.so.6.3.0\n",
            "\tlibvtkImagingMath-6.3.so.6.3 -> libvtkImagingMath-6.3.so.6.3.0\n",
            "\tlibnvidia-encode.so.1 -> libnvidia-encode.so.450.57\n",
            "\tlibboost_context.so.1.65.1 -> libboost_context.so.1.65.1\n",
            "\tlibgbm.so.1 -> libgbm.so.1.0.0\n",
            "\tlibvtkFiltersAMRTCL-6.3.so.6.3 -> libvtkFiltersAMRTCL-6.3.so.6.3.0\n",
            "\tlibIexMath-2_2.so.12 -> libIexMath.so\n",
            "\tlibcolord.so.2 -> libcolord.so.2.0.5\n",
            "\tlibvtkFiltersModeling-6.3.so.6.3 -> libvtkFiltersModeling-6.3.so.6.3.0\n",
            "\tlibvpx.so.5 -> libvpx.so.5.0.0\n",
            "\tlibepsilon.so.1 -> libepsilon.so.1.0.0\n",
            "\tlibvtkImagingHybridPython27D-6.3.so.6.3 -> libvtkImagingHybridPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOVideo-6.3.so.6.3 -> libvtkIOVideo-6.3.so.6.3.0\n",
            "\tlibGLESv1_CM_nvidia.so.1 -> libGLESv1_CM_nvidia.so.450.57\n",
            "\tlibgssapi_krb5.so.2 -> libgssapi_krb5.so.2.2\n",
            "\tlibvtkIOXdmfIITCL-6.3.so.6.3 -> libvtkIOXdmfIITCL-6.3.so.6.3.0\n",
            "\tlibapt-inst.so.2.0 -> libapt-inst.so.2.0.0\n",
            "\tlibboost_python-py27.so.1.65.1 -> libboost_python.so\n",
            "\tlibicu-le-hb.so.0 -> libicu-le-hb.so.0.0.0\n",
            "\tlibvtkFiltersParallelFlowPaths-6.3.so.6.3 -> libvtkFiltersParallelFlowPaths-6.3.so.6.3.0\n",
            "\tlibvtkGeovisCoreTCL-6.3.so.6.3 -> libvtkGeovisCoreTCL-6.3.so.6.3.0\n",
            "\tlibglut.so.3 -> libglut.so.3.9.0\n",
            "\tlibboost_numpy-py27.so.1.65.1 -> libboost_numpy.so\n",
            "\tlibvtkFiltersProgrammableTCL-6.3.so.6.3 -> libvtkFiltersProgrammableTCL-6.3.so.6.3.0\n",
            "\tlibaec.so.0 -> libaec.so.0.0.3\n",
            "\tlibhdf5_openmpi.so.100 -> libhdf5_openmpi.so.100.0.1\n",
            "\tlibvtkRenderingImagePython27D-6.3.so.6.3 -> libvtkRenderingImagePython27D-6.3.so.6.3.0\n",
            "\tlibpango-1.0.so.0 -> libpango-1.0.so.0.4000.14\n",
            "\tlibXdmcp.so.6 -> libXdmcp.so.6.0.0\n",
            "\tlibopencv_ccalib.so.3.2 -> libopencv_ccalib.so.3.2.0\n",
            "\tlibvtkGeovisCore-6.3.so.6.3 -> libvtkGeovisCore-6.3.so.6.3.0\n",
            "\tlibboost_signals.so.1.65.1 -> libboost_signals.so.1.65.1\n",
            "\tlibXmuu.so.1 -> libXmuu.so.1.0.0\n",
            "\tlibdrm.so.2 -> libdrm.so.2.4.0\n",
            "\tlibvtkImagingStencilPython27D-6.3.so.6.3 -> libvtkImagingStencilPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOImage-6.3.so.6.3 -> libvtkIOImage-6.3.so.6.3.0\n",
            "\tlibvtkIOInfovisTCL-6.3.so.6.3 -> libvtkIOInfovisTCL-6.3.so.6.3.0\n",
            "\tlibGLU.so.1 -> libGLU.so.1.3.1\n",
            "\tlibxcb-randr.so.0 -> libxcb-randr.so.0.1.0\n",
            "\tlibopencv_objdetect.so.3.2 -> libopencv_objdetect.so.3.2.0\n",
            "\tlibvtkImagingSources-6.3.so.6.3 -> libvtkImagingSources-6.3.so.6.3.0\n",
            "\tlibunwind.so.8 -> libunwind.so.8.0.1\n",
            "\tlibwebpmux.so.3 -> libwebpmux.so.3.0.1\n",
            "\tlibflite_cmu_grapheme_lex.so.1 -> libflite_cmu_grapheme_lex.so.2.1\n",
            "\tlibvtkIONetCDF-6.3.so.6.3 -> libvtkIONetCDF-6.3.so.6.3.0\n",
            "\tlibva-drm.so.2 -> libva-drm.so.2.100.0\n",
            "\tlibhdf5_openmpi_fortran.so.100 -> libhdf5_openmpi_fortran.so.100.0.1\n",
            "\tlibjbig.so.0 -> libjbig.so.0\n",
            "\tlibbs2b.so.0 -> libbs2b.so.0.0.0\n",
            "\tlibvtkIOAMRTCL-6.3.so.6.3 -> libvtkIOAMRTCL-6.3.so.6.3.0\n",
            "\tlibwacom.so.2 -> libwacom.so.2.6.1\n",
            "\tlibvtkRenderingContext2D-6.3.so.6.3 -> libvtkRenderingContext2D-6.3.so.6.3.0\n",
            "\tlibopen-rte.so.20 -> libopen-rte.so.20.10.1\n",
            "\tlibvtkIOMPIParallelTCL-6.3.so.6.3 -> libvtkIOMPIParallelTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersParallelStatisticsPython27D-6.3.so.6.3 -> libvtkFiltersParallelStatisticsPython27D-6.3.so.6.3.0\n",
            "\tlibopencv_surface_matching.so.3.2 -> libopencv_surface_matching.so.3.2.0\n",
            "\tlibvtkRenderingVolumeTCL-6.3.so.6.3 -> libvtkRenderingVolumeTCL-6.3.so.6.3.0\n",
            "\tlibopencv_photo.so.3.2 -> libopencv_photo.so.3.2.0\n",
            "\tlibfftw3_omp.so.3 -> libfftw3_omp.so.3.5.7\n",
            "\tlibvtkIOGeometryTCL-6.3.so.6.3 -> libvtkIOGeometryTCL-6.3.so.6.3.0\n",
            "\tlibwayland-client.so.0 -> libwayland-client.so.0.3.0\n",
            "\tlibvtkIOMoviePython27D-6.3.so.6.3 -> libvtkIOMoviePython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingParallel-6.3.so.6.3 -> libvtkRenderingParallel-6.3.so.6.3.0\n",
            "\tlibvtkRenderingContextIIDTCL-6.3.so.6.3 -> libvtkRenderingContextIIDTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOVideoTCL-6.3.so.6.3 -> libvtkIOVideoTCL-6.3.so.6.3.0\n",
            "\tlibXrandr.so.2 -> libXrandr.so.2.2.0\n",
            "\tlibvtkFiltersHybridTCL-6.3.so.6.3 -> libvtkFiltersHybridTCL-6.3.so.6.3.0\n",
            "\tlibxkbcommon-x11.so.0 -> libxkbcommon-x11.so.0.0.0\n",
            "\tlibavfilter.so.6 -> libavfilter.so.6.107.100\n",
            "\tlibFLAC.so.8 -> libFLAC.so.8.3.0\n",
            "\tlibvtkRenderingLabel-6.3.so.6.3 -> libvtkRenderingLabel-6.3.so.6.3.0\n",
            "\tlibvtkIOGeoJSONTCL-6.3.so.6.3 -> libvtkIOGeoJSONTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersHyperTreePython27D-6.3.so.6.3 -> libvtkFiltersHyperTreePython27D-6.3.so.6.3.0\n",
            "\tlibtcmalloc_minimal_debug.so.4 -> libtcmalloc_minimal_debug.so.4.3.0\n",
            "\tlibvdpau.so.1 -> libvdpau.so.1.0.0\n",
            "\tlibedit.so.2 -> libedit.so.2.0.56\n",
            "\tlibvtkFiltersGeneralTCL-6.3.so.6.3 -> libvtkFiltersGeneralTCL-6.3.so.6.3.0\n",
            "\tlibsocket++.so.1 -> libsocket++.so.1.0.2\n",
            "\tlibnuma.so.1 -> libnuma.so.1.0.0\n",
            "\tlibvtkRenderingParallelLICPython27D-6.3.so.6.3 -> libvtkRenderingParallelLICPython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingCoreTCL-6.3.so.6.3 -> libvtkRenderingCoreTCL-6.3.so.6.3.0\n",
            "\tlibvtkCommonColorPython27D-6.3.so.6.3 -> libvtkCommonColorPython27D-6.3.so.6.3.0\n",
            "\tlibfyut.so.0 -> libfyut.so.0.0.0\n",
            "\tlibvtkImagingSourcesPython27D-6.3.so.6.3 -> libvtkImagingSourcesPython27D-6.3.so.6.3.0\n",
            "\tlibopencv_structured_light.so.3.2 -> libopencv_structured_light.so.3.2.0\n",
            "\tlibvtkFiltersModelingPython27D-6.3.so.6.3 -> libvtkFiltersModelingPython27D-6.3.so.6.3.0\n",
            "\tlibcrystalhd.so.3 -> libcrystalhd.so.3.6\n",
            "\tlibvtkFiltersParallel-6.3.so.6.3 -> libvtkFiltersParallel-6.3.so.6.3.0\n",
            "\tlibnvidia-ngx.so.1 -> libnvidia-ngx.so.450.57\n",
            "\tlibvtkFiltersParallelGeometryPython27D-6.3.so.6.3 -> libvtkFiltersParallelGeometryPython27D-6.3.so.6.3.0\n",
            "\tlibgdcmjpeg12.so.2.8 -> libgdcmjpeg12.so.2.8.4\n",
            "\tlibvtkRenderingAnnotationPython27D-6.3.so.6.3 -> libvtkRenderingAnnotationPython27D-6.3.so.6.3.0\n",
            "\tlibgdk-3.so.0 -> libgdk-3.so.0.2200.30\n",
            "\tlibvtkInfovisCore-6.3.so.6.3 -> libvtkInfovisCore-6.3.so.6.3.0\n",
            "\tlibgtk-x11-2.0.so.0 -> libgtk-x11-2.0.so.0.2400.32\n",
            "\tlibvtkDomainsChemistryTCL-6.3.so.6.3 -> libvtkDomainsChemistryTCL-6.3.so.6.3.0\n",
            "\tlibdrm_intel.so.1 -> libdrm_intel.so.1.0.0\n",
            "\tlibvtkRenderingCore-6.3.so.6.3 -> libvtkRenderingCore-6.3.so.6.3.0\n",
            "\tlibvtkDomainsChemistry-6.3.so.6.3 -> libvtkDomainsChemistry-6.3.so.6.3.0\n",
            "\tlibmtdev.so.1 -> libmtdev.so.1.0.0\n",
            "\tlibmpi_java.so.20 -> libmpi_java.so.20.10.0\n",
            "\tlibGLX.so.0 -> libGLX.so.0.0.0\n",
            "\tlibxcb-xfixes.so.0 -> libxcb-xfixes.so.0.0.0\n",
            "\tlibboost_random.so.1.65.1 -> libboost_random.so.1.65.1\n",
            "\tlibgdcmDSED.so.2.8 -> libgdcmDSED.so.2.8.4\n",
            "\tlibasyncns.so.0 -> libasyncns.so.0.3.1\n",
            "\tlibvtkRenderingLODPython27D-6.3.so.6.3 -> libvtkRenderingLODPython27D-6.3.so.6.3.0\n",
            "\tlibvtkParallelMPIPython27D-6.3.so.6.3 -> libvtkParallelMPIPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOLSDynaPython27D-6.3.so.6.3 -> libvtkIOLSDynaPython27D-6.3.so.6.3.0\n",
            "\tlibspeex.so.1 -> libspeex.so.1.5.0\n",
            "\tlibx265.so.146 -> libx265.so.146\n",
            "\tlibflite_cmulex.so.1 -> libflite_cmulex.so.2.1\n",
            "\tlibvtkTestingRendering-6.3.so.6.3 -> libvtkTestingRendering-6.3.so.6.3.0\n",
            "\tlibqhull.so.7 -> libqhull.so.7.2.0\n",
            "\tlibproxy.so.1 -> libproxy.so.1.0.0\n",
            "\tlibvtkPythonInterpreterTCL-6.3.so.6.3 -> libvtkPythonInterpreterTCL-6.3.so.6.3.0\n",
            "\tlibdap.so.25 -> libdap.so.25.0.1\n",
            "\tlibobjc_gc.so.4 -> libobjc_gc.so.4.0.0\n",
            "\tlibpython2.7.so.1.0 -> libpython2.7.so.1.0\n",
            "\tlibvtkIOVPIC-6.3.so.6.3 -> libvtkIOVPIC-6.3.so.6.3.0\n",
            "\tlibxcb-sync.so.1 -> libxcb-sync.so.1.0.0\n",
            "\tlibchromaprint.so.1 -> libchromaprint.so.1.4.3\n",
            "\tlibopencv_xobjdetect.so.3.2 -> libopencv_xobjdetect.so.3.2.0\n",
            "\tlibopencv_line_descriptor.so.3.2 -> libopencv_line_descriptor.so.3.2.0\n",
            "\tlibmpi_mpifh.so.20 -> libmpi_mpifh.so.20.11.0\n",
            "\tlibxcb-render.so.0 -> libxcb-render.so.0.0.0\n",
            "\tlibvtkInteractionWidgets-6.3.so.6.3 -> libvtkInteractionWidgets-6.3.so.6.3.0\n",
            "\tlibvtkIOImportTCL-6.3.so.6.3 -> libvtkIOImportTCL-6.3.so.6.3.0\n",
            "\tlibharfbuzz-gobject.so.0 -> libharfbuzz-gobject.so.0.10702.0\n",
            "\tlibvtkFiltersImagingTCL-6.3.so.6.3 -> libvtkFiltersImagingTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOCorePython27D-6.3.so.6.3 -> libvtkIOCorePython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingLICTCL-6.3.so.6.3 -> libvtkRenderingLICTCL-6.3.so.6.3.0\n",
            "\tlibrom1394.so.0 -> librom1394.so.0.3.0\n",
            "\tlibboost_math_c99f.so.1.65.1 -> libboost_math_c99f.so.1.65.1\n",
            "\tlibvtkImagingMorphologicalPython27D-6.3.so.6.3 -> libvtkImagingMorphologicalPython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingParallelLICTCL-6.3.so.6.3 -> libvtkRenderingParallelLICTCL-6.3.so.6.3.0\n",
            "\tlibgl2ps.so.1.4 -> libgl2ps.so.1.4.0\n",
            "\tlibvtkFiltersFlowPaths-6.3.so.6.3 -> libvtkFiltersFlowPaths-6.3.so.6.3.0\n",
            "\tlibcroco-0.6.so.3 -> libcroco-0.6.so.3.0.1\n",
            "\tlibunwind-ptrace.so.0 -> libunwind-ptrace.so.0.0.0\n",
            "\tlibvtkFiltersAMRPython27D-6.3.so.6.3 -> libvtkFiltersAMRPython27D-6.3.so.6.3.0\n",
            "\tlibturbojpeg.so.0 -> libturbojpeg.so.0.1.0\n",
            "\tlibvtkInfovisCorePython27D-6.3.so.6.3 -> libvtkInfovisCorePython27D-6.3.so.6.3.0\n",
            "\tlibgeos_c.so.1 -> libgeos_c.so.1.10.2\n",
            "\tlibiculx.so.60 -> libiculx.so.60.2\n",
            "\tlibicutest.so.60 -> libicutest.so.60.2\n",
            "\tlibvtkGeovisCorePython27D-6.3.so.6.3 -> libvtkGeovisCorePython27D-6.3.so.6.3.0\n",
            "\tlibopencv_imgproc.so.3.2 -> libopencv_imgproc.so.3.2.0\n",
            "\tlibtbb.so.2 -> libtbb.so.2\n",
            "\tlibfreexl.so.1 -> libfreexl.so.1.1.0\n",
            "\tlibvtkFiltersParallelTCL-6.3.so.6.3 -> libvtkFiltersParallelTCL-6.3.so.6.3.0\n",
            "\tlibnvidia-ifr.so.1 -> libnvidia-ifr.so.450.57\n",
            "\tlibkrb5.so.3 -> libkrb5.so.3.3\n",
            "\tlibwayland-server.so.0 -> libwayland-server.so.0.1.0\n",
            "\tlibGL.so.1 -> libGL.so.1.0.0\n",
            "\tlibopenblas.so.0 -> libopenblasp-r0.2.20.so\n",
            "\tlibHalf.so.12 -> libHalf.so.12.0.0\n",
            "\tlibQt5DBus.so.5 -> libQt5DBus.so.5.9.5\n",
            "\tlibvtkIOAMR-6.3.so.6.3 -> libvtkIOAMR-6.3.so.6.3.0\n",
            "\tlibvtkRenderingVolumeOpenGLPython27D-6.3.so.6.3 -> libvtkRenderingVolumeOpenGLPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOVideoPython27D-6.3.so.6.3 -> libvtkIOVideoPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOAMRPython27D-6.3.so.6.3 -> libvtkIOAMRPython27D-6.3.so.6.3.0\n",
            "\tlibXcursor.so.1 -> libXcursor.so.1.0.2\n",
            "\tlibnvidia-ml.so.1 -> libnvidia-ml.so.450.57\n",
            "\tlibtcmalloc.so.4 -> libtcmalloc.so.4.3.0\n",
            "\tlibvtkIOExport-6.3.so.6.3 -> libvtkIOExport-6.3.so.6.3.0\n",
            "\tlibopencv_core.so.3.2 -> libopencv_core.so.3.2.0\n",
            "\tlibvtkFiltersGeometryPython27D-6.3.so.6.3 -> libvtkFiltersGeometryPython27D-6.3.so.6.3.0\n",
            "\tlibvtkFiltersProgrammable-6.3.so.6.3 -> libvtkFiltersProgrammable-6.3.so.6.3.0\n",
            "\tlibvtkIOParallelTCL-6.3.so.6.3 -> libvtkIOParallelTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOMPIParallel-6.3.so.6.3 -> libvtkIOMPIParallel-6.3.so.6.3.0\n",
            "\tlibgdcmMEXD.so.2.8 -> libgdcmMEXD.so.2.8.4\n",
            "\tlibmlx5.so.1 -> libmlx5.so.1.4.17.1\n",
            "\tlibvtkInteractionImageTCL-6.3.so.6.3 -> libvtkInteractionImageTCL-6.3.so.6.3.0\n",
            "\tlibvtkCommonSystem-6.3.so.6.3 -> libvtkCommonSystem-6.3.so.6.3.0\n",
            "\tlibpng16.so.16 -> libpng16.so.16.34.0\n",
            "\tlibnspr4.so -> libnspr4.so\n",
            "\tlibboost_coroutine.so.1.65.1 -> libboost_coroutine.so.1.65.1\n",
            "\tlibvtkIOXMLTCL-6.3.so.6.3 -> libvtkIOXMLTCL-6.3.so.6.3.0\n",
            "\tlibmca_common_verbs.so.20 -> libmca_common_verbs.so.20.10.0\n",
            "\tlibnssutil3.so -> libnssutil3.so\n",
            "\tlibvtkIOGDALPython27D-6.3.so.6.3 -> libvtkIOGDALPython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingLabelTCL-6.3.so.6.3 -> libvtkRenderingLabelTCL-6.3.so.6.3.0\n",
            "\tlibvtkIONetCDFTCL-6.3.so.6.3 -> libvtkIONetCDFTCL-6.3.so.6.3.0\n",
            "\tlibgdcmDICT.so.2.8 -> libgdcmDICT.so.2.8.4\n",
            "\tlibvtkFiltersProgrammablePython27D-6.3.so.6.3 -> libvtkFiltersProgrammablePython27D-6.3.so.6.3.0\n",
            "\tlibXmu.so.6 -> libXmu.so.6.2.0\n",
            "\tlibcc1.so.0 -> libcc1.so.0.0.0\n",
            "\tlibdapclient.so.6 -> libdapclient.so.6.1.7\n",
            "\tlibvtkFiltersGeometryTCL-6.3.so.6.3 -> libvtkFiltersGeometryTCL-6.3.so.6.3.0\n",
            "\tlibvtkViewsCore-6.3.so.6.3 -> libvtkViewsCore-6.3.so.6.3.0\n",
            "\tlibvtkInteractionWidgetsTCL-6.3.so.6.3 -> libvtkInteractionWidgetsTCL-6.3.so.6.3.0\n",
            "\tlibrbd.so.1 -> librbd.so.1.12.0\n",
            "\tlibvtkCommonMathTCL-6.3.so.6.3 -> libvtkCommonMathTCL-6.3.so.6.3.0\n",
            "\tlibEGL_mesa.so.0 -> libEGL_mesa.so.0.0.0\n",
            "\tlibvtkFiltersHyperTreeTCL-6.3.so.6.3 -> libvtkFiltersHyperTreeTCL-6.3.so.6.3.0\n",
            "\tlibvtkRenderingOpenGLPython27D-6.3.so.6.3 -> libvtkRenderingOpenGLPython27D-6.3.so.6.3.0\n",
            "\tlibvtkftgl-6.3.so.6.3 -> libvtkftgl-6.3.so.6.3.0\n",
            "\tlibvtkIOParallelLSDynaPython27D-6.3.so.6.3 -> libvtkIOParallelLSDynaPython27D-6.3.so.6.3.0\n",
            "\tlibGLX_nvidia.so.0 -> libGLX_nvidia.so.450.57\n",
            "\tlibvtkTestingIOSQL-6.3.so.6.3 -> libvtkTestingIOSQL-6.3.so.6.3.0\n",
            "\tlibxcb-image.so.0 -> libxcb-image.so.0.0.0\n",
            "\tlibvtkFiltersFlowPathsPython27D-6.3.so.6.3 -> libvtkFiltersFlowPathsPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOODBCTCL-6.3.so.6.3 -> libvtkIOODBCTCL-6.3.so.6.3.0\n",
            "\tlibXtst.so.6 -> libXtst.so.6.1.0\n",
            "\tlibvtkIOParallelXMLTCL-6.3.so.6.3 -> libvtkIOParallelXMLTCL-6.3.so.6.3.0\n",
            "\tlibdc1394.so.22 -> libdc1394.so.22.2.1\n",
            "\tlibvtkFiltersStatisticsPython27D-6.3.so.6.3 -> libvtkFiltersStatisticsPython27D-6.3.so.6.3.0\n",
            "\tlibmp3lame.so.0 -> libmp3lame.so.0.0.0\n",
            "\tlibboost_math_tr1.so.1.65.1 -> libboost_math_tr1.so.1.65.1\n",
            "\tlibvtkFiltersReebGraph-6.3.so.6.3 -> libvtkFiltersReebGraph-6.3.so.6.3.0\n",
            "\tlibflite_cmu_indic_lex.so.1 -> libflite_cmu_indic_lex.so.2.1\n",
            "\tlibboost_iostreams.so.1.65.1 -> libboost_iostreams.so.1.65.1\n",
            "\tlibglib-2.0.so.0 -> libglib-2.0.so.0.5600.4\n",
            "\tlibvtkFiltersGenericPython27D-6.3.so.6.3 -> libvtkFiltersGenericPython27D-6.3.so.6.3.0\n",
            "\tlibboost_system.so.1.65.1 -> libboost_system.so.1.65.1\n",
            "\tlibvtkRenderingGL2PS-6.3.so.6.3 -> libvtkRenderingGL2PS-6.3.so.6.3.0\n",
            "\tlibXcomposite.so.1 -> libXcomposite.so.1.0.0\n",
            "\tlibGLdispatch.so.0 -> libGLdispatch.so.0.0.0\n",
            "\tlibboost_mpi_python-py27.so.1.65.1 -> libboost_mpi_python.so\n",
            "\tlibvtkCommonExecutionModelTCL-6.3.so.6.3 -> libvtkCommonExecutionModelTCL-6.3.so.6.3.0\n",
            "\tlibvtkalglib-6.3.so.6.3 -> libvtkalglib-6.3.so.6.3.0\n",
            "\tlibvtkCommonMisc-6.3.so.6.3 -> libvtkCommonMisc-6.3.so.6.3.0\n",
            "\tlibXxf86vm.so.1 -> libXxf86vm.so.1.0.0\n",
            "\tlibprotoc.so.10 -> libprotoc.so.10.0.0\n",
            "\tlibsnappy.so.1 -> libsnappy.so.1.1.7\n",
            "\tlibEGL.so.1 -> libEGL.so.1.0.0\n",
            "\tlibvtkFiltersParallelStatisticsTCL-6.3.so.6.3 -> libvtkFiltersParallelStatisticsTCL-6.3.so.6.3.0\n",
            "\tlibnvidia-allocator.so.1 -> libnvidia-allocator.so.450.57\n",
            "\tlibvtkIOPLYPython27D-6.3.so.6.3 -> libvtkIOPLYPython27D-6.3.so.6.3.0\n",
            "\tlibsamplerate.so.0 -> libsamplerate.so.0.1.8\n",
            "\tlibopencv_superres.so.3.2 -> libopencv_superres.so.3.2.0\n",
            "\tlibvtkRenderingFreeType-6.3.so.6.3 -> libvtkRenderingFreeType-6.3.so.6.3.0\n",
            "\tlibtsan.so.0 -> libtsan.so.0.0.0\n",
            "\tlibvtkIOImagePython27D-6.3.so.6.3 -> libvtkIOImagePython27D-6.3.so.6.3.0\n",
            "\tlibvtkInfovisCoreTCL-6.3.so.6.3 -> libvtkInfovisCoreTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersSelectionTCL-6.3.so.6.3 -> libvtkFiltersSelectionTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersParallelStatistics-6.3.so.6.3 -> libvtkFiltersParallelStatistics-6.3.so.6.3.0\n",
            "\tlibhdf5_openmpi_hl.so.100 -> libhdf5_openmpi_hl.so.100.0.0\n",
            "\tlibvtkIOExportTCL-6.3.so.6.3 -> libvtkIOExportTCL-6.3.so.6.3.0\n",
            "\tlibboost_type_erasure.so.1.65.1 -> libboost_type_erasure.so.1.65.1\n",
            "\tlibatlas.so.3 -> libatlas.so.3.10.3\n",
            "\tlibvtkViewsGeovisTCL-6.3.so.6.3 -> libvtkViewsGeovisTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersSources-6.3.so.6.3 -> libvtkFiltersSources-6.3.so.6.3.0\n",
            "\tlibvtkFiltersCorePython27D-6.3.so.6.3 -> libvtkFiltersCorePython27D-6.3.so.6.3.0\n",
            "\tlibsz.so.2 -> libsz.so.2.0.1\n",
            "\tlibXss.so.1 -> libXss.so.1.0.0\n",
            "\tlibvtkFiltersCoreTCL-6.3.so.6.3 -> libvtkFiltersCoreTCL-6.3.so.6.3.0\n",
            "\tlibltdl.so.7 -> libltdl.so.7.3.1\n",
            "\tlibflite_usenglish.so.1 -> libflite_usenglish.so.2.1\n",
            "\tlibharfbuzz-icu.so.0 -> libharfbuzz-icu.so.0.10702.0\n",
            "\tlibvtkCommonMiscPython27D-6.3.so.6.3 -> libvtkCommonMiscPython27D-6.3.so.6.3.0\n",
            "\tlibvtkCommonMiscTCL-6.3.so.6.3 -> libvtkCommonMiscTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOMovieTCL-6.3.so.6.3 -> libvtkIOMovieTCL-6.3.so.6.3.0\n",
            "\tliblsan.so.0 -> liblsan.so.0.0.0\n",
            "\tlibnl-route-3.so.200 -> libnl-route-3.so.200.24.0\n",
            "\tlibvtkverdict-6.3.so.6.3 -> libvtkverdict-6.3.so.6.3.0\n",
            "\tlibgeos-3.6.2.so -> libgeos-3.6.2.so\n",
            "\tlibplds4.so -> libplds4.so\n",
            "\tlibdrm_radeon.so.1 -> libdrm_radeon.so.1.0.1\n",
            "\tlibvtkCommonComputationalGeometryPython27D-6.3.so.6.3 -> libvtkCommonComputationalGeometryPython27D-6.3.so.6.3.0\n",
            "\tlibvtkViewsContextIIDTCL-6.3.so.6.3 -> libvtkViewsContextIIDTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersCore-6.3.so.6.3 -> libvtkFiltersCore-6.3.so.6.3.0\n",
            "\tlibvtkCommonComputationalGeometry-6.3.so.6.3 -> libvtkCommonComputationalGeometry-6.3.so.6.3.0\n",
            "\tlibavformat.so.57 -> libavformat.so.57.83.100\n",
            "\tlibunwind-coredump.so.0 -> libunwind-coredump.so.0.0.0\n",
            "\tlibvtkIOEnSightPython27D-6.3.so.6.3 -> libvtkIOEnSightPython27D-6.3.so.6.3.0\n",
            "\tlibtiffxx.so.5 -> libtiffxx.so.5.3.0\n",
            "\tlibflite.so.1 -> libflite.so.2.1\n",
            "\tlibvtkFiltersTexture-6.3.so.6.3 -> libvtkFiltersTexture-6.3.so.6.3.0\n",
            "\tlibvtkIOVPICPython27D-6.3.so.6.3 -> libvtkIOVPICPython27D-6.3.so.6.3.0\n",
            "\tlibvtkFiltersImagingPython27D-6.3.so.6.3 -> libvtkFiltersImagingPython27D-6.3.so.6.3.0\n",
            "\tlibvtkImagingColorPython27D-6.3.so.6.3 -> libvtkImagingColorPython27D-6.3.so.6.3.0\n",
            "\tlibsmime3.so -> libsmime3.so\n",
            "\tlibtheoraenc.so.1 -> libtheoraenc.so.1.1.2\n",
            "\tlibvtkRenderingVolumeAMRPython27D-6.3.so.6.3 -> libvtkRenderingVolumeAMRPython27D-6.3.so.6.3.0\n",
            "\tlibvtkFiltersSelection-6.3.so.6.3 -> libvtkFiltersSelection-6.3.so.6.3.0\n",
            "\tlibQt5EglFSDeviceIntegration.so.5 -> libQt5EglFSDeviceIntegration.so.5.9.5\n",
            "\tlibavc1394.so.0 -> libavc1394.so.0.3.0\n",
            "\tlibcolordprivate.so.2 -> libcolordprivate.so.2.0.5\n",
            "\tlibopencv_plot.so.3.2 -> libopencv_plot.so.3.2.0\n",
            "\tlibvtkCommonColorTCL-6.3.so.6.3 -> libvtkCommonColorTCL-6.3.so.6.3.0\n",
            "\tlibvtkRenderingParallelLIC-6.3.so.6.3 -> libvtkRenderingParallelLIC-6.3.so.6.3.0\n",
            "\tlibgme.so.0 -> libgme.so.0.6.2\n",
            "\tlibOpenGL.so.0 -> libOpenGL.so.0.0.0\n",
            "\tlibvtkFiltersParallelImagingPython27D-6.3.so.6.3 -> libvtkFiltersParallelImagingPython27D-6.3.so.6.3.0\n",
            "\tlibgvpr.so.2 -> libgvpr.so.2.0.0\n",
            "\tlibSM.so.6 -> libSM.so.6.0.1\n",
            "\tlibvtkFiltersParallelFlowPathsTCL-6.3.so.6.3 -> libvtkFiltersParallelFlowPathsTCL-6.3.so.6.3.0\n",
            "\tlibnvidia-ptxjitcompiler.so.1 -> libnvidia-ptxjitcompiler.so.450.57\n",
            "\tlibgif.so.7 -> libgif.so.7.0.0\n",
            "\tlibopencv_freetype.so.3.2 -> libopencv_freetype.so.3.2.0\n",
            "\tlibvtkImagingCoreTCL-6.3.so.6.3 -> libvtkImagingCoreTCL-6.3.so.6.3.0\n",
            "\tlibtwolame.so.0 -> libtwolame.so.0.0.0\n",
            "\tlibflite_cmu_us_kal.so.1 -> libflite_cmu_us_kal.so.2.1\n",
            "\tlibvtkCommonColor-6.3.so.6.3 -> libvtkCommonColor-6.3.so.6.3.0\n",
            "\tlibasan.so.4 -> libasan.so.4.0.0\n",
            "\tlibboost_mpi.so.1.65.1 -> libboost_mpi.so.1.65.1\n",
            "\tlibrhash.so.0 -> librhash.so.0\n",
            "\tlibhdf5_openmpihl_fortran.so.100 -> libhdf5_openmpihl_fortran.so.100.0.0\n",
            "\tlibvtkInteractionImagePython27D-6.3.so.6.3 -> libvtkInteractionImagePython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingImageTCL-6.3.so.6.3 -> libvtkRenderingImageTCL-6.3.so.6.3.0\n",
            "\tlibvorbisenc.so.2 -> libvorbisenc.so.2.0.11\n",
            "\tlibfreetype.so.6 -> libfreetype.so.6.15.0\n",
            "\tlibpoppler.so.73 -> libpoppler.so.73.0.0\n",
            "\tlibvtkFiltersParallelPython27D-6.3.so.6.3 -> libvtkFiltersParallelPython27D-6.3.so.6.3.0\n",
            "\tlibflite_cmu_us_slt.so.1 -> libflite_cmu_us_slt.so.2.1\n",
            "\tlibvtkIOExportPython27D-6.3.so.6.3 -> libvtkIOExportPython27D-6.3.so.6.3.0\n",
            "\tlibboost_fiber.so.1.65.1 -> libboost_fiber.so.1.65.1\n",
            "\tlibboost_regex.so.1.65.1 -> libboost_regex.so.1.65.1\n",
            "\tlibvtkFiltersImaging-6.3.so.6.3 -> libvtkFiltersImaging-6.3.so.6.3.0\n",
            "\tlibvtkFiltersSMPTCL-6.3.so.6.3 -> libvtkFiltersSMPTCL-6.3.so.6.3.0\n",
            "\tlibvtkImagingColorTCL-6.3.so.6.3 -> libvtkImagingColorTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersParallelMPI-6.3.so.6.3 -> libvtkFiltersParallelMPI-6.3.so.6.3.0\n",
            "\tlibplc4.so -> libplc4.so\n",
            "\tlibvtkIOFFMPEGTCL-6.3.so.6.3 -> libvtkIOFFMPEGTCL-6.3.so.6.3.0\n",
            "\tlibtcmalloc_minimal.so.4 -> libtcmalloc_minimal.so.4.3.0\n",
            "\tlibvtkRenderingContextOpenGLTCL-6.3.so.6.3 -> libvtkRenderingContextOpenGLTCL-6.3.so.6.3.0\n",
            "\tlibvtkViewsContext2DPython27D-6.3.so.6.3 -> libvtkViewsContext2DPython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingCorePython27D-6.3.so.6.3 -> libvtkRenderingCorePython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOParallelNetCDFPython27D-6.3.so.6.3 -> libvtkIOParallelNetCDFPython27D-6.3.so.6.3.0\n",
            "\tlibboost_graph_parallel.so.1.65.1 -> libboost_graph_parallel.so.1.65.1\n",
            "\tlibcaca.so.0 -> libcaca.so.0.99.19\n",
            "\tlibnetcdf_c++.so.4 -> libnetcdf_c++.so.4.2.0\n",
            "\tlibvtkRenderingExternalPython27D-6.3.so.6.3 -> libvtkRenderingExternalPython27D-6.3.so.6.3.0\n",
            "\tlibvtkCommonTransformsTCL-6.3.so.6.3 -> libvtkCommonTransformsTCL-6.3.so.6.3.0\n",
            "\tlibnghttp2.so.14 -> libnghttp2.so.14.15.2\n",
            "\tlibvtkChartsCore-6.3.so.6.3 -> libvtkChartsCore-6.3.so.6.3.0\n",
            "\tlibXaw.so.7 -> libXaw7.so.7.0.0\n",
            "\tlibvtkIOGDAL-6.3.so.6.3 -> libvtkIOGDAL-6.3.so.6.3.0\n",
            "\tlibvtkImagingStatisticsPython27D-6.3.so.6.3 -> libvtkImagingStatisticsPython27D-6.3.so.6.3.0\n",
            "\tlibnvidia-rtcore.so.450.57 -> libnvidia-rtcore.so.450.57\n",
            "\tlibpsl.so.5 -> libpsl.so.5.2.0\n",
            "\tlibvtkIOParallelLSDyna-6.3.so.6.3 -> libvtkIOParallelLSDyna-6.3.so.6.3.0\n",
            "\tlibpolkit-agent-1.so.0 -> libpolkit-agent-1.so.0.0.0\n",
            "\tlibfabric.so.1 -> libfabric.so.1.9.3\n",
            "\tlibxcb-xinerama.so.0 -> libxcb-xinerama.so.0.0.0\n",
            "\tlibvtkIOODBC-6.3.so.6.3 -> libvtkIOODBC-6.3.so.6.3.0\n",
            "\tlibflite_cmu_indic_lang.so.1 -> libflite_cmu_indic_lang.so.2.1\n",
            "\tlibvtkInfovisBoostGraphAlgorithmsTCL-6.3.so.6.3 -> libvtkInfovisBoostGraphAlgorithmsTCL-6.3.so.6.3.0\n",
            "\tlibkmldom.so.1 -> libkmldom.so.1.3.0\n",
            "\tlibnvidia-glcore.so.450.57 -> libnvidia-glcore.so.450.57\n",
            "\tliburiparser.so.1 -> liburiparser.so.1.0.20\n",
            "\tlibvtkFiltersPython-6.3.so.6.3 -> libvtkFiltersPython-6.3.so.6.3.0\n",
            "\tlibvtkRenderingLODTCL-6.3.so.6.3 -> libvtkRenderingLODTCL-6.3.so.6.3.0\n",
            "\tlibQt5Core.so.5 -> libQt5Core.so.5.9.5\n",
            "\tlibIlmImfUtil-2_2.so.22 -> libIlmImfUtil.so\n",
            "\tlibpolkit-backend-1.so.0 -> libpolkit-backend-1.so.0.0.0\n",
            "\tlibboost_stacktrace_addr2line.so.1.65.1 -> libboost_stacktrace_addr2line.so.1.65.1\n",
            "\tlibhdf5_hl_cpp.so.100 -> libhdf5_hl_cpp.so.100.0.0\n",
            "\tlibcdt.so.5 -> libcdt.so.5.0.0\n",
            "\tlibvtkRenderingImage-6.3.so.6.3 -> libvtkRenderingImage-6.3.so.6.3.0\n",
            "\tlibflite_cmu_us_awb.so.1 -> libflite_cmu_us_awb.so.2.1\n",
            "\tlibvtkRenderingContext2DPython27D-6.3.so.6.3 -> libvtkRenderingContext2DPython27D-6.3.so.6.3.0\n",
            "\tlibssh-gcrypt_threads.so.4 -> libssh-gcrypt_threads.so.4.5.0\n",
            "\tlibproj.so.12 -> libproj.so.12.0.0\n",
            "\tlibvtkIOParallelExodus-6.3.so.6.3 -> libvtkIOParallelExodus-6.3.so.6.3.0\n",
            "\tlibgvc.so.6 -> libgvc.so.6.0.0\n",
            "\tlibvtkFiltersParallelFlowPathsPython27D-6.3.so.6.3 -> libvtkFiltersParallelFlowPathsPython27D-6.3.so.6.3.0\n",
            "\tlibvtkCommonDataModelTCL-6.3.so.6.3 -> libvtkCommonDataModelTCL-6.3.so.6.3.0\n",
            "\tlibpcre32.so.3 -> libpcre32.so.3.13.3\n",
            "\tlibboost_wave.so.1.65.1 -> libboost_wave.so.1.65.1\n",
            "\tlibatomic.so.1 -> libatomic.so.1.2.0\n",
            "\tlibvtkIOParallelLSDynaTCL-6.3.so.6.3 -> libvtkIOParallelLSDynaTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersGenericTCL-6.3.so.6.3 -> libvtkFiltersGenericTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOLegacy-6.3.so.6.3 -> libvtkIOLegacy-6.3.so.6.3.0\n",
            "\tlibvtkIOExodusPython27D-6.3.so.6.3 -> libvtkIOExodusPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOMPIImageTCL-6.3.so.6.3 -> libvtkIOMPIImageTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOSQL-6.3.so.6.3 -> libvtkIOSQL-6.3.so.6.3.0\n",
            "\tlibpolkit-gobject-1.so.0 -> libpolkit-gobject-1.so.0.0.0\n",
            "\tlibnvidia-cfg.so.1 -> libnvidia-cfg.so.450.57\n",
            "\tlibvtkIOXMLPython27D-6.3.so.6.3 -> libvtkIOXMLPython27D-6.3.so.6.3.0\n",
            "\tlibgts-0.7.so.5 -> libgts-0.7.so.5.0.1\n",
            "\tlibsodium.so.23 -> libsodium.so.23.1.0\n",
            "\tlibodbc.so.2 -> libodbc.so.2.0.0\n",
            "\tlibasound.so.2 -> libasound.so.2.0.0\n",
            "\tlibjpeg.so.8 -> libjpeg.so.8.1.2\n",
            "\tlibXv.so.1 -> libXv.so.1.0.0\n",
            "\tlibwayland-cursor.so.0 -> libwayland-cursor.so.0.0.0\n",
            "\tlibvtkIOGeoJSONPython27D-6.3.so.6.3 -> libvtkIOGeoJSONPython27D-6.3.so.6.3.0\n",
            "\tlibCharLS.so.1 -> libCharLS.so.1.0\n",
            "\tlibvtkViewsGeovisPython27D-6.3.so.6.3 -> libvtkViewsGeovisPython27D-6.3.so.6.3.0\n",
            "\tlibgmodule-2.0.so.0 -> libgmodule-2.0.so.0.5600.4\n",
            "\tlibevdev.so.2 -> libevdev.so.2.1.20\n",
            "\tlibQt5EglFsKmsSupport.so.5 -> libQt5EglFsKmsSupport.so.5.9.5\n",
            "\tlibvtkCommonMath-6.3.so.6.3 -> libvtkCommonMath-6.3.so.6.3.0\n",
            "\tlibglapi.so.0 -> libglapi.so.0.0.0\n",
            "\tlibvtkImagingColor-6.3.so.6.3 -> libvtkImagingColor-6.3.so.6.3.0\n",
            "\tlibvtkCommonDataModelPython27D-6.3.so.6.3 -> libvtkCommonDataModelPython27D-6.3.so.6.3.0\n",
            "\tlibvtkFiltersReebGraphTCL-6.3.so.6.3 -> libvtkFiltersReebGraphTCL-6.3.so.6.3.0\n",
            "\tlibpcre2-16.so.0 -> libpcre2-16.so.0.7.0\n",
            "\tlibvorbis.so.0 -> libvorbis.so.0.4.8\n",
            "\tlibvtkImagingStatisticsTCL-6.3.so.6.3 -> libvtkImagingStatisticsTCL-6.3.so.6.3.0\n",
            "\tlibX11-xcb.so.1 -> libX11-xcb.so.1.0.0\n",
            "\tlibxcb-present.so.0 -> libxcb-present.so.0.0.0\n",
            "\tlibgio-2.0.so.0 -> libgio-2.0.so.0.5600.4\n",
            "\tlibvtkIOParallel-6.3.so.6.3 -> libvtkIOParallel-6.3.so.6.3.0\n",
            "\tliblab_gamut.so.1 -> liblab_gamut.so.1.0.0\n",
            "\tlibnvidia-fbc.so.1 -> libnvidia-fbc.so.450.57\n",
            "\tlibvtkImagingSourcesTCL-6.3.so.6.3 -> libvtkImagingSourcesTCL-6.3.so.6.3.0\n",
            "\tlibgdcmjpeg16.so.2.8 -> libgdcmjpeg16.so.2.8.4\n",
            "\tlibGLESv2.so.2 -> libGLESv2.so.2.0.0\n",
            "\tlibvtkIOMPIImagePython27D-6.3.so.6.3 -> libvtkIOMPIImagePython27D-6.3.so.6.3.0\n",
            "\tlibvtkViewsGeovis-6.3.so.6.3 -> libvtkViewsGeovis-6.3.so.6.3.0\n",
            "\tlibgc.so.1 -> libgc.so.1.0.3\n",
            "\tlibXft.so.2 -> libXft.so.2.3.2\n",
            "\tlibboost_wserialization.so.1.65.1 -> libboost_wserialization.so.1.65.1\n",
            "\tlibvtkIOEnSightTCL-6.3.so.6.3 -> libvtkIOEnSightTCL-6.3.so.6.3.0\n",
            "\tlibf77blas.so.3 -> libf77blas.so.3.10.3\n",
            "\tlibelf.so.1 -> libelf-0.170.so\n",
            "\tlibvtkIOPLYTCL-6.3.so.6.3 -> libvtkIOPLYTCL-6.3.so.6.3.0\n",
            "\tlibsndfile.so.1 -> libsndfile.so.1.0.28\n",
            "\tlibsuperlu.so.5 -> libsuperlu.so.5.2.1\n",
            "\tlibvtkFiltersAMR-6.3.so.6.3 -> libvtkFiltersAMR-6.3.so.6.3.0\n",
            "\tlibatk-1.0.so.0 -> libatk-1.0.so.0.22810.1\n",
            "\tlibxkbcommon.so.0 -> libxkbcommon.so.0.0.0\n",
            "\tlibvtkFiltersGeneric-6.3.so.6.3 -> libvtkFiltersGeneric-6.3.so.6.3.0\n",
            "\tlibicuio.so.60 -> libicuio.so.60.2\n",
            "\tlibgdcmMSFF.so.2.8 -> libgdcmMSFF.so.2.8.4\n",
            "\tlibvtkImagingHybridTCL-6.3.so.6.3 -> libvtkImagingHybridTCL-6.3.so.6.3.0\n",
            "\tlibcgraph.so.6 -> libcgraph.so.6.0.0\n",
            "\tlibxml2.so.2 -> libxml2.so.2.9.4\n",
            "\tlibatk-bridge-2.0.so.0 -> libatk-bridge-2.0.so.0.0.0\n",
            "\tlibfontenc.so.1 -> libfontenc.so.1.0.0\n",
            "\tlibboost_graph.so.1.65.1 -> libboost_graph.so.1.65.1\n",
            "\tlibvtkRenderingAnnotation-6.3.so.6.3 -> libvtkRenderingAnnotation-6.3.so.6.3.0\n",
            "\tlibva-x11.so.2 -> libva-x11.so.2.100.0\n",
            "\tlibvtkRenderingGL2PSPython27D-6.3.so.6.3 -> libvtkRenderingGL2PSPython27D-6.3.so.6.3.0\n",
            "\tlibXi.so.6 -> libXi.so.6.1.0\n",
            "\tlibkmlbase.so.1 -> libkmlbase.so.1.3.0\n",
            "\tlibpangocairo-1.0.so.0 -> libpangocairo-1.0.so.0.4000.14\n",
            "\tlibxcb-glx.so.0 -> libxcb-glx.so.0.0.0\n",
            "\tlibvtkIOMINC-6.3.so.6.3 -> libvtkIOMINC-6.3.so.6.3.0\n",
            "\tlibjackserver.so.0 -> libjackserver.so.0.0.28\n",
            "\tlibvtkImagingFourierTCL-6.3.so.6.3 -> libvtkImagingFourierTCL-6.3.so.6.3.0\n",
            "\tlibgdk_pixbuf-2.0.so.0 -> libgdk_pixbuf-2.0.so.0.3611.0\n",
            "\tlibopencv_rgbd.so.3.2 -> libopencv_rgbd.so.3.2.0\n",
            "\tlibquadmath.so.0 -> libquadmath.so.0.0.0\n",
            "\tlibopus.so.0 -> libopus.so.0.5.2\n",
            "\tlibpq.so.5 -> libpq.so.5.10\n",
            "\tlibvtkViewsCorePython27D-6.3.so.6.3 -> libvtkViewsCorePython27D-6.3.so.6.3.0\n",
            "\tlibopencv_face.so.3.2 -> libopencv_face.so.3.2.0\n",
            "\tlibvtkIOEnSight-6.3.so.6.3 -> libvtkIOEnSight-6.3.so.6.3.0\n",
            "\tlibImath-2_2.so.12 -> libImath.so\n",
            "\tlibopencv_video.so.3.2 -> libopencv_video.so.3.2.0\n",
            "\tlibvtkIOGDALTCL-6.3.so.6.3 -> libvtkIOGDALTCL-6.3.so.6.3.0\n",
            "\tlibvtkRenderingFreeTypePython27D-6.3.so.6.3 -> libvtkRenderingFreeTypePython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOMINCTCL-6.3.so.6.3 -> libvtkIOMINCTCL-6.3.so.6.3.0\n",
            "\tlibvtkVPIC-6.3.so.6.3 -> libvtkVPIC-6.3.so.6.3.0\n",
            "\tlibfygm.so.0 -> libfygm.so.0.0.0\n",
            "\tlibmpi_usempi_ignore_tkr.so.20 -> libmpi_usempi_ignore_tkr.so.20.10.0\n",
            "\tlibk5crypto.so.3 -> libk5crypto.so.3.1\n",
            "\tlibvtkIOXdmf2-6.3.so.6.3 -> libvtkIOXdmf2-6.3.so.6.3.0\n",
            "\tlibvtkPythonInterpreterPython27D-6.3.so.6.3 -> libvtkPythonInterpreterPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOMovie-6.3.so.6.3 -> libvtkIOMovie-6.3.so.6.3.0\n",
            "\tlibxcb-icccm.so.4 -> libxcb-icccm.so.4.0.0\n",
            "\tlibvtkImagingStencil-6.3.so.6.3 -> libvtkImagingStencil-6.3.so.6.3.0\n",
            "\tlibtk8.6.so -> libtk8.6.so.0\n",
            "\tlibvtkInfovisLayoutTCL-6.3.so.6.3 -> libvtkInfovisLayoutTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOParallelPython27D-6.3.so.6.3 -> libvtkIOParallelPython27D-6.3.so.6.3.0\n",
            "\tlibopencv_reg.so.3.2 -> libopencv_reg.so.3.2.0\n",
            "\tlibhdf5_serialhl_fortran.so.100 -> libhdf5_serialhl_fortran.so.100.0.0\n",
            "\tlibtheora.so.0 -> libtheora.so.0.3.10\n",
            "\tlibvtkInteractionWidgetsPython27D-6.3.so.6.3 -> libvtkInteractionWidgetsPython27D-6.3.so.6.3.0\n",
            "\tlibvtkCommonCoreTCL-6.3.so.6.3 -> libvtkCommonCoreTCL-6.3.so.6.3.0\n",
            "\tlibXfixes.so.3 -> libXfixes.so.3.1.0\n",
            "\tlibvtkViewsInfovisTCL-6.3.so.6.3 -> libvtkViewsInfovisTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersVerdictPython27D-6.3.so.6.3 -> libvtkFiltersVerdictPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOImageTCL-6.3.so.6.3 -> libvtkIOImageTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersExtractionPython27D-6.3.so.6.3 -> libvtkFiltersExtractionPython27D-6.3.so.6.3.0\n",
            "\tlibdconf.so.1 -> libdconf.so.1.0.0\n",
            "\tlibvtkCommonSystemTCL-6.3.so.6.3 -> libvtkCommonSystemTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOFFMPEGPython27D-6.3.so.6.3 -> libvtkIOFFMPEGPython27D-6.3.so.6.3.0\n",
            "\tlibvtkWrappingJava-6.3.so.6.3 -> libvtkWrappingJava-6.3.so.6.3.0\n",
            "\tlibvtkRenderingAnnotationTCL-6.3.so.6.3 -> libvtkRenderingAnnotationTCL-6.3.so.6.3.0\n",
            "\tlibmlx4.so.1 -> libmlx4.so.1.0.17.1\n",
            "\tlibnvidia-opticalflow.so.1 -> libnvidia-opticalflow.so.450.57\n",
            "\tlibbluray.so.2 -> libbluray.so.2.0.2\n",
            "\tlibvtkViewsInfovis-6.3.so.6.3 -> libvtkViewsInfovis-6.3.so.6.3.0\n",
            "\tlibvtkFiltersSelectionPython27D-6.3.so.6.3 -> libvtkFiltersSelectionPython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingVolumeOpenGLTCL-6.3.so.6.3 -> libvtkRenderingVolumeOpenGLTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOParallelNetCDF-6.3.so.6.3 -> libvtkIOParallelNetCDF-6.3.so.6.3.0\n",
            "\tlibXinerama.so.1 -> libXinerama.so.1.0.0\n",
            "\tlibssl.so.1.1 -> libssl.so.1.1\n",
            "\tlibXNVCtrl.so.0 -> libXNVCtrl.so.0.0.0\n",
            "\tlibvtkFiltersParallelGeometryTCL-6.3.so.6.3 -> libvtkFiltersParallelGeometryTCL-6.3.so.6.3.0\n",
            "\tlibvtkImagingCore-6.3.so.6.3 -> libvtkImagingCore-6.3.so.6.3.0\n",
            "\tlibX11.so.6 -> libX11.so.6.3.0\n",
            "\tlibvtkLocalExampleTCL-6.3.so.6.3 -> libvtkLocalExampleTCL-6.3.so.6.3.0\n",
            "\tlibgccpp.so.1 -> libgccpp.so.1.0.3\n",
            "\tlibopen-pal.so.20 -> libopen-pal.so.20.10.1\n",
            "\tlibvtkIONetCDFPython27D-6.3.so.6.3 -> libvtkIONetCDFPython27D-6.3.so.6.3.0\n",
            "\tlibnvidia-compiler.so.450.57 -> libnvidia-compiler.so.450.57\n",
            "\tlibXext.so.6 -> libXext.so.6.4.0\n",
            "\tlibcdio.so.17 -> libcdio.so.17.0.0\n",
            "\tlibvtkFiltersReebGraphPython27D-6.3.so.6.3 -> libvtkFiltersReebGraphPython27D-6.3.so.6.3.0\n",
            "\tlibshine.so.3 -> libshine.so.3.0.1\n",
            "\tlibvtkIOLegacyTCL-6.3.so.6.3 -> libvtkIOLegacyTCL-6.3.so.6.3.0\n",
            "\tlibopencv_phase_unwrapping.so.3.2 -> libopencv_phase_unwrapping.so.3.2.0\n",
            "\tlibIlmImf-2_2.so.22 -> libIlmImf.so\n",
            "\tlibboost_unit_test_framework.so.1.65.1 -> libboost_unit_test_framework.so.1.65.1\n",
            "\tlibinfinipath.so.4 -> libinfinipath.so.4.0\n",
            "\tlibvtkFiltersHyperTree-6.3.so.6.3 -> libvtkFiltersHyperTree-6.3.so.6.3.0\n",
            "\tlibnvidia-glsi.so.450.57 -> libnvidia-glsi.so.450.57\n",
            "\tlibwebp.so.6 -> libwebp.so.6.0.2\n",
            "\tlibQt5PrintSupport.so.5 -> libQt5PrintSupport.so.5.9.5\n",
            "\tlibpcrecpp.so.0 -> libpcrecpp.so.0.0.1\n",
            "\tlibXrender.so.1 -> libXrender.so.1.3.0\n",
            "\tlibvtkInteractionStyleTCL-6.3.so.6.3 -> libvtkInteractionStyleTCL-6.3.so.6.3.0\n",
            "\tlibcairo.so.2 -> libcairo.so.2.11510.0\n",
            "\tlibQt5Sql.so.5 -> libQt5Sql.so.5.9.5\n",
            "\tlibvtkTestingGenericBridge-6.3.so.6.3 -> libvtkTestingGenericBridge-6.3.so.6.3.0\n",
            "\tlibvtkFiltersSMP-6.3.so.6.3 -> libvtkFiltersSMP-6.3.so.6.3.0\n",
            "\tlibavahi-common.so.3 -> libavahi-common.so.3.5.3\n",
            "\tlibopencv_stitching.so.3.2 -> libopencv_stitching.so.3.2.0\n",
            "\tlibvtkImagingCorePython27D-6.3.so.6.3 -> libvtkImagingCorePython27D-6.3.so.6.3.0\n",
            "\tlibrados.so.2 -> librados.so.2.0.0\n",
            "\tlibvtkRenderingMatplotlibTCL-6.3.so.6.3 -> libvtkRenderingMatplotlibTCL-6.3.so.6.3.0\n",
            "\tlibsoup-2.4.so.1 -> libsoup-2.4.so.1.8.0\n",
            "\tlibopencv_datasets.so.3.2 -> libopencv_datasets.so.3.2.0\n",
            "\tlibICE.so.6 -> libICE.so.6.3.0\n",
            "\tlibvtkCommonExecutionModel-6.3.so.6.3 -> libvtkCommonExecutionModel-6.3.so.6.3.0\n",
            "\tlibepoxy.so.0 -> libepoxy.so.0.0.0\n",
            "\tlibvtkDICOMParser-6.3.so.6.3 -> libvtkDICOMParser-6.3.so.6.3.0\n",
            "\tlibvtkTestingRenderingPython27D-6.3.so.6.3 -> libvtkTestingRenderingPython27D-6.3.so.6.3.0\n",
            "\tlibopencv_fuzzy.so.3.2 -> libopencv_fuzzy.so.3.2.0\n",
            "\tlibpangoft2-1.0.so.0 -> libpangoft2-1.0.so.0.4000.14\n",
            "\tlibibverbs.so.1 -> libibverbs.so.1.1.17.1\n",
            "\tlibodbccr.so.2 -> libodbccr.so.2.0.0\n",
            "\tlibvtksys-6.3.so.6.3 -> libvtksys-6.3.so.6.3.0\n",
            "\tlibvtkParallelMPI4PyPython27D-6.3.so.6.3 -> libvtkParallelMPI4PyPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOParallelXML-6.3.so.6.3 -> libvtkIOParallelXML-6.3.so.6.3.0\n",
            "\tlibxcb-shape.so.0 -> libxcb-shape.so.0.0.0\n",
            "\tlibxshmfence.so.1 -> libxshmfence.so.1.0.0\n",
            "\tlibnorm.so.1 -> libnorm.so.1.0.0\n",
            "\tlibarchive.so.13 -> libarchive.so.13.2.2\n",
            "\tlibvtkCommonComputationalGeometryTCL-6.3.so.6.3 -> libvtkCommonComputationalGeometryTCL-6.3.so.6.3.0\n",
            "\tlibxcb-shm.so.0 -> libxcb-shm.so.0.0.0\n",
            "\tlibpulse-simple.so.0 -> libpulse-simple.so.0.1.1\n",
            "\tliblapack_atlas.so.3 -> liblapack_atlas.so.3.10.3\n",
            "\tlibvtkIOGeometryPython27D-6.3.so.6.3 -> libvtkIOGeometryPython27D-6.3.so.6.3.0\n",
            "\tlibicudata.so.60 -> libicudata.so.60.2\n",
            "\tlibgdk-x11-2.0.so.0 -> libgdk-x11-2.0.so.0.2400.32\n",
            "\tlibgobject-2.0.so.0 -> libgobject-2.0.so.0.5600.4\n",
            "\tlibvtkRenderingParallelPython27D-6.3.so.6.3 -> libvtkRenderingParallelPython27D-6.3.so.6.3.0\n",
            "\tlibboost_thread.so.1.65.1 -> libboost_thread.so.1.65.1\n",
            "\tlibvtkIOCore-6.3.so.6.3 -> libvtkIOCore-6.3.so.6.3.0\n",
            "\tlibopencv_stereo.so.3.2 -> libopencv_stereo.so.3.2.0\n",
            "\tlibvtkRenderingExternalTCL-6.3.so.6.3 -> libvtkRenderingExternalTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOPostgreSQLPython27D-6.3.so.6.3 -> libvtkIOPostgreSQLPython27D-6.3.so.6.3.0\n",
            "\tlibvtkImagingStatistics-6.3.so.6.3 -> libvtkImagingStatistics-6.3.so.6.3.0\n",
            "\tlibx264.so.152 -> libx264.so.152\n",
            "\tlibboost_stacktrace_backtrace.so.1.65.1 -> libboost_stacktrace_backtrace.so.1.65.1\n",
            "\tlibSDL2-2.0.so.0 -> libSDL2-2.0.so.0.8.0\n",
            "\tlibQt5Concurrent.so.5 -> libQt5Concurrent.so.5.9.5\n",
            "\tlibvtkRenderingGLtoPSTCL-6.3.so.6.3 -> libvtkRenderingGLtoPSTCL-6.3.so.6.3.0\n",
            "\tlibopencv_videoio.so.3.2 -> libopencv_videoio.so.3.2.0\n",
            "\tlibvtkCommonSystemPython27D-6.3.so.6.3 -> libvtkCommonSystemPython27D-6.3.so.6.3.0\n",
            "\tlibEGL_nvidia.so.0 -> libEGL_nvidia.so.450.57\n",
            "\tlibvtkRenderingFreeTypeFontConfig-6.3.so.6.3 -> libvtkRenderingFreeTypeFontConfig-6.3.so.6.3.0\n",
            "\tlibvtkViewsInfovisPython27D-6.3.so.6.3 -> libvtkViewsInfovisPython27D-6.3.so.6.3.0\n",
            "\tlibvtkCommonTransformsPython27D-6.3.so.6.3 -> libvtkCommonTransformsPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOXMLParser-6.3.so.6.3 -> libvtkIOXMLParser-6.3.so.6.3.0\n",
            "\tlibcuda.so.1 -> libcuda.so.450.57\n",
            "\tlibvtkFiltersParallelImaging-6.3.so.6.3 -> libvtkFiltersParallelImaging-6.3.so.6.3.0\n",
            "\tlibip4tc.so.0 -> libip4tc.so.0.1.0\n",
            "\tlibvtkRenderingLabelPython27D-6.3.so.6.3 -> libvtkRenderingLabelPython27D-6.3.so.6.3.0\n",
            "\tlibvtkFiltersModelingTCL-6.3.so.6.3 -> libvtkFiltersModelingTCL-6.3.so.6.3.0\n",
            "\tlibgfortran.so.4 -> libgfortran.so.4.0.0\n",
            "\tlibvtkIOLSDyna-6.3.so.6.3 -> libvtkIOLSDyna-6.3.so.6.3.0\n",
            "\tlibvtkDomainsChemistryPython27D-6.3.so.6.3 -> libvtkDomainsChemistryPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOInfovisPython27D-6.3.so.6.3 -> libvtkIOInfovisPython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingMatplotlib-6.3.so.6.3 -> libvtkRenderingMatplotlib-6.3.so.6.3.0\n",
            "\tlibminizip.so.1 -> libminizip.so.1.0.0\n",
            "\tlibgdcmCommon.so.2.8 -> libgdcmCommon.so.2.8.4\n",
            "\tlibvtkIOPostgreSQL-6.3.so.6.3 -> libvtkIOPostgreSQL-6.3.so.6.3.0\n",
            "\tlibopencv_shape.so.3.2 -> libopencv_shape.so.3.2.0\n",
            "\tlibvtkImagingHybrid-6.3.so.6.3 -> libvtkImagingHybrid-6.3.so.6.3.0\n",
            "\tlibvtkParallelMPI-6.3.so.6.3 -> libvtkParallelMPI-6.3.so.6.3.0\n",
            "\tlibhdf5_serial_hl.so.100 -> libhdf5_serial_hl.so.100.0.0\n",
            "\tlibvtkIOVPICTCL-6.3.so.6.3 -> libvtkIOVPICTCL-6.3.so.6.3.0\n",
            "\tlibiec61883.so.0 -> libiec61883.so.0.1.1\n",
            "\tlibgomp.so.1 -> libgomp.so.1.0.0\n",
            "\tlibvtkViewsContext2D-6.3.so.6.3 -> libvtkViewsContext2D-6.3.so.6.3.0\n",
            "\tlibXdamage.so.1 -> libXdamage.so.1.1.0\n",
            "\tlibvtkRenderingVolumePython27D-6.3.so.6.3 -> libvtkRenderingVolumePython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingLOD-6.3.so.6.3 -> libvtkRenderingLOD-6.3.so.6.3.0\n",
            "\tlibgdcmjpeg8.so.2.8 -> libgdcmjpeg8.so.2.8.4\n",
            "\tlibhwloc.so.5 -> libhwloc.so.5.7.6\n",
            "\tlibkrb5support.so.0 -> libkrb5support.so.0.1\n",
            "\tlibfribidi.so.0 -> libfribidi.so.0.3.6\n",
            "\tlibvtkIOPostgreSQLTCL-6.3.so.6.3 -> libvtkIOPostgreSQLTCL-6.3.so.6.3.0\n",
            "\tlibxcb-dri3.so.0 -> libxcb-dri3.so.0.0.0\n",
            "\tlibvtkFiltersTexturePython27D-6.3.so.6.3 -> libvtkFiltersTexturePython27D-6.3.so.6.3.0\n",
            "\tlibQt5Network.so.5 -> libQt5Network.so.5.9.5\n",
            "\tlibvtkFiltersSMPPython27D-6.3.so.6.3 -> libvtkFiltersSMPPython27D-6.3.so.6.3.0\n",
            "\tlibvtkFiltersFlowPathsTCL-6.3.so.6.3 -> libvtkFiltersFlowPathsTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOMySQL-6.3.so.6.3 -> libvtkIOMySQL-6.3.so.6.3.0\n",
            "\tlibrest-0.7.so.0 -> librest-0.7.so.0.0.0\n",
            "\tlibopencv_flann.so.3.2 -> libopencv_flann.so.3.2.0\n",
            "\tlibvtkIOGeometry-6.3.so.6.3 -> libvtkIOGeometry-6.3.so.6.3.0\n",
            "\tlibxcb-xkb.so.1 -> libxcb-xkb.so.1.0.0\n",
            "\tlibvtkImagingMorphological-6.3.so.6.3 -> libvtkImagingMorphological-6.3.so.6.3.0\n",
            "\tlibpostproc.so.54 -> libpostproc.so.54.7.100\n",
            "\tlibraw1394.so.11 -> libraw1394.so.11.1.0\n",
            "\tlibvtkCommonCorePython27D-6.3.so.6.3 -> libvtkCommonCorePython27D-6.3.so.6.3.0\n",
            "\tlibvtkPythonInterpreter-6.3.so.6.3 -> libvtkPythonInterpreter-6.3.so.6.3.0\n",
            "\tlibpaper.so.1 -> libpaper.so.1.1.2\n",
            "\tlibvtkIOXMLParserTCL-6.3.so.6.3 -> libvtkIOXMLParserTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOMPIParallelPython27D-6.3.so.6.3 -> libvtkIOMPIParallelPython27D-6.3.so.6.3.0\n",
            "\tlibssl.so.1.0.0 -> libssl.so.1.0.0\n",
            "\tlibpcre2-posix.so.2 -> libpcre2-posix.so.2.0.0\n",
            "\tlibvtkFiltersSourcesTCL-6.3.so.6.3 -> libvtkFiltersSourcesTCL-6.3.so.6.3.0\n",
            "\tlibvtkTestingRenderingTCL-6.3.so.6.3 -> libvtkTestingRenderingTCL-6.3.so.6.3.0\n",
            "\tlibicutu.so.60 -> libicutu.so.60.2\n",
            "\tlibspatialite.so.7 -> libspatialite.so.7.1.0\n",
            "\tlibgraphite2.so.3 -> libgraphite2.so.3.0.1\n",
            "\tlibprotobuf.so.10 -> libprotobuf.so.10.0.0\n",
            "\tlibsensors.so.4 -> libsensors.so.4.4.0\n",
            "\tlibsoup-gnome-2.4.so.1 -> libsoup-gnome-2.4.so.1.8.0\n",
            "\tlibGLESv2_nvidia.so.2 -> libGLESv2_nvidia.so.450.57\n",
            "\tlibitm.so.1 -> libitm.so.1.0.0\n",
            "\tlibQt5Test.so.5 -> libQt5Test.so.5.9.5\n",
            "\tlibmpx.so.2 -> libmpx.so.2.0.1\n",
            "\tlibvtkFiltersParallelMPITCL-6.3.so.6.3 -> libvtkFiltersParallelMPITCL-6.3.so.6.3.0\n",
            "\tlibgphoto2.so.6 -> libgphoto2.so.6.0.0\n",
            "\tlibpcsclite.so.1 -> libpcsclite.so.1.0.0\n",
            "\tlibvtkParallelCore-6.3.so.6.3 -> libvtkParallelCore-6.3.so.6.3.0\n",
            "\tlibIex-2_2.so.12 -> libIex.so\n",
            "\tlibavdevice.so.57 -> libavdevice.so.57.10.100\n",
            "\tlibvtkRenderingTkTCL-6.3.so.6.3 -> libvtkRenderingTkTCL-6.3.so.6.3.0\n",
            "\tlibflite_cmu_time_awb.so.1 -> libflite_cmu_time_awb.so.2.1\n",
            "\tlibgsm.so.1 -> libgsm.so.1.0.12\n",
            "\tlibvtkRenderingOpenGL-6.3.so.6.3 -> libvtkRenderingOpenGL-6.3.so.6.3.0\n",
            "\tlibinput.so.10 -> libinput.so.10.13.0\n",
            "\tlibXau.so.6 -> libXau.so.6.0.0\n",
            "\tlibxcb-render-util.so.0 -> libxcb-render-util.so.0.0.0\n",
            "\tlibvtkIOXML-6.3.so.6.3 -> libvtkIOXML-6.3.so.6.3.0\n",
            "\tlibBlocksRuntime.so.0 -> libBlocksRuntime.so.0.0.0\n",
            "\tlibxcb-dri2.so.0 -> libxcb-dri2.so.0.0.0\n",
            "\tlibvtkFiltersParallelMPIPython27D-6.3.so.6.3 -> libvtkFiltersParallelMPIPython27D-6.3.so.6.3.0\n",
            "\tlibxcb-util.so.1 -> libxcb-util.so.1.0.0\n",
            "\tlibopencv_imgcodecs.so.3.2 -> libopencv_imgcodecs.so.3.2.0\n",
            "\tlibxerces-c-3.2.so -> libxerces-c-3.2.so\n",
            "\tlibvtkParallelCorePython27D-6.3.so.6.3 -> libvtkParallelCorePython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOParallelExodusTCL-6.3.so.6.3 -> libvtkIOParallelExodusTCL-6.3.so.6.3.0\n",
            "\tlibhdf5_serial_fortran.so.100 -> libhdf5_serial_fortran.so.100.0.1\n",
            "\tlibvtkIOExodusTCL-6.3.so.6.3 -> libvtkIOExodusTCL-6.3.so.6.3.0\n",
            "\tlibavutil.so.55 -> libavutil.so.55.78.100\n",
            "\tlibmpg123.so.0 -> libmpg123.so.0.44.8\n",
            "\tlibnvoptix.so.1 -> libnvoptix.so.450.57\n",
            "\tlibavahi-client.so.3 -> libavahi-client.so.3.2.9\n",
            "\tlibtesseract.so.4 -> libtesseract.so.4.0.0\n",
            "\tlibvtkWrappingPython27Core-6.3.so.6.3 -> libvtkWrappingPython27Core-6.3.so.6.3.0\n",
            "\tlibpipeline.so.1 -> libpipeline.so.1.5.0\n",
            "\tlibpixman-1.so.0 -> libpixman-1.so.0.34.0\n",
            "\tlibwavpack.so.1 -> libwavpack.so.1.2.0\n",
            "\tlibvtkCommonMathPython27D-6.3.so.6.3 -> libvtkCommonMathPython27D-6.3.so.6.3.0\n",
            "\tlibxvidcore.so.4 -> libxvidcore.so.4.3\n",
            "\tlibswscale.so.4 -> libswscale.so.4.8.100\n",
            "\tlibpulse.so.0 -> libpulse.so.0.20.2\n",
            "\tlibpython3.6m.so.1.0 -> libpython3.6m.so.1.0\n",
            "\tlibtcmalloc_and_profiler.so.4 -> libtcmalloc_and_profiler.so.4.3.0\n",
            "\tlibsndio.so.6.1 -> libsndio.so.6.1\n",
            "\tlibvtkIOODBCPython27D-6.3.so.6.3 -> libvtkIOODBCPython27D-6.3.so.6.3.0\n",
            "\tlibopencv_calib3d.so.3.2 -> libopencv_calib3d.so.3.2.0\n",
            "\tlibvtkRenderingFreeTypeTCL-6.3.so.6.3 -> libvtkRenderingFreeTypeTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersTextureTCL-6.3.so.6.3 -> libvtkFiltersTextureTCL-6.3.so.6.3.0\n",
            "\tlibopencv_bioinspired.so.3.2 -> libopencv_bioinspired.so.3.2.0\n",
            "\tlibprofiler.so.0 -> libprofiler.so.0.4.8\n",
            "\tlibxcb-keysyms.so.1 -> libxcb-keysyms.so.1.0.0\n",
            "\tlibvtkImagingStencilTCL-6.3.so.6.3 -> libvtkImagingStencilTCL-6.3.so.6.3.0\n",
            "\tlibcaca++.so.0 -> libcaca++.so.0.99.19\n",
            "\tlibass.so.9 -> libass.so.9.0.2\n",
            "\tlibboost_atomic.so.1.65.1 -> libboost_atomic.so.1.65.1\n",
            "\tlibmpi.so.20 -> libmpi.so.20.10.1\n",
            "\tlibboost_math_c99l.so.1.65.1 -> libboost_math_c99l.so.1.65.1\n",
            "\tlibcilkrts.so.5 -> libcilkrts.so.5.0.0\n",
            "\tlibvtkParallelCoreTCL-6.3.so.6.3 -> libvtkParallelCoreTCL-6.3.so.6.3.0\n",
            "\tlibxkbfile.so.1 -> libxkbfile.so.1.0.2\n",
            "\tlibgphoto2_port.so.12 -> libgphoto2_port.so.12.0.0\n",
            "\tlibvtkImagingGeneralTCL-6.3.so.6.3 -> libvtkImagingGeneralTCL-6.3.so.6.3.0\n",
            "\tlibkmlengine.so.1 -> libkmlengine.so.1.3.0\n",
            "\tlibvtkIOFFMPEG-6.3.so.6.3 -> libvtkIOFFMPEG-6.3.so.6.3.0\n",
            "\tlibvtkFiltersHybrid-6.3.so.6.3 -> libvtkFiltersHybrid-6.3.so.6.3.0\n",
            "\tlibvtkCommonDataModel-6.3.so.6.3 -> libvtkCommonDataModel-6.3.so.6.3.0\n",
            "\tlibmysofa.so.0 -> libmysofa.so.0.5.1\n",
            "\tlibdrm_nouveau.so.2 -> libdrm_nouveau.so.2.0.0\n",
            "\tlibvtkCommonCore-6.3.so.6.3 -> libvtkCommonCore-6.3.so.6.3.0\n",
            "\tlibvtkFiltersGeneral-6.3.so.6.3 -> libvtkFiltersGeneral-6.3.so.6.3.0\n",
            "\tlibvtkIOParallelNetCDFTCL-6.3.so.6.3 -> libvtkIOParallelNetCDFTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersParallelImagingTCL-6.3.so.6.3 -> libvtkFiltersParallelImagingTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOInfovis-6.3.so.6.3 -> libvtkIOInfovis-6.3.so.6.3.0\n",
            "\tlibdrm_amdgpu.so.1 -> libdrm_amdgpu.so.1.0.0\n",
            "\tlibopencv_ml.so.3.2 -> libopencv_ml.so.3.2.0\n",
            "\tlibopencv_xphoto.so.3.2 -> libopencv_xphoto.so.3.2.0\n",
            "\tlibvtkRenderingContextOpenGLPython27D-6.3.so.6.3 -> libvtkRenderingContextOpenGLPython27D-6.3.so.6.3.0\n",
            "\tlibcblas.so.3 -> libcblas.so.3.10.3\n",
            "\tlibQt5Gui.so.5 -> libQt5Gui.so.5.9.5\n",
            "\tlibvtkParallelMPITCL-6.3.so.6.3 -> libvtkParallelMPITCL-6.3.so.6.3.0\n",
            "\tlibodbcinst.so.2 -> libodbcinst.so.2.0.0\n",
            "\tlibopencv_viz.so.3.2 -> libopencv_viz.so.3.2.0\n",
            "\tlibQt5Xml.so.5 -> libQt5Xml.so.5.9.5\n",
            "\tlibQt5Widgets.so.5 -> libQt5Widgets.so.5.9.5\n",
            "\tlibgd.so.3 -> libgd.so.3.0.5\n",
            "\tlibvtkLocalExample-6.3.so.6.3 -> libvtkLocalExample-6.3.so.6.3.0\n",
            "\tlibdatrie.so.1 -> libdatrie.so.1.3.3\n",
            "\tlibssh-gcrypt.so.4 -> libssh-gcrypt.so.4.5.0\n",
            "\tlibxslt.so.1 -> libxslt.so.1.1.29\n",
            "\tlibpciaccess.so.0 -> libpciaccess.so.0.11.1\n",
            "\tlibvtkIOXMLParserPython27D-6.3.so.6.3 -> libvtkIOXMLParserPython27D-6.3.so.6.3.0\n",
            "\tlibvtkInteractionStylePython27D-6.3.so.6.3 -> libvtkInteractionStylePython27D-6.3.so.6.3.0\n",
            "\tlibva.so.2 -> libva.so.2.100.0\n",
            "\tlibharfbuzz.so.0 -> libharfbuzz.so.0.10702.0\n",
            "\tlibvtkRenderingExternal-6.3.so.6.3 -> libvtkRenderingExternal-6.3.so.6.3.0\n",
            "\tlibIlmThread-2_2.so.12 -> libIlmThread.so\n",
            "\tlibrsvg-2.so.2 -> librsvg-2.so.2.40.20\n",
            "\tlibpopt.so.0 -> libpopt.so.0.0.0\n",
            "\tlibvtkImagingFourier-6.3.so.6.3 -> libvtkImagingFourier-6.3.so.6.3.0\n",
            "\tlibQt5XcbQpa.so.5 -> libQt5XcbQpa.so.5.9.5\n",
            "\tlibopenjp2.so.7 -> libopenjp2.so.2.3.0\n",
            "\tlibpgm-5.2.so.0 -> libpgm-5.2.so.0.0.122\n",
            "\tlibvtkInfovisBoostGraphAlgorithms-6.3.so.6.3 -> libvtkInfovisBoostGraphAlgorithms-6.3.so.6.3.0\n",
            "\tlibvtkViewsCoreTCL-6.3.so.6.3 -> libvtkViewsCoreTCL-6.3.so.6.3.0\n",
            "\tlibfyba.so.0 -> libfyba.so.0.0.0\n",
            "\tlibXpm.so.4 -> libXpm.so.4.11.0\n",
            "\tlibcrypto.so.1.1 -> libcrypto.so.1.1\n",
            "\tlibjsoncpp.so.1 -> libjsoncpp.so.1.7.4\n",
            "\tlibmca_common_sm.so.20 -> libmca_common_sm.so.20.10.1\n",
            "\tlibflite_cmu_us_rms.so.1 -> libflite_cmu_us_rms.so.2.1\n",
            "\tlibpcre2-32.so.0 -> libpcre2-32.so.0.7.0\n",
            "\tlibmysqlclient.so.20 -> libmysqlclient.so.20.3.18\n",
            "\tlibvtkIOCoreTCL-6.3.so.6.3 -> libvtkIOCoreTCL-6.3.so.6.3.0\n",
            "\tlibboost_mpi_python3-py36.so.1.65.1 -> libboost_mpi_python3.so\n",
            "\tlibopencv_saliency.so.3.2 -> libopencv_saliency.so.3.2.0\n",
            "\tlibmpi_cxx.so.20 -> libmpi_cxx.so.20.10.0\n",
            "\tlibvtkIOGeoJSON-6.3.so.6.3 -> libvtkIOGeoJSON-6.3.so.6.3.0\n",
            "\tlibvtkIOLegacyPython27D-6.3.so.6.3 -> libvtkIOLegacyPython27D-6.3.so.6.3.0\n",
            "\tlibnetcdf.so.13 -> libnetcdf.so.13\n",
            "\tlibcrypto.so.1.0.0 -> libcrypto.so.1.0.0\n",
            "\tlibzvbi.so.0 -> libzvbi.so.0.13.2\n",
            "\tliblcms2.so.2 -> liblcms2.so.2.0.8\n",
            "\tlibflite_cmu_grapheme_lang.so.1 -> libflite_cmu_grapheme_lang.so.2.1\n",
            "\tlibvtkInteractionStyle-6.3.so.6.3 -> libvtkInteractionStyle-6.3.so.6.3.0\n",
            "\tlibcurl.so.4 -> libcurl.so.4.5.0\n",
            "\tlibOpenCL.so.1 -> libOpenCL.so.1.0.0\n",
            "\tlibvtkRenderingVolume-6.3.so.6.3 -> libvtkRenderingVolume-6.3.so.6.3.0\n",
            "\tlibvtkImagingMathPython27D-6.3.so.6.3 -> libvtkImagingMathPython27D-6.3.so.6.3.0\n",
            "\tlibubsan.so.0 -> libubsan.so.0.0.0\n",
            "\tlibzvbi-chains.so.0 -> libzvbi-chains.so.0.0.0\n",
            "\tlibrdmacm.so.1 -> librdmacm.so.1.1.17.1\n",
            "\tlibGLESv1_CM.so.1 -> libGLESv1_CM.so.1.0.0\n",
            "\tlibvtkChartsCoreTCL-6.3.so.6.3 -> libvtkChartsCoreTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersVerdict-6.3.so.6.3 -> libvtkFiltersVerdict-6.3.so.6.3.0\n",
            "\tlibfontconfig.so.1 -> libfontconfig.so.1.10.1\n",
            "\tlibatspi.so.0 -> libatspi.so.0.0.1\n",
            "\tlibgirepository-1.0.so.1 -> libgirepository-1.0.so.1.0.0\n",
            "\tlibnvidia-opencl.so.1 -> libnvidia-opencl.so.450.57\n",
            "\tlibcairo-gobject.so.2 -> libcairo-gobject.so.2.11510.0\n",
            "\tlibvtkRenderingLIC-6.3.so.6.3 -> libvtkRenderingLIC-6.3.so.6.3.0\n",
            "\tlibvtkFiltersStatisticsTCL-6.3.so.6.3 -> libvtkFiltersStatisticsTCL-6.3.so.6.3.0\n",
            "\tlibGLX_mesa.so.0 -> libGLX_mesa.so.0.0.0\n",
            "\tlibvtkIOExodus-6.3.so.6.3 -> libvtkIOExodus-6.3.so.6.3.0\n",
            "\tlibtcl8.6.so -> libtcl8.6.so.0\n",
            "\tlibvtkRenderingOpenGLTCL-6.3.so.6.3 -> libvtkRenderingOpenGLTCL-6.3.so.6.3.0\n",
            "\tlibuv.so.1 -> libuv.so.1.0.0\n",
            "\tlibvtkIOMySQLTCL-6.3.so.6.3 -> libvtkIOMySQLTCL-6.3.so.6.3.0\n",
            "\tlibflite_cmu_us_kal16.so.1 -> libflite_cmu_us_kal16.so.2.1\n",
            "\tlibvtkIOPLY-6.3.so.6.3 -> libvtkIOPLY-6.3.so.6.3.0\n",
            "\tlibboost_stacktrace_basic.so.1.65.1 -> libboost_stacktrace_basic.so.1.65.1\n",
            "\tlibvtkRenderingVolumeAMR-6.3.so.6.3 -> libvtkRenderingVolumeAMR-6.3.so.6.3.0\n",
            "\tlibcdio_cdda.so.2 -> libcdio_cdda.so.2.0.0\n",
            "\tlibmca_common_libfabric.so.20 -> libmca_common_libfabric.so.20.10.0\n",
            "\tlibvtkmetaio-6.3.so.6.3 -> libvtkmetaio-6.3.so.6.3.0\n",
            "\tlibarpack.so.2 -> libarpack.so.2.0.0\n",
            "\tlibtcmalloc_debug.so.4 -> libtcmalloc_debug.so.4.3.0\n",
            "\tlibopencv_aruco.so.3.2 -> libopencv_aruco.so.3.2.0\n",
            "\tlibrubberband.so.2 -> librubberband.so.2.1.0\n",
            "\tlibopencv_videostab.so.3.2 -> libopencv_videostab.so.3.2.0\n",
            "\tlibvtkIOXdmf2Python27D-6.3.so.6.3 -> libvtkIOXdmf2Python27D-6.3.so.6.3.0\n",
            "\tlibcurl-gnutls.so.4 -> libcurl-gnutls.so.4.5.0\n",
            "\tlibavresample.so.3 -> libavresample.so.3.7.0\n",
            "\tlibgudev-1.0.so.0 -> libgudev-1.0.so.0.2.0\n",
            "\tlibvtkInteractionImage-6.3.so.6.3 -> libvtkInteractionImage-6.3.so.6.3.0\n",
            "\tlibboost_numpy3-py36.so.1.65.1 -> libboost_numpy3.so\n",
            "\tlibtheoradec.so.1 -> libtheoradec.so.1.1.4\n",
            "\tlibvtkxdmf2-6.3.so.6.3 -> libvtkxdmf2-6.3.so.6.3.0\n",
            "\tlibdouble-conversion.so.1 -> libdouble-conversion.so.1.0\n",
            "\tlibvtkRenderingVolumeAMRTCL-6.3.so.6.3 -> libvtkRenderingVolumeAMRTCL-6.3.so.6.3.0\n",
            "\tlibvtkRenderingParallelTCL-6.3.so.6.3 -> libvtkRenderingParallelTCL-6.3.so.6.3.0\n",
            "\tlibvtkFiltersVerdictTCL-6.3.so.6.3 -> libvtkFiltersVerdictTCL-6.3.so.6.3.0\n",
            "\tlibzmq.so.5 -> libzmq.so.5.1.5\n",
            "\tlibvtkexoIIc-6.3.so.6.3 -> libvtkexoIIc-6.3.so.6.3.0\n",
            "\tlibvtkIOImportPython27D-6.3.so.6.3 -> libvtkIOImportPython27D-6.3.so.6.3.0\n",
            "\tlibfftw3_threads.so.3 -> libfftw3_threads.so.3.5.7\n",
            "\tlibexslt.so.0 -> libexslt.so.0.8.17\n",
            "\tlibvtkFiltersParallelGeometry-6.3.so.6.3 -> libvtkFiltersParallelGeometry-6.3.so.6.3.0\n",
            "\tlibpcre16.so.3 -> libpcre16.so.3.13.3\n",
            "\tlibswresample.so.2 -> libswresample.so.2.9.100\n",
            "\tlibboost_python3-py36.so.1.65.1 -> libboost_python3.so\n",
            "\tlibopenal.so.1 -> libopenal.so.1.18.2\n",
            "\tlibthai.so.0 -> libthai.so.0.3.0\n",
            "\tlibmpdec.so.2 -> libmpdec.so.2.4.2\n",
            "\tlibvtkFiltersStatistics-6.3.so.6.3 -> libvtkFiltersStatistics-6.3.so.6.3.0\n",
            "\tlibXfont2.so.2 -> libXfont2.so.2.0.0\n",
            "\tlibexpatw.so.1 -> libexpatw.so.1.6.7\n",
            "\tlibopencv_bgsegm.so.3.2 -> libopencv_bgsegm.so.3.2.0\n",
            "\tlibvtkFiltersSourcesPython27D-6.3.so.6.3 -> libvtkFiltersSourcesPython27D-6.3.so.6.3.0\n",
            "\tlibvtkRenderingVolumeOpenGL-6.3.so.6.3 -> libvtkRenderingVolumeOpenGL-6.3.so.6.3.0\n",
            "\tlibvtkChartsCorePython27D-6.3.so.6.3 -> libvtkChartsCorePython27D-6.3.so.6.3.0\n",
            "\tlibopencv_hdf.so.3.2 -> libopencv_hdf.so.3.2.0\n",
            "\tlibogg.so.0 -> libogg.so.0.8.2\n",
            "\tlibobjc.so.4 -> libobjc.so.4.0.0\n",
            "\tlibvtkIOLSDynaTCL-6.3.so.6.3 -> libvtkIOLSDynaTCL-6.3.so.6.3.0\n",
            "\tlibvtkImagingMorphologicalTCL-6.3.so.6.3 -> libvtkImagingMorphologicalTCL-6.3.so.6.3.0\n",
            "\tlibvtkIOParallelXMLPython27D-6.3.so.6.3 -> libvtkIOParallelXMLPython27D-6.3.so.6.3.0\n",
            "\tlibicuuc.so.60 -> libicuuc.so.60.2\n",
            "\tlibboost_math_tr1f.so.1.65.1 -> libboost_math_tr1f.so.1.65.1\n",
            "\tlibgthread-2.0.so.0 -> libgthread-2.0.so.0.5600.4\n",
            "\tlibmpi_usempif08.so.20 -> libmpi_usempif08.so.20.10.0\n",
            "\tlibvtkFiltersPythonPython27D-6.3.so.6.3 -> libvtkFiltersPythonPython27D-6.3.so.6.3.0\n",
            "\tlibgtk-3.so.0 -> libgtk-3.so.0.2200.30\n",
            "\tlibjson-glib-1.0.so.0 -> libjson-glib-1.0.so.0.400.2\n",
            "\tlibfftw3.so.3 -> libfftw3.so.3.5.7\n",
            "\tlibunwind-x86_64.so.8 -> libunwind-x86_64.so.8.0.1\n",
            "\tlibxcb.so.1 -> libxcb.so.1.1.0\n",
            "\tlibwebpdemux.so.2 -> libwebpdemux.so.2.0.3\n",
            "\tlibopencv_optflow.so.3.2 -> libopencv_optflow.so.3.2.0\n",
            "\tlibgdcmIOD.so.2.8 -> libgdcmIOD.so.2.8.4\n",
            "\tlibvtkFiltersExtraction-6.3.so.6.3 -> libvtkFiltersExtraction-6.3.so.6.3.0\n",
            "\tlibvtkIOMySQLPython27D-6.3.so.6.3 -> libvtkIOMySQLPython27D-6.3.so.6.3.0\n",
            "\tlibopencv_highgui.so.3.2 -> libopencv_highgui.so.3.2.0\n",
            "\tlibgeotiff.so.2 -> libgeotiff.so.2.1.2\n",
            "\tlibnvidia-eglcore.so.450.57 -> libnvidia-eglcore.so.450.57\n",
            "\tlibicui18n.so.60 -> libicui18n.so.60.2\n",
            "\tlibvtkParallelMPI4Py-6.3.so.6.3 -> libvtkParallelMPI4Py-6.3.so.6.3.0\n",
            "\tlibompitrace.so.20 -> libompitrace.so.20.10.0\n",
            "\tlibvorbisfile.so.3 -> libvorbisfile.so.3.3.7\n",
            "\tlibvtkImagingFourierPython27D-6.3.so.6.3 -> libvtkImagingFourierPython27D-6.3.so.6.3.0\n",
            "\tlibvtkIOImport-6.3.so.6.3 -> libvtkIOImport-6.3.so.6.3.0\n",
            "\tliblua5.1.so.0 -> liblua5.1.so.0.0.0\n",
            "\tlibyaml-0.so.2 -> libyaml-0.so.2.0.5\n",
            "\tlibluajit-5.1.so.2 -> libluajit-5.1.so.2.1.0\n",
            "\tliblua5.1-c++.so.0 -> liblua5.1-c++.so.0.0.0\n",
            "\tlibsundials_nvecserial.so.2 -> libsundials_nvecserial.so.2.7.0\n",
            "\tlibbtf.so.1 -> libbtf.so.1.2.6\n",
            "\tlibcolamd.so.2 -> libcolamd.so.2.9.6\n",
            "\tlibsuitesparseconfig.so.5 -> libsuitesparseconfig.so.5.1.2\n",
            "\tlibsundials_fnvecserial.so.2 -> libsundials_fnvecserial.so.2.7.0\n",
            "\tlibklu.so.1 -> libklu.so.1.3.8\n",
            "\tlibsundials_cvode.so.2 -> libsundials_cvode.so.2.9.0\n",
            "\tlibamd.so.2 -> libamd.so.2.4.6\n",
            "\tlibdb-5.3.so -> libdb-5.3.so\n",
            "\tlibzstd.so.1 -> libzstd.so.1.3.3\n",
            "\tlibtasn1.so.6 -> libtasn1.so.6.5.5\n",
            "\tlibp11-kit.so.0 -> libp11-kit.so.0.3.0\n",
            "\tlibnettle.so.6 -> libnettle.so.6.4\n",
            "\tlibmenuw.so.5 -> libmenuw.so.5.9\n",
            "\tlibform.so.5 -> libform.so.5.9\n",
            "\tlibgnutls.so.30 -> libgnutls.so.30.14.10\n",
            "\tlibhogweed.so.4 -> libhogweed.so.4.4\n",
            "\tlibunistring.so.2 -> libunistring.so.2.1.0\n",
            "\tlibdebconfclient.so.0 -> libdebconfclient.so.0.0.0\n",
            "\tlibgmp.so.10 -> libgmp.so.10.3.2\n",
            "\tlibstdc++.so.6 -> libstdc++.so.6.0.25\n",
            "\tlibpanelw.so.5 -> libpanelw.so.5.9\n",
            "\tliblz4.so.1 -> liblz4.so.1.7.1\n",
            "\tlibapt-private.so.0.0 -> libapt-private.so.0.0.0\n",
            "\tlibsemanage.so.1 -> libsemanage.so.1\n",
            "\tlibapt-pkg.so.5.0 -> libapt-pkg.so.5.0.2\n",
            "\tlibpanel.so.5 -> libpanel.so.5.9\n",
            "\tlibtic.so.5 -> libtic.so.5.9\n",
            "\tlibidn2.so.0 -> libidn2.so.0.3.3\n",
            "\tlibformw.so.5 -> libformw.so.5.9\n",
            "\tlibmenu.so.5 -> libmenu.so.5.9\n",
            "\tlibffi.so.6 -> libffi.so.6.0.4\n",
            "\tlibpcreposix.so.3 -> libpcreposix.so.3.13.3\n",
            "/lib32:\n",
            "\tlibnss_nisplus.so.2 -> libnss_nisplus-2.27.so\n",
            "\tlibcrypt.so.1 -> libcrypt-2.27.so\n",
            "\tlibdl.so.2 -> libdl-2.27.so\n",
            "/sbin/ldconfig.real: /lib32/ld-2.27.so is the dynamic linker, ignoring\n",
            "\n",
            "\tld-linux.so.2 -> ld-2.27.so\n",
            "\tlibcidn.so.1 -> libcidn-2.27.so\n",
            "\tlibpthread.so.0 -> libpthread-2.27.so\n",
            "\tlibnss_hesiod.so.2 -> libnss_hesiod-2.27.so\n",
            "\tlibpcprofile.so -> libpcprofile.so\n",
            "\tlibutil.so.1 -> libutil-2.27.so\n",
            "\tlibnss_compat.so.2 -> libnss_compat-2.27.so\n",
            "\tlibnss_nis.so.2 -> libnss_nis-2.27.so\n",
            "\tlibanl.so.1 -> libanl-2.27.so\n",
            "\tlibc.so.6 -> libc-2.27.so\n",
            "\tlibnsl.so.1 -> libnsl-2.27.so\n",
            "\tlibnss_dns.so.2 -> libnss_dns-2.27.so\n",
            "\tlibrt.so.1 -> librt-2.27.so\n",
            "\tlibmemusage.so -> libmemusage.so\n",
            "\tlibnss_files.so.2 -> libnss_files-2.27.so\n",
            "\tlibm.so.6 -> libm-2.27.so\n",
            "\tlibBrokenLocale.so.1 -> libBrokenLocale-2.27.so\n",
            "\tlibSegFault.so -> libSegFault.so\n",
            "\tlibthread_db.so.1 -> libthread_db-1.0.so\n",
            "\tlibresolv.so.2 -> libresolv-2.27.so\n",
            "/usr/lib32:\n",
            "\tlibstdc++.so.6 -> libstdc++.so.6.0.25\n",
            "\tlibgcc_s.so.1 -> libgcc_s.so.1\n",
            "/lib:\n",
            "/usr/lib:\n",
            "\tlibBLTlite.2.5.so.8.6 -> libBLTlite.2.5.so.8.6\n",
            "\tlibnvidia-gtk3.so.450.51.06 -> libnvidia-gtk3.so.450.51.06\n",
            "\tlibBLT.2.5.so.8.6 -> libBLT.2.5.so.8.6\n",
            "\tlibarmadillo.so.8 -> libarmadillo.so.8.400.0\n",
            "\tlibdfalt.so.0 -> libdfalt.so.0.0.0\n",
            "\tlibann.so.0 -> libann.so.0.0.0\n",
            "\tlibgdal.so.20 -> libgdal.so.20.3.2\n",
            "\tlibogdi.so.3.2 -> libogdi.so.3.2\n",
            "\tlibvpf.so.3.2 -> libvpf.so.3.2\n",
            "\tlibmfhdfalt.so.0 -> libmfhdfalt.so.0.0.0\n",
            "\tlibnvidia-gtk2.so.450.51.06 -> libnvidia-gtk2.so.450.51.06\n",
            "\tlibcln.so.6 -> libcln.so.6.0.4\n",
            "\tlibginac.so.6 -> libginac.so.6.2.0\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "GzInNwTb-dvn"
      },
      "source": [
        "2. Install JEMRIS onto the virtual machine. After this step, JEMRIS can be called from the command line with various options: \n",
        "* Generate sequence plots from JEMRIS .xml format\n",
        "* Generate pulseq file from JEMRIS .xml format\n",
        "* Perform simulation using information and references stored in \"simu.xml\"\n",
        "* etc... (see http://www.jemris.org/ug_command_line.html) \n"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "mSFAMSR6Qq_p",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 106
        },
        "outputId": "1bacad83-910c-41fb-deee-749471ced7df"
      },
      "source": [
        "# Install JEMRIS \n",
        "!sudo dpkg -i jemris-2.8.3-Linux.deb"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Selecting previously unselected package jemris.\n",
            "(Reading database ... \r(Reading database ... 5%\r(Reading database ... 10%\r(Reading database ... 15%\r(Reading database ... 20%\r(Reading database ... 25%\r(Reading database ... 30%\r(Reading database ... 35%\r(Reading database ... 40%\r(Reading database ... 45%\r(Reading database ... 50%\r(Reading database ... 55%\r(Reading database ... 60%\r(Reading database ... 65%\r(Reading database ... 70%\r(Reading database ... 75%\r(Reading database ... 80%\r(Reading database ... 85%\r(Reading database ... 90%\r(Reading database ... 95%\r(Reading database ... 100%\r(Reading database ... 144693 files and directories currently installed.)\n",
            "Preparing to unpack jemris-2.8.3-Linux.deb ...\n",
            "Unpacking jemris (2.8.3) ...\n",
            "Setting up jemris (2.8.3) ...\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_vB73SRPABXu"
      },
      "source": [
        "Call JEMRIS command to check that it works:"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "I3b5cYSmZYV9",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 355
        },
        "outputId": "059e32a4-6dbe-4db3-eb46-c112b542bc8e"
      },
      "source": [
        "# The following should run and explain how to use the JEMRIS command \n",
        "!jemris "
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "\n",
            "jemris 2.8.3 (3ce3164b704394c4c1a8a3746b3ddc1296727458)\n",
            "\n",
            "\n",
            "  Usage:\n",
            "\n",
            "  1. jemris <xml-file>        \n",
            "     The file could be either a a) Simulation, b) Sequence, or c) Coilarray file, \n",
            "     so that a) the simultion is performed, b) a sequence diagram is written, \n",
            "     or c) the sensitivity maps are dumped, respectively.\n",
            "\n",
            "  2. jemris modlist           \n",
            "     Writes the file mod.xml containing a list of all available modules.\n",
            "\n",
            "  Parameters:\n",
            "     -o <output_dir>: Output directory\n",
            "     -f <filename>:   Output filename (without extension)\n",
            "     -x: Output sequence file for execution\n",
            "     -d <def>=<val>:  Define custom sequence variable\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "h4poETMMZEHl"
      },
      "source": [
        "## Install py2jemris"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "trKD-7zaAzrr"
      },
      "source": [
        "Install virtual scanner - the simulation portion contains py2jemris code. "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "BZI55OO4Aj8Y",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "outputId": "b8a258db-0ccb-4775-cc41-2622e961b5d0"
      },
      "source": [
        "# Install latest dev build of virtualscanner to grab the py2jemris functionalities \n",
        "!pip install git+https://github.com/imr-framework/virtual-scanner.git@dev"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Collecting git+https://github.com/imr-framework/virtual-scanner.git@dev\n",
            "  Cloning https://github.com/imr-framework/virtual-scanner.git (to revision dev) to /tmp/pip-req-build-rumicjzi\n",
            "  Running command git clone -q https://github.com/imr-framework/virtual-scanner.git /tmp/pip-req-build-rumicjzi\n",
            "  Running command git checkout -b dev --track origin/dev\n",
            "  Switched to a new branch 'dev'\n",
            "  Branch 'dev' set up to track remote branch 'dev' from 'origin'.\n",
            "Collecting absl-py==0.7.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/da/3f/9b0355080b81b15ba6a9ffcf1f5ea39e307a2778b2f2dc8694724e8abd5b/absl-py-0.7.1.tar.gz (99kB)\n",
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            "\u001b[?25hCollecting astor==0.7.1\n",
            "  Downloading https://files.pythonhosted.org/packages/35/6b/11530768cac581a12952a2aad00e1526b89d242d0b9f59534ef6e6a1752f/astor-0.7.1-py2.py3-none-any.whl\n",
            "Collecting Click==7.0\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/fa/37/45185cb5abbc30d7257104c434fe0b07e5a195a6847506c074527aa599ec/Click-7.0-py2.py3-none-any.whl (81kB)\n",
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            "Collecting Flask==1.0.2\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/7f/e7/08578774ed4536d3242b14dacb4696386634607af824ea997202cd0edb4b/Flask-1.0.2-py2.py3-none-any.whl (91kB)\n",
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            "\u001b[?25hCollecting gast==0.2.2\n",
            "  Downloading https://files.pythonhosted.org/packages/4e/35/11749bf99b2d4e3cceb4d55ca22590b0d7c2c62b9de38ac4a4a7f4687421/gast-0.2.2.tar.gz\n",
            "Collecting grpcio==1.20.0\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/39/a8/8eeb117c46a53768008a7e3892746aa0ea8ea0b669a2a06712eec11ecc33/grpcio-1.20.0-cp36-cp36m-manylinux1_x86_64.whl (2.1MB)\n",
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            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/30/99/d7d4fbf2d02bb30fb76179911a250074b55b852d34e98dd452a9f394ac06/h5py-2.9.0-cp36-cp36m-manylinux1_x86_64.whl (2.8MB)\n",
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            "Collecting Jinja2==2.10.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl (124kB)\n",
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            "\u001b[?25hCollecting Keras==2.2.4\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/5e/10/aa32dad071ce52b5502266b5c659451cfd6ffcbf14e6c8c4f16c0ff5aaab/Keras-2.2.4-py2.py3-none-any.whl (312kB)\n",
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            "\u001b[?25hCollecting Keras-Applications==1.0.7\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/90/85/64c82949765cfb246bbdaf5aca2d55f400f792655927a017710a78445def/Keras_Applications-1.0.7-py2.py3-none-any.whl (51kB)\n",
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            "\u001b[?25hCollecting Keras-Preprocessing==1.0.9\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/c0/bf/0315ef6a9fd3fc2346e85b0ff1f5f83ca17073f2c31ac719ab2e4da0d4a3/Keras_Preprocessing-1.0.9-py2.py3-none-any.whl (59kB)\n",
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            "\u001b[?25hCollecting kiwisolver==1.0.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/69/a7/88719d132b18300b4369fbffa741841cfd36d1e637e1990f27929945b538/kiwisolver-1.0.1-cp36-cp36m-manylinux1_x86_64.whl (949kB)\n",
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            "\u001b[?25hCollecting Markdown==3.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/f5/e4/d8c18f2555add57ff21bf25af36d827145896a07607486cc79a2aea641af/Markdown-3.1-py2.py3-none-any.whl (87kB)\n",
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            "Collecting matplotlib==3.0.3\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/e9/69/f5e05f578585ed9935247be3788b374f90701296a70c8871bcd6d21edb00/matplotlib-3.0.3-cp36-cp36m-manylinux1_x86_64.whl (13.0MB)\n",
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            "\u001b[?25hCollecting mock==2.0.0\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/e6/35/f187bdf23be87092bd0f1200d43d23076cee4d0dec109f195173fd3ebc79/mock-2.0.0-py2.py3-none-any.whl (56kB)\n",
            "\u001b[K     |████████████████████████████████| 61kB 6.8MB/s \n",
            "\u001b[?25hCollecting nibabel==2.4.0\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/93/ed/35768f663a361030233a2357de0a482ea46e246af4fc9817dcd5273ee3a7/nibabel-2.4.0-py3-none-any.whl (3.3MB)\n",
            "\u001b[K     |████████████████████████████████| 3.3MB 36.7MB/s \n",
            "\u001b[?25hCollecting numpy==1.16.2\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/35/d5/4f8410ac303e690144f0a0603c4b8fd3b986feb2749c435f7cdbb288f17e/numpy-1.16.2-cp36-cp36m-manylinux1_x86_64.whl (17.3MB)\n",
            "\u001b[K     |████████████████████████████████| 17.3MB 238kB/s \n",
            "\u001b[?25hCollecting opencv-python==4.0.0.21\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/37/49/874d119948a5a084a7ebe98308214098ef3471d76ab74200f9800efeef15/opencv_python-4.0.0.21-cp36-cp36m-manylinux1_x86_64.whl (25.4MB)\n",
            "\u001b[K     |████████████████████████████████| 25.4MB 21.1MB/s \n",
            "\u001b[?25hCollecting pbr==5.1.3\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/14/09/12fe9a14237a6b7e0ba3a8d6fcf254bf4b10ec56a0185f73d651145e9222/pbr-5.1.3-py2.py3-none-any.whl (107kB)\n",
            "\u001b[K     |████████████████████████████████| 112kB 46.2MB/s \n",
            "\u001b[?25hCollecting Pillow==6.0.0\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/d2/c2/f84b1e57416755e967236468dcfb0fad7fd911f707185efc4ba8834a1a94/Pillow-6.0.0-cp36-cp36m-manylinux1_x86_64.whl (2.0MB)\n",
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            "\u001b[?25hCollecting protobuf==3.7.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/5a/aa/a858df367b464f5e9452e1c538aa47754d467023850c00b000287750fa77/protobuf-3.7.1-cp36-cp36m-manylinux1_x86_64.whl (1.2MB)\n",
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            "\u001b[?25hCollecting pydicom==1.2.2\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/43/88/d3c419ab2e753e7651510882a53219373e78fb55294cb247dffd3934ea55/pydicom-1.2.2-py2.py3-none-any.whl (7.0MB)\n",
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            "\u001b[?25hCollecting pyparsing==2.3.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/de/0a/001be530836743d8be6c2d85069f46fecf84ac6c18c7f5fb8125ee11d854/pyparsing-2.3.1-py2.py3-none-any.whl (61kB)\n",
            "\u001b[K     |████████████████████████████████| 71kB 8.5MB/s \n",
            "\u001b[?25hCollecting pypulseq==1.2.0.post1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/78/2a/3cddbd9e9345134d858dfb561248cc00b9d9a5fca3b1fee0a617f24f61c3/pypulseq-1.2.0.post1-py3-none-any.whl (55kB)\n",
            "\u001b[K     |████████████████████████████████| 61kB 7.1MB/s \n",
            "\u001b[?25hCollecting python-dateutil==2.8.0\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl (226kB)\n",
            "\u001b[K     |████████████████████████████████| 235kB 39.0MB/s \n",
            "\u001b[?25hCollecting PyYAML==5.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/9f/2c/9417b5c774792634834e730932745bc09a7d36754ca00acf1ccd1ac2594d/PyYAML-5.1.tar.gz (274kB)\n",
            "\u001b[K     |████████████████████████████████| 276kB 45.5MB/s \n",
            "\u001b[?25hCollecting scipy==1.2.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/7f/5f/c48860704092933bf1c4c1574a8de1ffd16bf4fde8bab190d747598844b2/scipy-1.2.1-cp36-cp36m-manylinux1_x86_64.whl (24.8MB)\n",
            "\u001b[K     |████████████████████████████████| 24.8MB 129kB/s \n",
            "\u001b[?25hCollecting six==1.12.0\n",
            "  Downloading https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl\n",
            "Collecting tensorboard==1.13.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/0f/39/bdd75b08a6fba41f098b6cb091b9e8c7a80e1b4d679a581a0ccd17b10373/tensorboard-1.13.1-py3-none-any.whl (3.2MB)\n",
            "\u001b[K     |████████████████████████████████| 3.2MB 45.0MB/s \n",
            "\u001b[?25hCollecting tensorflow==1.13.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/77/63/a9fa76de8dffe7455304c4ed635be4aa9c0bacef6e0633d87d5f54530c5c/tensorflow-1.13.1-cp36-cp36m-manylinux1_x86_64.whl (92.5MB)\n",
            "\u001b[K     |████████████████████████████████| 92.5MB 55kB/s \n",
            "\u001b[?25hCollecting tensorflow-estimator==1.13.0\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/bb/48/13f49fc3fa0fdf916aa1419013bb8f2ad09674c275b4046d5ee669a46873/tensorflow_estimator-1.13.0-py2.py3-none-any.whl (367kB)\n",
            "\u001b[K     |████████████████████████████████| 368kB 37.1MB/s \n",
            "\u001b[?25hRequirement already satisfied: termcolor==1.1.0 in /usr/local/lib/python3.6/dist-packages (from virtual-scanner==1.0.26) (1.1.0)\n",
            "Collecting Werkzeug==0.15.2\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/18/79/84f02539cc181cdbf5ff5a41b9f52cae870b6f632767e43ba6ac70132e92/Werkzeug-0.15.2-py2.py3-none-any.whl (328kB)\n",
            "\u001b[K     |████████████████████████████████| 337kB 38.5MB/s \n",
            "\u001b[?25hCollecting scikit-image==0.15.0\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/d4/ab/674e168bf7d0bc597218b3bec858d02c23fbac9ec1fec9cad878c6cee95f/scikit_image-0.15.0-cp36-cp36m-manylinux1_x86_64.whl (26.3MB)\n",
            "\u001b[K     |████████████████████████████████| 26.3MB 52.8MB/s \n",
            "\u001b[?25hRequirement already satisfied: setuptools in /usr/local/lib/python3.6/dist-packages (from kiwisolver==1.0.1->virtual-scanner==1.0.26) (49.6.0)\n",
            "Requirement already satisfied: wheel>=0.26; python_version >= \"3\" in /usr/local/lib/python3.6/dist-packages (from tensorboard==1.13.1->virtual-scanner==1.0.26) (0.35.1)\n",
            "Requirement already satisfied: networkx>=2.0 in /usr/local/lib/python3.6/dist-packages (from scikit-image==0.15.0->virtual-scanner==1.0.26) (2.5)\n",
            "Requirement already satisfied: PyWavelets>=0.4.0 in /usr/local/lib/python3.6/dist-packages (from scikit-image==0.15.0->virtual-scanner==1.0.26) (1.1.1)\n",
            "Requirement already satisfied: imageio>=2.0.1 in /usr/local/lib/python3.6/dist-packages (from scikit-image==0.15.0->virtual-scanner==1.0.26) (2.4.1)\n",
            "Requirement already satisfied: decorator>=4.3.0 in /usr/local/lib/python3.6/dist-packages (from networkx>=2.0->scikit-image==0.15.0->virtual-scanner==1.0.26) (4.4.2)\n",
            "Building wheels for collected packages: virtual-scanner, absl-py, gast, PyYAML\n",
            "  Building wheel for virtual-scanner (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for virtual-scanner: filename=virtual_scanner-1.0.26-cp36-none-any.whl size=17243744 sha256=1f0e4ffebe2edde2a83ff6f8b4060fe58d4a6335cbd4aad63cddd028d84707af\n",
            "  Stored in directory: /tmp/pip-ephem-wheel-cache-d3_up173/wheels/fe/da/be/530de1c0e943f2c3b941b1b0567c1942792906d5d1cc0fa8c2\n",
            "  Building wheel for absl-py (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for absl-py: filename=absl_py-0.7.1-cp36-none-any.whl size=117848 sha256=f53097b04b2aa0cf62652f663d5402045fc8e596e6b368719d4307133487cf24\n",
            "  Stored in directory: /root/.cache/pip/wheels/ee/98/38/46cbcc5a93cfea5492d19c38562691ddb23b940176c14f7b48\n",
            "  Building wheel for gast (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for gast: filename=gast-0.2.2-cp36-none-any.whl size=7542 sha256=9e8ef9a612c453debd328c43b46b68c4b7b252d0705d222cdbb9f68fea3ec59b\n",
            "  Stored in directory: /root/.cache/pip/wheels/5c/2e/7e/a1d4d4fcebe6c381f378ce7743a3ced3699feb89bcfbdadadd\n",
            "  Building wheel for PyYAML (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for PyYAML: filename=PyYAML-5.1-cp36-cp36m-linux_x86_64.whl size=44075 sha256=c45218d8f8bb22916fe4d72bf940e7d505cb33ca7e917afc35eb9ec61d328f51\n",
            "  Stored in directory: /root/.cache/pip/wheels/ad/56/bc/1522f864feb2a358ea6f1a92b4798d69ac783a28e80567a18b\n",
            "Successfully built virtual-scanner absl-py gast PyYAML\n",
            "\u001b[31mERROR: umap-learn 0.4.6 has requirement numpy>=1.17, but you'll have numpy 1.16.2 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: umap-learn 0.4.6 has requirement scipy>=1.3.1, but you'll have scipy 1.2.1 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: tensorflow-probability 0.11.0 has requirement gast>=0.3.2, but you'll have gast 0.2.2 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: tensorflow-hub 0.9.0 has requirement protobuf>=3.8.0, but you'll have protobuf 3.7.1 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: plotnine 0.6.0 has requirement matplotlib>=3.1.1, but you'll have matplotlib 3.0.3 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: mizani 0.6.0 has requirement matplotlib>=3.1.1, but you'll have matplotlib 3.0.3 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: google-colab 1.0.0 has requirement six~=1.15.0, but you'll have six 1.12.0 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: datascience 0.10.6 has requirement folium==0.2.1, but you'll have folium 0.8.3 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: albumentations 0.1.12 has requirement imgaug<0.2.7,>=0.2.5, but you'll have imgaug 0.2.9 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: pypulseq 1.2.0.post1 has requirement numpy>=1.16.3, but you'll have numpy 1.16.2 which is incompatible.\u001b[0m\n",
            "Installing collected packages: six, absl-py, astor, Click, Werkzeug, Jinja2, Flask, gast, grpcio, numpy, h5py, Keras-Preprocessing, scipy, Keras-Applications, PyYAML, Keras, kiwisolver, Markdown, pyparsing, python-dateutil, matplotlib, pbr, mock, nibabel, opencv-python, Pillow, protobuf, pydicom, pypulseq, tensorboard, tensorflow-estimator, tensorflow, scikit-image, virtual-scanner\n",
            "  Found existing installation: six 1.15.0\n",
            "    Uninstalling six-1.15.0:\n",
            "      Successfully uninstalled six-1.15.0\n",
            "  Found existing installation: absl-py 0.8.1\n",
            "    Uninstalling absl-py-0.8.1:\n",
            "      Successfully uninstalled absl-py-0.8.1\n",
            "  Found existing installation: astor 0.8.1\n",
            "    Uninstalling astor-0.8.1:\n",
            "      Successfully uninstalled astor-0.8.1\n",
            "  Found existing installation: click 7.1.2\n",
            "    Uninstalling click-7.1.2:\n",
            "      Successfully uninstalled click-7.1.2\n",
            "  Found existing installation: Werkzeug 1.0.1\n",
            "    Uninstalling Werkzeug-1.0.1:\n",
            "      Successfully uninstalled Werkzeug-1.0.1\n",
            "  Found existing installation: Jinja2 2.11.2\n",
            "    Uninstalling Jinja2-2.11.2:\n",
            "      Successfully uninstalled Jinja2-2.11.2\n",
            "  Found existing installation: Flask 1.1.2\n",
            "    Uninstalling Flask-1.1.2:\n",
            "      Successfully uninstalled Flask-1.1.2\n",
            "  Found existing installation: gast 0.3.3\n",
            "    Uninstalling gast-0.3.3:\n",
            "      Successfully uninstalled gast-0.3.3\n",
            "  Found existing installation: grpcio 1.31.0\n",
            "    Uninstalling grpcio-1.31.0:\n",
            "      Successfully uninstalled grpcio-1.31.0\n",
            "  Found existing installation: numpy 1.18.5\n",
            "    Uninstalling numpy-1.18.5:\n",
            "      Successfully uninstalled numpy-1.18.5\n",
            "  Found existing installation: h5py 2.10.0\n",
            "    Uninstalling h5py-2.10.0:\n",
            "      Successfully uninstalled h5py-2.10.0\n",
            "  Found existing installation: Keras-Preprocessing 1.1.2\n",
            "    Uninstalling Keras-Preprocessing-1.1.2:\n",
            "      Successfully uninstalled Keras-Preprocessing-1.1.2\n",
            "  Found existing installation: scipy 1.4.1\n",
            "    Uninstalling scipy-1.4.1:\n",
            "      Successfully uninstalled scipy-1.4.1\n",
            "  Found existing installation: PyYAML 3.13\n",
            "    Uninstalling PyYAML-3.13:\n",
            "      Successfully uninstalled PyYAML-3.13\n",
            "  Found existing installation: Keras 2.4.3\n",
            "    Uninstalling Keras-2.4.3:\n",
            "      Successfully uninstalled Keras-2.4.3\n",
            "  Found existing installation: kiwisolver 1.2.0\n",
            "    Uninstalling kiwisolver-1.2.0:\n",
            "      Successfully uninstalled kiwisolver-1.2.0\n",
            "  Found existing installation: Markdown 3.2.2\n",
            "    Uninstalling Markdown-3.2.2:\n",
            "      Successfully uninstalled Markdown-3.2.2\n",
            "  Found existing installation: pyparsing 2.4.7\n",
            "    Uninstalling pyparsing-2.4.7:\n",
            "      Successfully uninstalled pyparsing-2.4.7\n",
            "  Found existing installation: python-dateutil 2.8.1\n",
            "    Uninstalling python-dateutil-2.8.1:\n",
            "      Successfully uninstalled python-dateutil-2.8.1\n",
            "  Found existing installation: matplotlib 3.2.2\n",
            "    Uninstalling matplotlib-3.2.2:\n",
            "      Successfully uninstalled matplotlib-3.2.2\n",
            "  Found existing installation: nibabel 3.0.2\n",
            "    Uninstalling nibabel-3.0.2:\n",
            "      Successfully uninstalled nibabel-3.0.2\n",
            "  Found existing installation: opencv-python 4.1.2.30\n",
            "    Uninstalling opencv-python-4.1.2.30:\n",
            "      Successfully uninstalled opencv-python-4.1.2.30\n",
            "  Found existing installation: Pillow 7.0.0\n",
            "    Uninstalling Pillow-7.0.0:\n",
            "      Successfully uninstalled Pillow-7.0.0\n",
            "  Found existing installation: protobuf 3.12.4\n",
            "    Uninstalling protobuf-3.12.4:\n",
            "      Successfully uninstalled protobuf-3.12.4\n",
            "  Found existing installation: tensorboard 2.3.0\n",
            "    Uninstalling tensorboard-2.3.0:\n",
            "      Successfully uninstalled tensorboard-2.3.0\n",
            "  Found existing installation: tensorflow-estimator 2.3.0\n",
            "    Uninstalling tensorflow-estimator-2.3.0:\n",
            "      Successfully uninstalled tensorflow-estimator-2.3.0\n",
            "  Found existing installation: tensorflow 2.3.0\n",
            "    Uninstalling tensorflow-2.3.0:\n",
            "      Successfully uninstalled tensorflow-2.3.0\n",
            "  Found existing installation: scikit-image 0.16.2\n",
            "    Uninstalling scikit-image-0.16.2:\n",
            "      Successfully uninstalled scikit-image-0.16.2\n",
            "Successfully installed Click-7.0 Flask-1.0.2 Jinja2-2.10.1 Keras-2.2.4 Keras-Applications-1.0.7 Keras-Preprocessing-1.0.9 Markdown-3.1 Pillow-6.0.0 PyYAML-5.1 Werkzeug-0.15.2 absl-py-0.7.1 astor-0.7.1 gast-0.2.2 grpcio-1.20.0 h5py-2.9.0 kiwisolver-1.0.1 matplotlib-3.0.3 mock-2.0.0 nibabel-2.4.0 numpy-1.16.2 opencv-python-4.0.0.21 pbr-5.1.3 protobuf-3.7.1 pydicom-1.2.2 pyparsing-2.3.1 pypulseq-1.2.0.post1 python-dateutil-2.8.0 scikit-image-0.15.0 scipy-1.2.1 six-1.12.0 tensorboard-1.13.1 tensorflow-1.13.1 tensorflow-estimator-1.13.0 virtual-scanner-1.0.26\n"
          ],
          "name": "stdout"
        },
        {
          "output_type": "display_data",
          "data": {
            "application/vnd.colab-display-data+json": {
              "pip_warning": {
                "packages": [
                  "PIL",
                  "dateutil",
                  "google",
                  "kiwisolver",
                  "matplotlib",
                  "mpl_toolkits",
                  "numpy",
                  "pyparsing",
                  "six"
                ]
              }
            }
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          "metadata": {
            "tags": []
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        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "51im7HLxA57P"
      },
      "source": [
        "Re-install pypulseq (even though it was installed with virtual scanner) to get to the dev branch so that importing works later. "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "_JxDlX3EZDAK",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 925
        },
        "outputId": "33552a1c-e822-4956-d220-1d14a07211d6"
      },
      "source": [
        "# Reinstall pypulseq to dev in order to fix import problem \n",
        "!pip install git+https://github.com/imr-framework/pypulseq.git@dev"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Collecting git+https://github.com/imr-framework/pypulseq.git@dev\n",
            "  Cloning https://github.com/imr-framework/pypulseq.git (to revision dev) to /tmp/pip-req-build-lbrd28wd\n",
            "  Running command git clone -q https://github.com/imr-framework/pypulseq.git /tmp/pip-req-build-lbrd28wd\n",
            "  Running command git checkout -b dev --track origin/dev\n",
            "  Switched to a new branch 'dev'\n",
            "  Branch 'dev' set up to track remote branch 'dev' from 'origin'.\n",
            "Requirement already satisfied: matplotlib>=3.0.3 in /usr/local/lib/python3.6/dist-packages (from pypulseq==1.2.0.post3) (3.0.3)\n",
            "Collecting numpy>=1.16.3\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/b1/9a/7d474ba0860a41f771c9523d8c4ea56b084840b5ca4092d96bdee8a3b684/numpy-1.19.1-cp36-cp36m-manylinux2010_x86_64.whl (14.5MB)\n",
            "\u001b[K     |████████████████████████████████| 14.5MB 316kB/s \n",
            "\u001b[?25hCollecting scipy>=1.4.1\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/2b/a8/f4c66eb529bb252d50e83dbf2909c6502e2f857550f22571ed8556f62d95/scipy-1.5.2-cp36-cp36m-manylinux1_x86_64.whl (25.9MB)\n",
            "\u001b[K     |████████████████████████████████| 25.9MB 1.4MB/s \n",
            "\u001b[?25hRequirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=3.0.3->pypulseq==1.2.0.post3) (0.10.0)\n",
            "Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=3.0.3->pypulseq==1.2.0.post3) (1.0.1)\n",
            "Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=3.0.3->pypulseq==1.2.0.post3) (2.8.0)\n",
            "Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.6/dist-packages (from matplotlib>=3.0.3->pypulseq==1.2.0.post3) (2.3.1)\n",
            "Requirement already satisfied: six in /usr/local/lib/python3.6/dist-packages (from cycler>=0.10->matplotlib>=3.0.3->pypulseq==1.2.0.post3) (1.12.0)\n",
            "Requirement already satisfied: setuptools in /usr/local/lib/python3.6/dist-packages (from kiwisolver>=1.0.1->matplotlib>=3.0.3->pypulseq==1.2.0.post3) (49.6.0)\n",
            "Building wheels for collected packages: pypulseq\n",
            "  Building wheel for pypulseq (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for pypulseq: filename=pypulseq-1.2.0.post3-cp36-none-any.whl size=73258 sha256=06f95944627de2f875a836a6e996503a1bff21be626f89701feb5320049d588f\n",
            "  Stored in directory: /tmp/pip-ephem-wheel-cache-jk476hde/wheels/18/dd/da/be52d6c4f99b9ccc0d8320b3862f73b03cf4e9a51c1299b008\n",
            "Successfully built pypulseq\n",
            "\u001b[31mERROR: virtual-scanner 1.0.26 has requirement numpy==1.16.2, but you'll have numpy 1.19.1 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: virtual-scanner 1.0.26 has requirement pypulseq==1.2.0.post1, but you'll have pypulseq 1.2.0.post3 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: virtual-scanner 1.0.26 has requirement scipy==1.2.1, but you'll have scipy 1.5.2 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: tensorflow-probability 0.11.0 has requirement gast>=0.3.2, but you'll have gast 0.2.2 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: tensorflow-hub 0.9.0 has requirement protobuf>=3.8.0, but you'll have protobuf 3.7.1 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: plotnine 0.6.0 has requirement matplotlib>=3.1.1, but you'll have matplotlib 3.0.3 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: mizani 0.6.0 has requirement matplotlib>=3.1.1, but you'll have matplotlib 3.0.3 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: google-colab 1.0.0 has requirement six~=1.15.0, but you'll have six 1.12.0 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: datascience 0.10.6 has requirement folium==0.2.1, but you'll have folium 0.8.3 which is incompatible.\u001b[0m\n",
            "\u001b[31mERROR: albumentations 0.1.12 has requirement imgaug<0.2.7,>=0.2.5, but you'll have imgaug 0.2.9 which is incompatible.\u001b[0m\n",
            "Installing collected packages: numpy, scipy, pypulseq\n",
            "  Found existing installation: numpy 1.16.2\n",
            "    Uninstalling numpy-1.16.2:\n",
            "      Successfully uninstalled numpy-1.16.2\n",
            "  Found existing installation: scipy 1.2.1\n",
            "    Uninstalling scipy-1.2.1:\n",
            "      Successfully uninstalled scipy-1.2.1\n",
            "  Found existing installation: pypulseq 1.2.0.post1\n",
            "    Uninstalling pypulseq-1.2.0.post1:\n",
            "      Successfully uninstalled pypulseq-1.2.0.post1\n",
            "Successfully installed numpy-1.19.1 pypulseq-1.2.0.post3 scipy-1.5.2\n"
          ],
          "name": "stdout"
        },
        {
          "output_type": "display_data",
          "data": {
            "application/vnd.colab-display-data+json": {
              "pip_warning": {
                "packages": [
                  "numpy"
                ]
              }
            }
          },
          "metadata": {
            "tags": []
          }
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Vg65dHO5BHtO"
      },
      "source": [
        "## Import necessary code for this demo "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "1Egi0RiPWceG"
      },
      "source": [
        "# Import modules \n",
        "\n",
        "from pypulseq.Sequence.sequence import Sequence\n",
        "from virtualscanner.server.simulation.py2jemris.coil2xml import coil2xml\n",
        "from virtualscanner.server.simulation.py2jemris.seq2xml import seq2xml\n",
        "from virtualscanner.server.simulation.py2jemris.sim_jemris import sim_jemris\n",
        "from virtualscanner.server.simulation.py2jemris.pulseq_jemris_simulator import simulate_pulseq_jemris, create_and_save_phantom\n",
        "from virtualscanner.server.simulation.py2jemris.recon_jemris import recon_jemris\n",
        "from virtualscanner.server.simulation.py2jemris.sim2xml import sim2xml \n",
        "import virtualscanner.server.simulation.bloch.phantom as pht\n",
        "from virtualscanner.server.simulation.bloch.pulseq_library import make_pulseq_irse, make_pulseq_se_oblique\n",
        "import numpy as np\n",
        "import matplotlib.pyplot as plt\n",
        "from scipy.io import loadmat, savemat\n",
        "from virtualscanner.utils.constants import SERVER_SIM_BLOCH_PY2JEMRIS_PATH\n",
        "import os\n",
        "import h5py\n"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "PNFBaXHLWnDv"
      },
      "source": [
        "## Set output paths "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "wL9BngTQWlf9"
      },
      "source": [
        "utest_path =  'sim/utest_outputs'\n",
        "sim_path = 'sim'"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "QO1kiOfUbBl4",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 53
        },
        "outputId": "b4af6b48-2da3-428f-e315-ff9a46c44bd4"
      },
      "source": [
        "# Make directory for storing outputs \n",
        "%cd /content \n",
        "!mkdir sim/utest_outputs -p \n",
        "!mkdir sim/custom -p \n",
        "!pwd"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/content\n",
            "/content\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "5vaB22C8WqJh"
      },
      "source": [
        "## Demo 1: Test coil2xml and visualize "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "OxF1fLjSW7Jh",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 326
        },
        "outputId": "43638500-421c-47e2-9043-fe85bf374cbe"
      },
      "source": [
        "# Always go back to content folder first \n",
        "%cd /content\n",
        "\n",
        "!pwd\n",
        " # Example on using coil2xml\n",
        "# Generate coil using B1 maps and plot\n",
        "# 4 channels with different B1 maps\n",
        "\n",
        "b1 = np.ones((32,32))\n",
        "XY = np.meshgrid(np.linspace(0,1,32), np.linspace(0,1,32))\n",
        "X = XY[0]\n",
        "Y = XY[1]\n",
        "\n",
        "# Define coil sensitivity maps (complex arrays, in general)\n",
        "b1_ch1 = np.sqrt(X**2 + Y**2)\n",
        "b1_ch2 = np.rot90(b1_ch1)\n",
        "b1_ch3 = np.rot90(b1_ch2)\n",
        "b1_ch4 = np.rot90(b1_ch3)\n",
        "\n",
        "coil2xml(b1maps=[b1_ch1, b1_ch2, b1_ch3, b1_ch4], fov=200, name='test_coil', out_folder=utest_path)\n",
        "\n",
        "# Generate sensmaps.h5 using JEMRIS command\n",
        "\n",
        "%cd sim/utest_outputs\n",
        "out = os.system('jemris test_coil.xml') # Run jemris to create h5 sensitivity maps \n",
        "print(out)\n",
        "\n",
        "# Load sensmaps.h5 and plot coil\n",
        "a = h5py.File('sensmaps.h5', 'r')\n",
        "maps_magnitude = a['maps/magnitude']\n",
        "maps_phase = a['maps/phase']\n",
        "plt.figure(1)\n",
        "plt.title('Coil sensitivity maps')\n",
        "for u in range(4):\n",
        "    plt.subplot(2,4,u+1)\n",
        "    plt.gray()\n",
        "    plt.imshow(maps_magnitude[f'0{u}'])\n",
        "    plt.title(f'Magnitude Ch #{u+1}')\n",
        "    plt.subplot(2,4,u+5)\n",
        "    plt.gray()\n",
        "    plt.imshow(maps_phase[f'0{u}'])\n",
        "    plt.title(f'Phase Ch #{u+1}')\n",
        "plt.show()\n",
        "\n"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/content\n",
            "/content\n",
            "/content/sim/utest_outputs\n",
            "0\n"
          ],
          "name": "stdout"
        },
        {
          "output_type": "display_data",
          "data": {
            "image/png": "[encoded data, 23236 characters]\n",
            "text/plain": [
              "<Figure size 432x288 with 8 Axes>"
            ]
          },
          "metadata": {
            "tags": [],
            "needs_background": "light"
          }
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "35fWjPhDIniV"
      },
      "source": [
        "## Demo 2: Seq2xml  \n",
        "In this section, a pulseq sequence is generate from the Virtual Scanner sequence library and converted to a set of files that together make up a JEMRIS sequence:\n",
        "- An (.xml) file that records the sequence structure and most high-level data\n",
        "- An arbitrary number of (.h5) files that store (1) all unique RF pulses; (2) any unique non-trapezoid gradients"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "68yWH1rXXRZx",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 106
        },
        "outputId": "139ee462-b17b-423a-c7be-b6aac6b4911b"
      },
      "source": [
        "%cd /content \n",
        "# Seq2xml test \n",
        "# Make a sequence\n",
        "seq = make_pulseq_irse(fov=0.256, n=16, thk=0.01, fa=15, tr=150, te=30, ti=10,\n",
        "                        enc='xyz', slice_locs=None, write=False)\n",
        "\n",
        "# Convert to .xml format\n",
        "seq2xml(seq, seq_name='irse16_pulseq', out_folder=utest_path)\n",
        "\n",
        "# Use JEMRIS to generate sequence diagrams from .xml sequence\n",
        "os.chdir(utest_path)\n",
        "print(os.system('dir'))\n"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/content\n",
            "dur rf 0.00213 dur gss: 0.00214\n",
            "IRSE sequence constructed\n",
            "{}\n",
            "0\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "dFRhs6E0cyD7",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "outputId": "a22aee9e-e8fb-436a-c5d9-83d4b4388234"
      },
      "source": [
        "!jemris -x -d id=1 -f irse16_pulseq irse16_pulseq.xml\n",
        "#out = os.system(f'jemris -x -d id=1 -f irse16_pulseq irse16_pulseq.xml')\n",
        "#print(out)"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "\n",
            "jemris 2.8.3 (3ce3164b704394c4c1a8a3746b3ddc1296727458)\n",
            "\n",
            "dump of sequence tree\n",
            "                        TYPE              CLASS        NAME  duration      ADCs     TPOIs |  module specific\n",
            "                        ----------------------------------------------------------------- |  ---------------\n",
            "sequence-root------>   CONCAT       CONCATSEQUENCEConcatSequence2560000.160      256     98208  |  Repetitions = 1\n",
            "  |_ child 1   ---->     ATOM       ATOMICSEQUENCE       C1     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE       R1     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       G1     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 2   ---->     ATOM       ATOMICSEQUENCE       C2     0.000        0         0  | \n",
            "  |_ child 3   ---->     ATOM  DELAYATOMICSEQUENCE       D1  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE    eP_D1  9997.870        0         2  |  Axis = none \n",
            "  |_ child 4   ---->     ATOM       ATOMICSEQUENCE       C3     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE       R2     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       G2     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 5   ---->     ATOM       ATOMICSEQUENCE       C4     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE       G3     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       G4     2.000        0         4  |  Axis = GY  , Area = -0.19635 , FlatTop: (Area,time)= (-0.195363,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE       G5     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 6   ---->     ATOM       ATOMICSEQUENCE       C5     0.000        0         0  | \n",
            "  |_ child 7   ---->     ATOM  DELAYATOMICSEQUENCE       D2 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE    eP_D2 14995.860        0         2  |  Axis = none \n",
            "  |_ child 8   ---->     ATOM       ATOMICSEQUENCE       C6     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE       R3     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       G6     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 9   ---->     ATOM       ATOMICSEQUENCE       C7     0.000        0         0  | \n",
            "  |_ child 10   ---->     ATOM  DELAYATOMICSEQUENCE       D3 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE    eP_D3 14995.720        0         2  |  Axis = none \n",
            "  |_ child 11   ---->     ATOM       ATOMICSEQUENCE       C8     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE       G7     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       S1     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 12   ---->     ATOM       ATOMICSEQUENCE       C9     0.000        0         0  | \n",
            "  |_ child 13   ---->     ATOM  DELAYATOMICSEQUENCE       D4119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE    eP_D4119995.720        0         2  |  Axis = none \n",
            "  |_ child 14   ---->     ATOM       ATOMICSEQUENCE      C10     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE       R4     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       G8     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 15   ---->     ATOM       ATOMICSEQUENCE      C11     0.000        0         0  | \n",
            "  |_ child 16   ---->     ATOM  DELAYATOMICSEQUENCE       D5  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE    eP_D5  9997.870        0         2  |  Axis = none \n",
            "  |_ child 17   ---->     ATOM       ATOMICSEQUENCE      C12     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE       R5     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       G9     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 18   ---->     ATOM       ATOMICSEQUENCE      C13     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G10     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G11     2.000        0         4  |  Axis = GY  , Area = -0.171806 , FlatTop: (Area,time)= (-0.170943,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G12     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 19   ---->     ATOM       ATOMICSEQUENCE      C14     0.000        0         0  | \n",
            "  |_ child 20   ---->     ATOM  DELAYATOMICSEQUENCE       D6 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE    eP_D6 14995.860        0         2  |  Axis = none \n",
            "  |_ child 21   ---->     ATOM       ATOMICSEQUENCE      C15     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE       R6     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G13     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 22   ---->     ATOM       ATOMICSEQUENCE      C16     0.000        0         0  | \n",
            "  |_ child 23   ---->     ATOM  DELAYATOMICSEQUENCE       D7 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE    eP_D7 14995.720        0         2  |  Axis = none \n",
            "  |_ child 24   ---->     ATOM       ATOMICSEQUENCE      C17     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G14     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       S2     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 25   ---->     ATOM       ATOMICSEQUENCE      C18     0.000        0         0  | \n",
            "  |_ child 26   ---->     ATOM  DELAYATOMICSEQUENCE       D8119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE    eP_D8119995.720        0         2  |  Axis = none \n",
            "  |_ child 27   ---->     ATOM       ATOMICSEQUENCE      C19     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE       R7     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G15     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 28   ---->     ATOM       ATOMICSEQUENCE      C20     0.000        0         0  | \n",
            "  |_ child 29   ---->     ATOM  DELAYATOMICSEQUENCE       D9  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE    eP_D9  9997.870        0         2  |  Axis = none \n",
            "  |_ child 30   ---->     ATOM       ATOMICSEQUENCE      C21     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE       R8     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G16     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 31   ---->     ATOM       ATOMICSEQUENCE      C22     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G17     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G18     2.000        0         4  |  Axis = GY  , Area = -0.147262 , FlatTop: (Area,time)= (-0.146522,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G19     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 32   ---->     ATOM       ATOMICSEQUENCE      C23     0.000        0         0  | \n",
            "  |_ child 33   ---->     ATOM  DELAYATOMICSEQUENCE      D10 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D10 14995.860        0         2  |  Axis = none \n",
            "  |_ child 34   ---->     ATOM       ATOMICSEQUENCE      C24     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE       R9     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G20     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 35   ---->     ATOM       ATOMICSEQUENCE      C25     0.000        0         0  | \n",
            "  |_ child 36   ---->     ATOM  DELAYATOMICSEQUENCE      D11 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D11 14995.720        0         2  |  Axis = none \n",
            "  |_ child 37   ---->     ATOM       ATOMICSEQUENCE      C26     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G21     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       S3     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 38   ---->     ATOM       ATOMICSEQUENCE      C27     0.000        0         0  | \n",
            "  |_ child 39   ---->     ATOM  DELAYATOMICSEQUENCE      D12119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D12119995.720        0         2  |  Axis = none \n",
            "  |_ child 40   ---->     ATOM       ATOMICSEQUENCE      C28     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R10     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G22     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 41   ---->     ATOM       ATOMICSEQUENCE      C29     0.000        0         0  | \n",
            "  |_ child 42   ---->     ATOM  DELAYATOMICSEQUENCE      D13  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D13  9997.870        0         2  |  Axis = none \n",
            "  |_ child 43   ---->     ATOM       ATOMICSEQUENCE      C30     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R11     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G23     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 44   ---->     ATOM       ATOMICSEQUENCE      C31     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G24     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G25     2.000        0         4  |  Axis = GY  , Area = -0.122718 , FlatTop: (Area,time)= (-0.122102,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G26     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 45   ---->     ATOM       ATOMICSEQUENCE      C32     0.000        0         0  | \n",
            "  |_ child 46   ---->     ATOM  DELAYATOMICSEQUENCE      D14 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D14 14995.860        0         2  |  Axis = none \n",
            "  |_ child 47   ---->     ATOM       ATOMICSEQUENCE      C33     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R12     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G27     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 48   ---->     ATOM       ATOMICSEQUENCE      C34     0.000        0         0  | \n",
            "  |_ child 49   ---->     ATOM  DELAYATOMICSEQUENCE      D15 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D15 14995.720        0         2  |  Axis = none \n",
            "  |_ child 50   ---->     ATOM       ATOMICSEQUENCE      C35     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G28     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       S4     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 51   ---->     ATOM       ATOMICSEQUENCE      C36     0.000        0         0  | \n",
            "  |_ child 52   ---->     ATOM  DELAYATOMICSEQUENCE      D16119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D16119995.720        0         2  |  Axis = none \n",
            "  |_ child 53   ---->     ATOM       ATOMICSEQUENCE      C37     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R13     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G29     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 54   ---->     ATOM       ATOMICSEQUENCE      C38     0.000        0         0  | \n",
            "  |_ child 55   ---->     ATOM  DELAYATOMICSEQUENCE      D17  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D17  9997.870        0         2  |  Axis = none \n",
            "  |_ child 56   ---->     ATOM       ATOMICSEQUENCE      C39     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R14     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G30     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 57   ---->     ATOM       ATOMICSEQUENCE      C40     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G31     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G32     2.000        0         4  |  Axis = GY  , Area = -0.0981748 , FlatTop: (Area,time)= (-0.0976814,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G33     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 58   ---->     ATOM       ATOMICSEQUENCE      C41     0.000        0         0  | \n",
            "  |_ child 59   ---->     ATOM  DELAYATOMICSEQUENCE      D18 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D18 14995.860        0         2  |  Axis = none \n",
            "  |_ child 60   ---->     ATOM       ATOMICSEQUENCE      C42     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R15     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G34     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 61   ---->     ATOM       ATOMICSEQUENCE      C43     0.000        0         0  | \n",
            "  |_ child 62   ---->     ATOM  DELAYATOMICSEQUENCE      D19 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D19 14995.720        0         2  |  Axis = none \n",
            "  |_ child 63   ---->     ATOM       ATOMICSEQUENCE      C44     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G35     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       S5     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 64   ---->     ATOM       ATOMICSEQUENCE      C45     0.000        0         0  | \n",
            "  |_ child 65   ---->     ATOM  DELAYATOMICSEQUENCE      D20119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D20119995.720        0         2  |  Axis = none \n",
            "  |_ child 66   ---->     ATOM       ATOMICSEQUENCE      C46     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R16     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G36     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 67   ---->     ATOM       ATOMICSEQUENCE      C47     0.000        0         0  | \n",
            "  |_ child 68   ---->     ATOM  DELAYATOMICSEQUENCE      D21  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D21  9997.870        0         2  |  Axis = none \n",
            "  |_ child 69   ---->     ATOM       ATOMICSEQUENCE      C48     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R17     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G37     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 70   ---->     ATOM       ATOMICSEQUENCE      C49     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G38     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G39     2.000        0         4  |  Axis = GY  , Area = -0.0736311 , FlatTop: (Area,time)= (-0.0732611,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G40     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 71   ---->     ATOM       ATOMICSEQUENCE      C50     0.000        0         0  | \n",
            "  |_ child 72   ---->     ATOM  DELAYATOMICSEQUENCE      D22 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D22 14995.860        0         2  |  Axis = none \n",
            "  |_ child 73   ---->     ATOM       ATOMICSEQUENCE      C51     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R18     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G41     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 74   ---->     ATOM       ATOMICSEQUENCE      C52     0.000        0         0  | \n",
            "  |_ child 75   ---->     ATOM  DELAYATOMICSEQUENCE      D23 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D23 14995.720        0         2  |  Axis = none \n",
            "  |_ child 76   ---->     ATOM       ATOMICSEQUENCE      C53     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G42     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       S6     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 77   ---->     ATOM       ATOMICSEQUENCE      C54     0.000        0         0  | \n",
            "  |_ child 78   ---->     ATOM  DELAYATOMICSEQUENCE      D24119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D24119995.720        0         2  |  Axis = none \n",
            "  |_ child 79   ---->     ATOM       ATOMICSEQUENCE      C55     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R19     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G43     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 80   ---->     ATOM       ATOMICSEQUENCE      C56     0.000        0         0  | \n",
            "  |_ child 81   ---->     ATOM  DELAYATOMICSEQUENCE      D25  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D25  9997.870        0         2  |  Axis = none \n",
            "  |_ child 82   ---->     ATOM       ATOMICSEQUENCE      C57     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R20     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G44     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 83   ---->     ATOM       ATOMICSEQUENCE      C58     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G45     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G46     2.000        0         4  |  Axis = GY  , Area = -0.0490874 , FlatTop: (Area,time)= (-0.0488407,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G47     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 84   ---->     ATOM       ATOMICSEQUENCE      C59     0.000        0         0  | \n",
            "  |_ child 85   ---->     ATOM  DELAYATOMICSEQUENCE      D26 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D26 14995.860        0         2  |  Axis = none \n",
            "  |_ child 86   ---->     ATOM       ATOMICSEQUENCE      C60     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R21     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G48     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 87   ---->     ATOM       ATOMICSEQUENCE      C61     0.000        0         0  | \n",
            "  |_ child 88   ---->     ATOM  DELAYATOMICSEQUENCE      D27 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D27 14995.720        0         2  |  Axis = none \n",
            "  |_ child 89   ---->     ATOM       ATOMICSEQUENCE      C62     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G49     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       S7     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 90   ---->     ATOM       ATOMICSEQUENCE      C63     0.000        0         0  | \n",
            "  |_ child 91   ---->     ATOM  DELAYATOMICSEQUENCE      D28119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D28119995.720        0         2  |  Axis = none \n",
            "  |_ child 92   ---->     ATOM       ATOMICSEQUENCE      C64     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R22     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G50     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 93   ---->     ATOM       ATOMICSEQUENCE      C65     0.000        0         0  | \n",
            "  |_ child 94   ---->     ATOM  DELAYATOMICSEQUENCE      D29  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D29  9997.870        0         2  |  Axis = none \n",
            "  |_ child 95   ---->     ATOM       ATOMICSEQUENCE      C66     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R23     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G51     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 96   ---->     ATOM       ATOMICSEQUENCE      C67     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G52     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G53     2.000        0         4  |  Axis = GY  , Area = -0.0245437 , FlatTop: (Area,time)= (-0.0244204,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G54     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 97   ---->     ATOM       ATOMICSEQUENCE      C68     0.000        0         0  | \n",
            "  |_ child 98   ---->     ATOM  DELAYATOMICSEQUENCE      D30 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D30 14995.860        0         2  |  Axis = none \n",
            "  |_ child 99   ---->     ATOM       ATOMICSEQUENCE      C69     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R24     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G55     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 100   ---->     ATOM       ATOMICSEQUENCE      C70     0.000        0         0  | \n",
            "  |_ child 101   ---->     ATOM  DELAYATOMICSEQUENCE      D31 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D31 14995.720        0         2  |  Axis = none \n",
            "  |_ child 102   ---->     ATOM       ATOMICSEQUENCE      C71     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G56     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       S8     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 103   ---->     ATOM       ATOMICSEQUENCE      C72     0.000        0         0  | \n",
            "  |_ child 104   ---->     ATOM  DELAYATOMICSEQUENCE      D32119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D32119995.720        0         2  |  Axis = none \n",
            "  |_ child 105   ---->     ATOM       ATOMICSEQUENCE      C73     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R25     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G57     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 106   ---->     ATOM       ATOMICSEQUENCE      C74     0.000        0         0  | \n",
            "  |_ child 107   ---->     ATOM  DELAYATOMICSEQUENCE      D33  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D33  9997.870        0         2  |  Axis = none \n",
            "  |_ child 108   ---->     ATOM       ATOMICSEQUENCE      C75     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R26     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G58     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 109   ---->     ATOM       ATOMICSEQUENCE      C76     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G59     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G60     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 110   ---->     ATOM       ATOMICSEQUENCE      C77     0.000        0         0  | \n",
            "  |_ child 111   ---->     ATOM  DELAYATOMICSEQUENCE      D34 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D34 14995.860        0         2  |  Axis = none \n",
            "  |_ child 112   ---->     ATOM       ATOMICSEQUENCE      C78     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R27     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G61     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 113   ---->     ATOM       ATOMICSEQUENCE      C79     0.000        0         0  | \n",
            "  |_ child 114   ---->     ATOM  DELAYATOMICSEQUENCE      D35 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D35 14995.720        0         2  |  Axis = none \n",
            "  |_ child 115   ---->     ATOM       ATOMICSEQUENCE      C80     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G62     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE       S9     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 116   ---->     ATOM       ATOMICSEQUENCE      C81     0.000        0         0  | \n",
            "  |_ child 117   ---->     ATOM  DELAYATOMICSEQUENCE      D36119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D36119995.720        0         2  |  Axis = none \n",
            "  |_ child 118   ---->     ATOM       ATOMICSEQUENCE      C82     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R28     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G63     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 119   ---->     ATOM       ATOMICSEQUENCE      C83     0.000        0         0  | \n",
            "  |_ child 120   ---->     ATOM  DELAYATOMICSEQUENCE      D37  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D37  9997.870        0         2  |  Axis = none \n",
            "  |_ child 121   ---->     ATOM       ATOMICSEQUENCE      C84     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R29     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G64     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 122   ---->     ATOM       ATOMICSEQUENCE      C85     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G65     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G66     2.000        0         4  |  Axis = GY  , Area = 0.0245437 , FlatTop: (Area,time)= (0.0244204,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G67     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 123   ---->     ATOM       ATOMICSEQUENCE      C86     0.000        0         0  | \n",
            "  |_ child 124   ---->     ATOM  DELAYATOMICSEQUENCE      D38 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D38 14995.860        0         2  |  Axis = none \n",
            "  |_ child 125   ---->     ATOM       ATOMICSEQUENCE      C87     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R30     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G68     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 126   ---->     ATOM       ATOMICSEQUENCE      C88     0.000        0         0  | \n",
            "  |_ child 127   ---->     ATOM  DELAYATOMICSEQUENCE      D39 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D39 14995.720        0         2  |  Axis = none \n",
            "  |_ child 128   ---->     ATOM       ATOMICSEQUENCE      C89     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G69     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      S10     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 129   ---->     ATOM       ATOMICSEQUENCE      C90     0.000        0         0  | \n",
            "  |_ child 130   ---->     ATOM  DELAYATOMICSEQUENCE      D40119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D40119995.720        0         2  |  Axis = none \n",
            "  |_ child 131   ---->     ATOM       ATOMICSEQUENCE      C91     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R31     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G70     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 132   ---->     ATOM       ATOMICSEQUENCE      C92     0.000        0         0  | \n",
            "  |_ child 133   ---->     ATOM  DELAYATOMICSEQUENCE      D41  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D41  9997.870        0         2  |  Axis = none \n",
            "  |_ child 134   ---->     ATOM       ATOMICSEQUENCE      C93     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R32     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G71     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 135   ---->     ATOM       ATOMICSEQUENCE      C94     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G72     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G73     2.000        0         4  |  Axis = GY  , Area = 0.0490874 , FlatTop: (Area,time)= (0.0488407,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G74     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 136   ---->     ATOM       ATOMICSEQUENCE      C95     0.000        0         0  | \n",
            "  |_ child 137   ---->     ATOM  DELAYATOMICSEQUENCE      D42 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D42 14995.860        0         2  |  Axis = none \n",
            "  |_ child 138   ---->     ATOM       ATOMICSEQUENCE      C96     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R33     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G75     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 139   ---->     ATOM       ATOMICSEQUENCE      C97     0.000        0         0  | \n",
            "  |_ child 140   ---->     ATOM  DELAYATOMICSEQUENCE      D43 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D43 14995.720        0         2  |  Axis = none \n",
            "  |_ child 141   ---->     ATOM       ATOMICSEQUENCE      C98     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G76     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      S11     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 142   ---->     ATOM       ATOMICSEQUENCE      C99     0.000        0         0  | \n",
            "  |_ child 143   ---->     ATOM  DELAYATOMICSEQUENCE      D44119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D44119995.720        0         2  |  Axis = none \n",
            "  |_ child 144   ---->     ATOM       ATOMICSEQUENCE     C100     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R34     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G77     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 145   ---->     ATOM       ATOMICSEQUENCE     C101     0.000        0         0  | \n",
            "  |_ child 146   ---->     ATOM  DELAYATOMICSEQUENCE      D45  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D45  9997.870        0         2  |  Axis = none \n",
            "  |_ child 147   ---->     ATOM       ATOMICSEQUENCE     C102     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R35     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G78     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 148   ---->     ATOM       ATOMICSEQUENCE     C103     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G79     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G80     2.000        0         4  |  Axis = GY  , Area = 0.0736311 , FlatTop: (Area,time)= (0.0732611,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G81     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 149   ---->     ATOM       ATOMICSEQUENCE     C104     0.000        0         0  | \n",
            "  |_ child 150   ---->     ATOM  DELAYATOMICSEQUENCE      D46 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D46 14995.860        0         2  |  Axis = none \n",
            "  |_ child 151   ---->     ATOM       ATOMICSEQUENCE     C105     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R36     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G82     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 152   ---->     ATOM       ATOMICSEQUENCE     C106     0.000        0         0  | \n",
            "  |_ child 153   ---->     ATOM  DELAYATOMICSEQUENCE      D47 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D47 14995.720        0         2  |  Axis = none \n",
            "  |_ child 154   ---->     ATOM       ATOMICSEQUENCE     C107     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G83     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      S12     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 155   ---->     ATOM       ATOMICSEQUENCE     C108     0.000        0         0  | \n",
            "  |_ child 156   ---->     ATOM  DELAYATOMICSEQUENCE      D48119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D48119995.720        0         2  |  Axis = none \n",
            "  |_ child 157   ---->     ATOM       ATOMICSEQUENCE     C109     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R37     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G84     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 158   ---->     ATOM       ATOMICSEQUENCE     C110     0.000        0         0  | \n",
            "  |_ child 159   ---->     ATOM  DELAYATOMICSEQUENCE      D49  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D49  9997.870        0         2  |  Axis = none \n",
            "  |_ child 160   ---->     ATOM       ATOMICSEQUENCE     C111     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R38     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G85     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 161   ---->     ATOM       ATOMICSEQUENCE     C112     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G86     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G87     2.000        0         4  |  Axis = GY  , Area = 0.0981748 , FlatTop: (Area,time)= (0.0976814,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G88     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 162   ---->     ATOM       ATOMICSEQUENCE     C113     0.000        0         0  | \n",
            "  |_ child 163   ---->     ATOM  DELAYATOMICSEQUENCE      D50 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D50 14995.860        0         2  |  Axis = none \n",
            "  |_ child 164   ---->     ATOM       ATOMICSEQUENCE     C114     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R39     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G89     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 165   ---->     ATOM       ATOMICSEQUENCE     C115     0.000        0         0  | \n",
            "  |_ child 166   ---->     ATOM  DELAYATOMICSEQUENCE      D51 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D51 14995.720        0         2  |  Axis = none \n",
            "  |_ child 167   ---->     ATOM       ATOMICSEQUENCE     C116     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G90     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      S13     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 168   ---->     ATOM       ATOMICSEQUENCE     C117     0.000        0         0  | \n",
            "  |_ child 169   ---->     ATOM  DELAYATOMICSEQUENCE      D52119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D52119995.720        0         2  |  Axis = none \n",
            "  |_ child 170   ---->     ATOM       ATOMICSEQUENCE     C118     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R40     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G91     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 171   ---->     ATOM       ATOMICSEQUENCE     C119     0.000        0         0  | \n",
            "  |_ child 172   ---->     ATOM  DELAYATOMICSEQUENCE      D53  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D53  9997.870        0         2  |  Axis = none \n",
            "  |_ child 173   ---->     ATOM       ATOMICSEQUENCE     C120     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R41     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G92     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 174   ---->     ATOM       ATOMICSEQUENCE     C121     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G93     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G94     2.000        0         4  |  Axis = GY  , Area = 0.122718 , FlatTop: (Area,time)= (0.122102,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE      G95     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 175   ---->     ATOM       ATOMICSEQUENCE     C122     0.000        0         0  | \n",
            "  |_ child 176   ---->     ATOM  DELAYATOMICSEQUENCE      D54 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D54 14995.860        0         2  |  Axis = none \n",
            "  |_ child 177   ---->     ATOM       ATOMICSEQUENCE     C123     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R42     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G96     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 178   ---->     ATOM       ATOMICSEQUENCE     C124     0.000        0         0  | \n",
            "  |_ child 179   ---->     ATOM  DELAYATOMICSEQUENCE      D55 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D55 14995.720        0         2  |  Axis = none \n",
            "  |_ child 180   ---->     ATOM       ATOMICSEQUENCE     C125     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE      G97     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      S14     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 181   ---->     ATOM       ATOMICSEQUENCE     C126     0.000        0         0  | \n",
            "  |_ child 182   ---->     ATOM  DELAYATOMICSEQUENCE      D56119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D56119995.720        0         2  |  Axis = none \n",
            "  |_ child 183   ---->     ATOM       ATOMICSEQUENCE     C127     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R43     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G98     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 184   ---->     ATOM       ATOMICSEQUENCE     C128     0.000        0         0  | \n",
            "  |_ child 185   ---->     ATOM  DELAYATOMICSEQUENCE      D57  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D57  9997.870        0         2  |  Axis = none \n",
            "  |_ child 186   ---->     ATOM       ATOMICSEQUENCE     C129     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R44     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      G99     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 187   ---->     ATOM       ATOMICSEQUENCE     C130     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE     G100     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE     G101     2.000        0         4  |  Axis = GY  , Area = 0.147262 , FlatTop: (Area,time)= (0.146522,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE     G102     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 188   ---->     ATOM       ATOMICSEQUENCE     C131     0.000        0         0  | \n",
            "  |_ child 189   ---->     ATOM  DELAYATOMICSEQUENCE      D58 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D58 14995.860        0         2  |  Axis = none \n",
            "  |_ child 190   ---->     ATOM       ATOMICSEQUENCE     C132     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R45     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE     G103     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 191   ---->     ATOM       ATOMICSEQUENCE     C133     0.000        0         0  | \n",
            "  |_ child 192   ---->     ATOM  DELAYATOMICSEQUENCE      D59 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D59 14995.720        0         2  |  Axis = none \n",
            "  |_ child 193   ---->     ATOM       ATOMICSEQUENCE     C134     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE     G104     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      S15     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 194   ---->     ATOM       ATOMICSEQUENCE     C135     0.000        0         0  | \n",
            "  |_ child 195   ---->     ATOM  DELAYATOMICSEQUENCE      D60119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D60119995.720        0         2  |  Axis = none \n",
            "  |_ child 196   ---->     ATOM       ATOMICSEQUENCE     C136     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R46     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE     G105     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 197   ---->     ATOM       ATOMICSEQUENCE     C137     0.000        0         0  | \n",
            "  |_ child 198   ---->     ATOM  DELAYATOMICSEQUENCE      D61  9997.870        0         2  |  DelayType = B2E  , Delay = 9997.87\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D61  9997.870        0         2  |  Axis = none \n",
            "  |_ child 199   ---->     ATOM       ATOMICSEQUENCE     C138     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R47     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_2.h5,0.288128,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE     G106     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 200   ---->     ATOM       ATOMICSEQUENCE     C139     2.000        0         6  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE     G107     2.000        0         4  |  Axis = GX  , Area = 0.196656 , FlatTop: (Area,time)= (0.195668,1.98)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE     G108     2.000        0         4  |  Axis = GY  , Area = 0.171806 , FlatTop: (Area,time)= (0.170943,1.98)\n",
            "    |_ child 3   -->    PULSE        TRAPGRADPULSE     G109     2.000        0         4  |  Axis = GZ  , Area = -1.28177 , FlatTop: (Area,time)= (-1.26882,1.96)\n",
            "  |_ child 201   ---->     ATOM       ATOMICSEQUENCE     C140     0.000        0         0  | \n",
            "  |_ child 202   ---->     ATOM  DELAYATOMICSEQUENCE      D62 14995.860        0         2  |  DelayType = B2E  , Delay = 14995.9\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D62 14995.860        0         2  |  Axis = none \n",
            "  |_ child 203   ---->     ATOM       ATOMICSEQUENCE     C141     2.140        0      2034  | \n",
            "    |_ child 1   -->    PULSE      EXTERNALRFPULSE      R48     2.029        0      2032  |  Axis = RF  , InitDelay = 0.1 , (Flipangle,Phase,Bandwidth,Channel,Symmetry) = (0,0,1e+16,0,0.5)  , (Filename,Energy,TPOIs) = (rf_1.h5,3.45753,2032)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE     G110     2.080        0         4  |  Axis = GZ  , InitDelay = 0.06 , Area = 2.56354 , FlatTop: (Area,time)= (2.51327,2)\n",
            "  |_ child 204   ---->     ATOM       ATOMICSEQUENCE     C142     0.000        0         0  | \n",
            "  |_ child 205   ---->     ATOM  DELAYATOMICSEQUENCE      D63 14995.720        0         2  |  DelayType = B2E  , Delay = 14995.7\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D63 14995.720        0         2  |  Axis = none \n",
            "  |_ child 206   ---->     ATOM       ATOMICSEQUENCE     C143     6.420       16        22  | \n",
            "    |_ child 1   -->    PULSE        TRAPGRADPULSE     G111     6.420        0         4  |  Axis = GX  , Area = 0.393313 , FlatTop: (Area,time)= (0.392699,6.4)\n",
            "    |_ child 2   -->    PULSE        TRAPGRADPULSE      S16     6.400       16        20  |  Axis = GX  , InitDelay = 0.02 , Area = 0 , FlatTop: (Area,time)= (0,6.4)\n",
            "  |_ child 207   ---->     ATOM       ATOMICSEQUENCE     C144     0.000        0         0  | \n",
            "  |_ child 208   ---->     ATOM  DELAYATOMICSEQUENCE      D64119995.720        0         2  |  DelayType = B2E  , Delay = 119996\n",
            "    |_ child 1   -->    PULSE           EMPTYPULSE   eP_D64119995.720        0         2  |  Axis = none \n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "e8awrRCaIiNo"
      },
      "source": [
        "Plot the resulting waveforms, as interpreted and generated by JEMRIS: "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "MDqodOQbIOIh",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 295
        },
        "outputId": "e6227943-ea8d-4618-df32-6e1fc847580f"
      },
      "source": [
        "# Read sequence diagram and plot\n",
        "data = h5py.File('irse16_pulseq.h5','r')\n",
        "diag = data['seqdiag']\n",
        "\n",
        "t = diag['T']\n",
        "gx = diag['GX']\n",
        "gy = diag['GY']\n",
        "gz = diag['GZ']\n",
        "rxp = diag['RXP']\n",
        "txm = diag['TXM']\n",
        "txp = diag['TXP']\n",
        "\n",
        "ylist = [txm, txp, gx, gy, gz, rxp]\n",
        "title_list = ['RF Tx magnitude', 'RF Tx phase', 'Gx', 'Gy', 'Gz', 'RF Rx phase']\n",
        "styles = ['r-', 'g-', 'k-', 'k-', 'k-', 'bx']\n",
        "plt.figure(1)\n",
        "for v in range(6):\n",
        "    plt.subplot(6,1,v+1)\n",
        "    plt.plot(t, ylist[v], styles[v])\n",
        "    plt.title(title_list[v])\n",
        "    plt.xlabel('Time')\n",
        "\n",
        "plt.show()\n",
        "\n"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "display_data",
          "data": {
            "image/png": "[encoded data, 18704 characters]\n",
            "text/plain": [
              "<Figure size 432x288 with 6 Axes>"
            ]
          },
          "metadata": {
            "tags": [],
            "needs_background": "light"
          }
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "aCJeu74Ie7xx"
      },
      "source": [
        "## Demo 3: create_and_save_phantom \n",
        "Make standard phantom from Virtual Scanner and convert it into JEMRIS-compatible (.h5) file format\n",
        "\n",
        "Note: this must be run before the sim_jemris demo can run "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "tSSHSQ13XU6K",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 88
        },
        "outputId": "4debeba6-7e55-4407-efdf-af2f562ae50a"
      },
      "source": [
        "%cd /content \n",
        "# Creates a virtual scanner phantom and save it as an .h5 file (per JEMRIS standard)\n",
        "phantom_info = {'fov': 0.256, 'N': 32, 'type': 'cylindrical', 'dim': 2, 'dir': 'z'}\n",
        "create_and_save_phantom(phantom_info, out_folder=utest_path)\n",
        "print(\"The phantom is saved as cylindrical.h5\")"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/content\n",
            "Making cylindrical phantom\n",
            "<class 'numpy.ndarray'>\n",
            "The phantom is saved as cylindrical.h5\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "oFQTbA8fJt-U"
      },
      "source": [
        "## Demo 4: sim_jemris\n",
        "\n",
        "1. Take a list of existing sim file names and generate simu.xml \n",
        "2. Runs JEMRIS on the command line using these files\n",
        "3. Reads the JEMRIS output and return them as a dictionary of data (in numpy array)\n",
        "\n",
        "Make sure you run the phantom creation code above first. \n",
        "  "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "3buUr0Raijx3",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 464
        },
        "outputId": "59675e65-8c94-48a8-c4ac-a7d2c99b4486"
      },
      "source": [
        "# Download gre32.xml from Github for sim purposes \n",
        "%cd /content/sim/utest_outputs \n",
        "!wget https://raw.githubusercontent.com/imr-framework/virtual-scanner/dev/virtualscanner/server/simulation/py2jemris/sim/utest_outputs/gre32.xml\n",
        "!wget https://raw.githubusercontent.com/imr-framework/virtual-scanner/dev/virtualscanner/server/simulation/py2jemris/sim/uniform.xml\n",
        "%cd ../.."
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/content/sim/utest_outputs\n",
            "--2020-08-27 18:02:37--  https://raw.githubusercontent.com/imr-framework/virtual-scanner/dev/virtualscanner/server/simulation/py2jemris/sim/utest_outputs/gre32.xml\n",
            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...\n",
            "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 1500 (1.5K) [text/plain]\n",
            "Saving to: ‘gre32.xml’\n",
            "\n",
            "gre32.xml           100%[===================>]   1.46K  --.-KB/s    in 0s      \n",
            "\n",
            "2020-08-27 18:02:38 (13.3 MB/s) - ‘gre32.xml’ saved [1500/1500]\n",
            "\n",
            "--2020-08-27 18:02:38--  https://raw.githubusercontent.com/imr-framework/virtual-scanner/dev/virtualscanner/server/simulation/py2jemris/sim/uniform.xml\n",
            "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...\n",
            "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 79 [text/plain]\n",
            "Saving to: ‘uniform.xml’\n",
            "\n",
            "uniform.xml         100%[===================>]      79  --.-KB/s    in 0s      \n",
            "\n",
            "2020-08-27 18:02:38 (2.94 MB/s) - ‘uniform.xml’ saved [79/79]\n",
            "\n",
            "/content\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "R9J67xCcht3k",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 177
        },
        "outputId": "521c8492-1253-45d2-ea1b-fbf46268dac0"
      },
      "source": [
        "%cd /content\n",
        "\n",
        "#******************** grab gre32.xml *****************************#\n",
        "list_sim_orig = {'seq_xml': 'gre32.xml', 'pht_h5': 'cylindrical.h5', 'tx_xml':'uniform.xml',\n",
        "                    'rx_xml': 'uniform.xml'}\n",
        "out = sim_jemris(list_sim_orig, working_folder = utest_path)\n",
        "\n",
        "%cd /content/sim/utest_outputs \n",
        "savemat('data32_orig.mat',out)\n",
        "print('Data is saved in py2jemris/sim/utest_outputs/data32_orig.mat')\n"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/content\n",
            "Simulating using JEMRIS ...\n",
            "0\n",
            "0\n",
            "sim/utest_outputs/signals.h5\n",
            "/content/sim/utest_outputs/signals.h5\n",
            "True\n",
            "/content/sim/utest_outputs\n",
            "Data is saved in py2jemris/sim/utest_outputs/data32_orig.mat\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Q3hYZ0QpG-c9",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "e54cde32-e91b-4c1e-ad6e-8219e82577d5"
      },
      "source": [
        "# Run this cell after JEMRIS finishes to save data \n",
        "%cd /content/\n",
        "savemat('data32_orig.mat',out)\n",
        "%cd /content \n",
        "print('Data is saved in py2jemris/sim/utest_outputs/data32_orig.mat')"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/content\n",
            "/content\n",
            "Data is saved in py2jemris/sim/utest_outputs/data32_orig.mat\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "mZnTYGkWL6eq",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 52
        },
        "outputId": "4dcc0607-6be3-4f9a-f0bb-7b38186669d8"
      },
      "source": [
        " # Optional code to download data \n",
        " %cd /content \n",
        " from google.colab import files\n",
        " files.download('sim/utest_outputs/data32_orig.mat')  # Download locally"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/content\n"
          ],
          "name": "stdout"
        },
        {
          "output_type": "display_data",
          "data": {
            "application/javascript": [
              "\n",
              "    async function download(id, filename, size) {\n",
              "      if (!google.colab.kernel.accessAllowed) {\n",
              "        return;\n",
              "      }\n",
              "      const div = document.createElement('div');\n",
              "      const label = document.createElement('label');\n",
              "      label.textContent = `Downloading \"${filename}\": `;\n",
              "      div.appendChild(label);\n",
              "      const progress = document.createElement('progress');\n",
              "      progress.max = size;\n",
              "      div.appendChild(progress);\n",
              "      document.body.appendChild(div);\n",
              "\n",
              "      const buffers = [];\n",
              "      let downloaded = 0;\n",
              "\n",
              "      const channel = await google.colab.kernel.comms.open(id);\n",
              "      // Send a message to notify the kernel that we're ready.\n",
              "      channel.send({})\n",
              "\n",
              "      for await (const message of channel.messages) {\n",
              "        // Send a message to notify the kernel that we're ready.\n",
              "        channel.send({})\n",
              "        if (message.buffers) {\n",
              "          for (const buffer of message.buffers) {\n",
              "            buffers.push(buffer);\n",
              "            downloaded += buffer.byteLength;\n",
              "            progress.value = downloaded;\n",
              "          }\n",
              "        }\n",
              "      }\n",
              "      const blob = new Blob(buffers, {type: 'application/binary'});\n",
              "      const a = document.createElement('a');\n",
              "      a.href = window.URL.createObjectURL(blob);\n",
              "      a.download = filename;\n",
              "      div.appendChild(a);\n",
              "      a.click();\n",
              "      div.remove();\n",
              "    }\n",
              "  "
            ],
            "text/plain": [
              "<IPython.core.display.Javascript object>"
            ]
          },
          "metadata": {
            "tags": []
          }
        },
        {
          "output_type": "display_data",
          "data": {
            "application/javascript": [
              "download(\"download_6c71fc35-2c5b-4b02-85e1-d81f2ec21c2c\", \"data32_orig.mat\", 49472)"
            ],
            "text/plain": [
              "<IPython.core.display.Javascript object>"
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            "tags": []
          }
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "yDwQPa7PLkK5"
      },
      "source": [
        "## **Final demo: Simulation pipeline for checking custom seq files**\n",
        "Option 1: Upload your own seq file to be simulated (this is to be tested)!\n"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "Z-5vrFmjKCVS",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 427
        },
        "outputId": "0ce89f01-6a1f-46ea-9dff-8d88f62ee29c"
      },
      "source": [
        "# Option 1: Upload your seq file\n",
        "from google.colab import files\n",
        "%cd /content/sim/custom\n",
        "uploaded = files.upload()\n",
        "\n",
        "for fn in uploaded.keys():\n",
        "  print('User uploaded file \"{name}\" with length {length} bytes'.format(\n",
        "      name=fn, length=len(uploaded[fn])))\n",
        "\n",
        "seqfile = uploaded.keys()[0] # Use the 1st file uploaded\n",
        "# Alternatively, upload on the Files panel & change the filename (it needs to be inside /content/sim/custom) above  "
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "/content/sim/custom\n"
          ],
          "name": "stdout"
        },
        {
          "output_type": "display_data",
          "data": {
            "text/html": [
              "\n",
              "     <input type=\"file\" id=\"files-8655e92a-49a9-4f9e-8c0e-df8f03b22845\" name=\"files[]\" multiple disabled\n",
              "        style=\"border:none\" />\n",
              "     <output id=\"result-8655e92a-49a9-4f9e-8c0e-df8f03b22845\">\n",
              "      Upload widget is only available when the cell has been executed in the\n",
              "      current browser session. Please rerun this cell to enable.\n",
              "      </output>\n",
              "      <script src=\"/nbextensions/google.colab/files.js\"></script> "
            ],
            "text/plain": [
              "<IPython.core.display.HTML object>"
            ]
          },
          "metadata": {
            "tags": []
          }
        },
        {
          "output_type": "error",
          "ename": "MessageError",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mMessageError\u001b[0m                              Traceback (most recent call last)",
            "\u001b[0;32m<ipython-input-20-e22e0fabf205>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mgoogle\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolab\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mfiles\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmagic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'cd /content/sim/custom'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0muploaded\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfiles\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mupload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      5\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      6\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mfn\u001b[0m \u001b[0;32min\u001b[0m \u001b[0muploaded\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mkeys\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/google/colab/files.py\u001b[0m in \u001b[0;36mupload\u001b[0;34m()\u001b[0m\n\u001b[1;32m     62\u001b[0m   result = _output.eval_js(\n\u001b[1;32m     63\u001b[0m       'google.colab._files._uploadFiles(\"{input_id}\", \"{output_id}\")'.format(\n\u001b[0;32m---> 64\u001b[0;31m           input_id=input_id, output_id=output_id))\n\u001b[0m\u001b[1;32m     65\u001b[0m   \u001b[0mfiles\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_collections\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdefaultdict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_six\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbinary_type\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     66\u001b[0m   \u001b[0;31m# Mapping from original filename to filename as saved locally.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/google/colab/output/_js.py\u001b[0m in \u001b[0;36meval_js\u001b[0;34m(script, ignore_result)\u001b[0m\n\u001b[1;32m     37\u001b[0m   \u001b[0;32mif\u001b[0m \u001b[0mignore_result\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     38\u001b[0m     \u001b[0;32mreturn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 39\u001b[0;31m   \u001b[0;32mreturn\u001b[0m \u001b[0m_message\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread_reply_from_input\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrequest_id\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     40\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     41\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;32m/usr/local/lib/python3.6/dist-packages/google/colab/_message.py\u001b[0m in \u001b[0;36mread_reply_from_input\u001b[0;34m(message_id, timeout_sec)\u001b[0m\n\u001b[1;32m    104\u001b[0m         reply.get('colab_msg_id') == message_id):\n\u001b[1;32m    105\u001b[0m       \u001b[0;32mif\u001b[0m \u001b[0;34m'error'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mreply\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 106\u001b[0;31m         \u001b[0;32mraise\u001b[0m \u001b[0mMessageError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mreply\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'error'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    107\u001b[0m       \u001b[0;32mreturn\u001b[0m \u001b[0mreply\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'data'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    108\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;31mMessageError\u001b[0m: TypeError: Cannot read property '_uploadFiles' of undefined"
          ]
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "JGYN7Dmk-sei"
      },
      "source": [
        "Option 2: Construct a default sequence here instead"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "8bg7X-M4Q53d"
      },
      "source": [
        "\n",
        "# We use one from Virtual Scanner \n",
        "%cd /content/sim/custom \n",
        "make_pulseq_se_oblique(fov=0.256,n=5, thk=0.005, tr=0.2, te=0.05, fa=90,\n",
        "                          enc='xyz', slice_locs=[0], write=True)\n",
        "seqfile =  'se_fov256mm_Nf15_Np15_TE50ms_TR200ms_FA90deg.seq'"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "3c2fSFNY-2_H"
      },
      "source": [
        "Next, we grab uniform.xml, the default/ideal RF coil configuration file used in JEMRIS."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "F8yneD4IRcUo"
      },
      "source": [
        "# Download uniform.xml from Github for sim purposes \n",
        "%cd /content/sim/custom \n",
        "!wget https://raw.githubusercontent.com/imr-framework/virtual-scanner/dev/virtualscanner/server/simulation/py2jemris/sim/uniform.xml\n",
        "%cd ../.."
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "shiud7Ed_Avn"
      },
      "source": [
        "Let's run the `simulate_pulseq_jemris()` function, designed for quick testing of custom pulseq files. "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "HzSqDI9VZDEp"
      },
      "source": [
        "# Go back\n",
        "%cd /content\n",
        "\n",
        "# Define phantom \n",
        "# Using N=15; change this to have higher-resolution phantoms when needed \n",
        "phantom_info = {'fov': 0.256, 'N': 5, 'type': 'cylindrical', 'dim': 2, 'dir': 'z'}\n",
        "sim_name = 'custom'\n",
        "\n",
        "out = simulate_pulseq_jemris(seq_path='sim/custom/' + seqfile, phantom_info=phantom_info, sim_name=sim_name,\n",
        "                        coil_fov=0.256, env_option='colab')\n",
        "print(out)\n",
        "print(\"Simulated!\")"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "MYuZSlkX_LyU"
      },
      "source": [
        "Then, load the signal, perform basic Cartesian reconstruction, and display: "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "g_SUHN5Cx-R-"
      },
      "source": [
        "%cd /content \n",
        "kk, im, images = recon_jemris(file='sim/' + sim_name + '/signals.h5', dims=[15, 15])\n",
        "\n",
        "savemat('sim/' + sim_name + '/pulseq_sim_output.mat', {'images': images, 'kspace': kk, 'imspace': im})\n",
        "print('Simulation result is in sim/custom/pulseq_sim_output.mat')\n",
        "\n",
        "# Plot results\n",
        "plt.figure(1)\n",
        "plt.gray()\n",
        "plt.imshow(np.squeeze(images))\n",
        "plt.show()\n"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "zT9XgPrn_Tt4"
      },
      "source": [
        "Run the following cell to download the data as a MATLAB .mat file. "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "weQ2Sh1Re182"
      },
      "source": [
        " # Optional code to download data \n",
        " %cd /content \n",
        " from google.colab import files\n",
        " files.download('sim/custom/pulseq_sim_output.mat')  # Download locally"
      ],
      "execution_count": null,
      "outputs": []
    }
  ]
}