NoduleNet.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "NoduleNet.ipynb",
      "provenance": [],
      "collapsed_sections": [],
      "authorship_tag": "ABX9TyPv/Md7vztiXDBrMWAzbSvJ",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "accelerator": "TPU"
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/SnehaShukla937/ComputerVision_OpenCV/blob/master/NoduleNet.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "b1wVz-m2EsTf",
        "outputId": "a1f96bf6-5c38-4bc1-cb3c-4971fe33b7ac"
      },
      "source": [
        "!git clone /~https://github.com/uci-cbcl/NoduleNet.git "
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "fatal: destination path 'NoduleNet' already exists and is not an empty directory.\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "NDDUaOv3H6UU",
        "outputId": "394700a6-6d7a-4fb8-ca90-582cf395ea82"
      },
      "source": [
        "!wget https://wiki.cancerimagingarchive.net/download/attachments/1966254/LIDC-XML-only.zip?version=1&modificationDate=1530215018015&api=v2"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2021-01-28 14:53:53--  https://wiki.cancerimagingarchive.net/download/attachments/1966254/LIDC-XML-only.zip?version=1\n",
            "Resolving wiki.cancerimagingarchive.net (wiki.cancerimagingarchive.net)... 144.30.169.13\n",
            "Connecting to wiki.cancerimagingarchive.net (wiki.cancerimagingarchive.net)|144.30.169.13|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 \n",
            "Length: 9034311 (8.6M) [application/zip]\n",
            "Saving to: ‘LIDC-XML-only.zip?version=1’\n",
            "\n",
            "LIDC-XML-only.zip?v 100%[===================>]   8.62M  20.6MB/s    in 0.4s    \n",
            "\n",
            "Last-modified header invalid -- time-stamp ignored.\n",
            "2021-01-28 14:53:54 (20.6 MB/s) - ‘LIDC-XML-only.zip?version=1’ saved [9034311/9034311]\n",
            "\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "8qvLiNO3IMPq",
        "outputId": "e0fe38ce-1637-4eb1-fe11-39932efb11e3"
      },
      "source": [
        "!unzip LIDC-XML-only.zip\r\n",
        "!rm -rf LIDC-XML-only.zip"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Archive:  LIDC-XML-only.zip\n",
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            "  inflating: tcia-lidc-xml/189/052.xml  \n",
            "  inflating: tcia-lidc-xml/189/053.xml  \n",
            "  inflating: tcia-lidc-xml/189/054.xml  \n",
            "  inflating: tcia-lidc-xml/189/055.xml  \n",
            "  inflating: tcia-lidc-xml/189/056.xml  \n",
            "  inflating: tcia-lidc-xml/189/057.xml  \n",
            "  inflating: tcia-lidc-xml/189/058.xml  \n",
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            "  inflating: tcia-lidc-xml/189/077.xml  \n",
            "  inflating: tcia-lidc-xml/189/078.xml  \n",
            "  inflating: tcia-lidc-xml/189/079.xml  \n",
            "  inflating: tcia-lidc-xml/189/080.xml  \n",
            "  inflating: tcia-lidc-xml/189/081.xml  \n",
            "  inflating: tcia-lidc-xml/189/082.xml  \n",
            "  inflating: tcia-lidc-xml/189/083.xml  \n",
            "  inflating: tcia-lidc-xml/189/084.xml  \n",
            "  inflating: tcia-lidc-xml/189/085.xml  \n",
            "  inflating: tcia-lidc-xml/189/086.xml  \n",
            "  inflating: tcia-lidc-xml/189/087.xml  \n",
            "  inflating: tcia-lidc-xml/189/088.xml  \n",
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            "  inflating: tcia-lidc-xml/189/095.xml  \n",
            "  inflating: tcia-lidc-xml/189/096.xml  \n",
            "  inflating: tcia-lidc-xml/189/097.xml  \n",
            "  inflating: tcia-lidc-xml/189/098.xml  \n",
            "  inflating: tcia-lidc-xml/189/099.xml  \n",
            "  inflating: tcia-lidc-xml/189/100.xml  \n",
            "  inflating: tcia-lidc-xml/189/101.xml  \n",
            "  inflating: tcia-lidc-xml/189/102.xml  \n",
            "  inflating: tcia-lidc-xml/189/103.xml  \n",
            "  inflating: tcia-lidc-xml/189/104.xml  \n",
            "  inflating: tcia-lidc-xml/189/105.xml  \n",
            "  inflating: tcia-lidc-xml/189/106.xml  \n",
            "  inflating: tcia-lidc-xml/189/107.xml  \n",
            "  inflating: tcia-lidc-xml/189/108.xml  \n",
            "  inflating: tcia-lidc-xml/189/109.xml  \n",
            "  inflating: tcia-lidc-xml/189/110.xml  \n",
            "  inflating: tcia-lidc-xml/189/111.xml  \n",
            "  inflating: tcia-lidc-xml/189/112.xml  \n",
            "  inflating: tcia-lidc-xml/189/113.xml  \n",
            "  inflating: tcia-lidc-xml/189/114.xml  \n",
            "  inflating: tcia-lidc-xml/189/115.xml  \n",
            "  inflating: tcia-lidc-xml/189/116.xml  \n",
            "  inflating: tcia-lidc-xml/189/117.xml  \n",
            "  inflating: tcia-lidc-xml/189/118.xml  \n",
            "  inflating: tcia-lidc-xml/189/119.xml  \n",
            "  inflating: tcia-lidc-xml/189/120.xml  \n",
            "  inflating: tcia-lidc-xml/189/121.xml  \n",
            "  inflating: tcia-lidc-xml/189/122.xml  \n",
            "  inflating: tcia-lidc-xml/189/123.xml  \n",
            "  inflating: tcia-lidc-xml/189/124.xml  \n",
            "  inflating: tcia-lidc-xml/189/125.xml  \n",
            "  inflating: tcia-lidc-xml/189/126.xml  \n",
            "  inflating: tcia-lidc-xml/189/127.xml  \n",
            "  inflating: tcia-lidc-xml/189/128.xml  \n",
            "  inflating: tcia-lidc-xml/189/129.xml  \n",
            "  inflating: tcia-lidc-xml/189/130.xml  \n",
            "  inflating: tcia-lidc-xml/189/131.xml  \n",
            "  inflating: tcia-lidc-xml/189/132.xml  \n",
            "  inflating: tcia-lidc-xml/189/133.xml  \n",
            "  inflating: tcia-lidc-xml/189/134.xml  \n",
            "  inflating: tcia-lidc-xml/189/135.xml  \n",
            "  inflating: tcia-lidc-xml/189/136.xml  \n",
            "  inflating: tcia-lidc-xml/189/137.xml  \n",
            "  inflating: tcia-lidc-xml/189/138.xml  \n",
            "  inflating: tcia-lidc-xml/189/139.xml  \n",
            "  inflating: tcia-lidc-xml/189/140.xml  \n",
            "  inflating: tcia-lidc-xml/189/141.xml  \n",
            "  inflating: tcia-lidc-xml/189/142.xml  \n",
            "  inflating: tcia-lidc-xml/189/143.xml  \n",
            "  inflating: tcia-lidc-xml/189/144.xml  \n",
            "  inflating: tcia-lidc-xml/189/145.xml  \n",
            "  inflating: tcia-lidc-xml/189/146.xml  \n",
            "  inflating: tcia-lidc-xml/189/147.xml  \n",
            "  inflating: tcia-lidc-xml/189/148.xml  \n",
            "  inflating: tcia-lidc-xml/189/149.xml  \n",
            "  inflating: tcia-lidc-xml/189/150.xml  \n",
            "  inflating: tcia-lidc-xml/189/151.xml  \n",
            "  inflating: tcia-lidc-xml/189/152.xml  \n",
            "  inflating: tcia-lidc-xml/189/153.xml  \n",
            "  inflating: tcia-lidc-xml/189/154.xml  \n",
            "  inflating: tcia-lidc-xml/189/155.xml  \n",
            "  inflating: tcia-lidc-xml/189/156.xml  \n",
            "  inflating: tcia-lidc-xml/189/157.xml  \n",
            "  inflating: tcia-lidc-xml/189/158.xml  \n",
            "  inflating: tcia-lidc-xml/189/159.xml  \n",
            "  inflating: tcia-lidc-xml/189/160.xml  \n",
            "  inflating: tcia-lidc-xml/189/161.xml  \n",
            "  inflating: tcia-lidc-xml/189/162.xml  \n",
            "  inflating: tcia-lidc-xml/189/163.xml  \n",
            "  inflating: tcia-lidc-xml/189/164.xml  \n",
            "  inflating: tcia-lidc-xml/189/165.xml  \n",
            "  inflating: tcia-lidc-xml/189/166.xml  \n",
            "  inflating: tcia-lidc-xml/189/167.xml  \n",
            "  inflating: tcia-lidc-xml/189/168.xml  \n",
            "  inflating: tcia-lidc-xml/189/169.xml  \n",
            "  inflating: tcia-lidc-xml/189/170.xml  \n",
            "  inflating: tcia-lidc-xml/189/171.xml  \n",
            "  inflating: tcia-lidc-xml/189/172.xml  \n",
            "  inflating: tcia-lidc-xml/189/173.xml  \n",
            "  inflating: tcia-lidc-xml/189/174.xml  \n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "MRcsJaS4IcEg",
        "outputId": "5de36d8c-9b09-4264-e5ce-e7fb20fa7378"
      },
      "source": [
        "!wget https://zenodo.org/record/3723295/files/subset0.zip?download=1"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2021-01-28 14:55:02--  https://zenodo.org/record/3723295/files/subset0.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 6811924508 (6.3G) [application/octet-stream]\n",
            "Saving to: ‘subset0.zip?download=1’\n",
            "\n",
            "subset0.zip?downloa 100%[===================>]   6.34G  5.40MB/s    in 12m 5s  \n",
            "\n",
            "2021-01-28 15:07:08 (8.97 MB/s) - ‘subset0.zip?download=1’ saved [6811924508/6811924508]\n",
            "\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "v3f37vgBMB3T",
        "outputId": "0bc0950f-1c39-46d8-fd03-be5e4783a9b0"
      },
      "source": [
        "!wget https://zenodo.org/record/3723295/files/subset1.zip?download=1"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2021-01-28 15:07:08--  https://zenodo.org/record/3723295/files/subset1.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 6334778552 (5.9G) [application/octet-stream]\n",
            "Saving to: ‘subset1.zip?download=1’\n",
            "\n",
            "subset1.zip?downloa 100%[===================>]   5.90G  10.2MB/s    in 11m 21s \n",
            "\n",
            "2021-01-28 15:18:30 (8.87 MB/s) - ‘subset1.zip?download=1’ saved [6334778552/6334778552]\n",
            "\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "G5Mem7WsNOE2",
        "outputId": "e81934ff-29cc-4645-b7cf-01854e2a6d70"
      },
      "source": [
        "!wget https://zenodo.org/record/3723295/files/subset3.zip?download=1"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2021-01-28 15:18:30--  https://zenodo.org/record/3723295/files/subset3.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 6896620114 (6.4G) [application/octet-stream]\n",
            "Saving to: ‘subset3.zip?download=1’\n",
            "\n",
            "subset3.zip?downloa 100%[===================>]   6.42G  11.1MB/s    in 11m 16s \n",
            "\n",
            "2021-01-28 15:29:48 (9.73 MB/s) - ‘subset3.zip?download=1’ saved [6896620114/6896620114]\n",
            "\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "SJQ7Hx_INvMi",
        "outputId": "295d2ff6-2d67-493b-ce15-5f121088debf"
      },
      "source": [
        "!wget https://zenodo.org/record/3723295/files/subset2.zip?download=1\r\n",
        "!wget https://zenodo.org/record/3723295/files/subset4.zip?download=1\r\n",
        "!wget https://zenodo.org/record/3723295/files/subset5.zip?download=1"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2021-01-28 15:29:48--  https://zenodo.org/record/3723295/files/subset2.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 7257937108 (6.8G) [application/octet-stream]\n",
            "Saving to: ‘subset2.zip?download=1’\n",
            "\n",
            "subset2.zip?downloa 100%[===================>]   6.76G  20.2MB/s    in 9m 57s  \n",
            "\n",
            "utime(subset2.zip?download=1): No such file or directory\n",
            "2021-01-28 15:39:46 (11.6 MB/s) - ‘subset2.zip?download=1’ saved [7257937108/7257937108]\n",
            "\n",
            "--2021-01-28 15:39:46--  https://zenodo.org/record/3723295/files/subset4.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 6856144330 (6.4G) [application/octet-stream]\n",
            "Saving to: ‘subset4.zip?download=1’\n",
            "\n",
            "subset4.zip?downloa 100%[===================>]   6.38G  14.0MB/s    in 8m 24s  \n",
            "\n",
            "2021-01-28 15:48:11 (13.0 MB/s) - ‘subset4.zip?download=1’ saved [6856144330/6856144330]\n",
            "\n",
            "--2021-01-28 15:48:11--  https://zenodo.org/record/3723295/files/subset5.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 6610460097 (6.2G) [application/octet-stream]\n",
            "Saving to: ‘subset5.zip?download=1’\n",
            "\n",
            "subset5.zip?downloa 100%[===================>]   6.16G  5.29MB/s    in 10m 11s \n",
            "\n",
            "2021-01-28 15:58:24 (10.3 MB/s) - ‘subset5.zip?download=1’ saved [6610460097/6610460097]\n",
            "\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "hXZqpW0PWJyv",
        "outputId": "ba096901-a24e-478d-b22e-3e1fc7d57d8a"
      },
      "source": [
        "!wget https://zenodo.org/record/3723295/files/subset6.zip?download=1\r\n",
        "!wget https://zenodo.org/record/4121926/files/subset7.zip?download=1\r\n",
        "!wget https://zenodo.org/record/4121926/files/subset8.zip?download=1\r\n",
        "!wget https://zenodo.org/record/4121926/files/subset9.zip?download=1"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2021-01-28 15:58:24--  https://zenodo.org/record/3723295/files/subset6.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 6531050274 (6.1G) [application/octet-stream]\n",
            "Saving to: ‘subset6.zip?download=1’\n",
            "\n",
            "subset6.zip?downloa 100%[===================>]   6.08G  5.78MB/s    in 11m 29s \n",
            "\n",
            "2021-01-28 16:09:55 (9.04 MB/s) - ‘subset6.zip?download=1’ saved [6531050274/6531050274]\n",
            "\n",
            "--2021-01-28 16:09:55--  https://zenodo.org/record/4121926/files/subset7.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 6313598213 (5.9G) [application/octet-stream]\n",
            "Saving to: ‘subset7.zip?download=1’\n",
            "\n",
            "subset7.zip?downloa 100%[===================>]   5.88G  12.7MB/s    in 10m 56s \n",
            "\n",
            "2021-01-28 16:20:52 (9.18 MB/s) - ‘subset7.zip?download=1’ saved [6313598213/6313598213]\n",
            "\n",
            "--2021-01-28 16:20:52--  https://zenodo.org/record/4121926/files/subset8.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 6025767505 (5.6G) [application/octet-stream]\n",
            "Saving to: ‘subset8.zip?download=1’\n",
            "\n",
            "subset8.zip?downloa 100%[===================>]   5.61G  6.57MB/s    in 9m 15s  \n",
            "\n",
            "utime(subset8.zip?download=1): No such file or directory\n",
            "2021-01-28 16:30:09 (10.4 MB/s) - ‘subset8.zip?download=1’ saved [6025767505/6025767505]\n",
            "\n",
            "--2021-01-28 16:30:09--  https://zenodo.org/record/4121926/files/subset9.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 6699650017 (6.2G) [application/octet-stream]\n",
            "Saving to: ‘subset9.zip?download=1’\n",
            "\n",
            "subset9.zip?downloa 100%[===================>]   6.24G  16.2MB/s    in 12m 39s \n",
            "\n",
            "2021-01-28 16:42:49 (8.42 MB/s) - ‘subset9.zip?download=1’ saved [6699650017/6699650017]\n",
            "\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "-aVzT2KLm46E",
        "outputId": "6a8bf908-beb8-4750-d5fa-b1af82586769"
      },
      "source": [
        "!wget https://zenodo.org/record/3723295/files/seg-lungs-LUNA16.zip?download=1"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2021-01-28 16:42:51--  https://zenodo.org/record/3723295/files/seg-lungs-LUNA16.zip?download=1\n",
            "Resolving zenodo.org (zenodo.org)... 137.138.76.77\n",
            "Connecting to zenodo.org (zenodo.org)|137.138.76.77|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 303871549 (290M) [application/octet-stream]\n",
            "Saving to: ‘seg-lungs-LUNA16.zip?download=1’\n",
            "\n",
            "seg-lungs-LUNA16.zi 100%[===================>] 289.79M  21.2MB/s    in 13s     \n",
            "\n",
            "2021-01-28 16:43:06 (21.9 MB/s) - ‘seg-lungs-LUNA16.zip?download=1’ saved [303871549/303871549]\n",
            "\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "_wBKTKsQ4MXm",
        "outputId": "d8049560-869c-4258-d254-f6fb78c474be"
      },
      "source": [
        "!unzip seg-lungs-LUNA16.zip"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Archive:  seg-lungs-LUNA16.zip\n",
            "  inflating: seg-lungs-LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.100225287222365663678666836860.mhd  \n",
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            "  inflating: seg-lungs-LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.980362852713685276785310240144.mhd  \n",
            "  inflating: seg-lungs-LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.980362852713685276785310240144.zraw  \n",
            "  inflating: seg-lungs-LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.986011151772797848993829243183.mhd  \n",
            "  inflating: seg-lungs-LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.986011151772797848993829243183.zraw  \n",
            "  inflating: seg-lungs-LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.994459772950022352718462251777.mhd  \n",
            "  inflating: seg-lungs-LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.994459772950022352718462251777.zraw  \n",
            "  inflating: seg-lungs-LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.997611074084993415992563148335.mhd  \n",
            "  inflating: seg-lungs-LUNA16/1.3.6.1.4.1.14519.5.2.1.6279.6001.997611074084993415992563148335.zraw  \n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "bE6z8i234gPB"
      },
      "source": [
        "!rm -rf seg-lungs-LUNA16.zip"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "OWO7Kvu82Gdq"
      },
      "source": [
        "!mv \"/content/subset9.zip\" \"/content/NoduleNet/data/LIDC/combined/\""
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "8mA7pYKK6QV_",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "689264f3-5fd1-43c3-c016-5404c751fd18"
      },
      "source": [
        "!python3 /content/NoduleNet/utils/LIDC/preprocess.py"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "nod mask dir /content/NoduleNet/data/LIDC/masks_test/3\n",
            "save dir  /content/NoduleNet/data/LIDC/preprocessed_test/3\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "EPUJ7kSmFysE",
        "outputId": "108d5d35-7504-4c21-d656-f5ea85735f9f"
      },
      "source": [
        "!pip3 install http.client"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Collecting http.client\n",
            "  Downloading https://files.pythonhosted.org/packages/94/e5/2e8134353629a91854c50a228f1624e21985aca1abc9d0ef0ce25bf5f389/http_client-0.1.22.tar.gz\n",
            "Collecting pycurl\n",
            "\u001b[?25l  Downloading https://files.pythonhosted.org/packages/50/1a/35b1d8b8e4e23a234f1b17a8a40299fd550940b16866c9a1f2d47a04b969/pycurl-7.43.0.6.tar.gz (222kB)\n",
            "\u001b[K     |████████████████████████████████| 225kB 6.0MB/s \n",
            "\u001b[?25hRequirement already satisfied: six in /usr/local/lib/python3.6/dist-packages (from http.client) (1.15.0)\n",
            "Building wheels for collected packages: http.client, pycurl\n",
            "  Building wheel for http.client (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for http.client: filename=http_client-0.1.22-cp36-none-any.whl size=2210 sha256=d8a52f2617b3ae00467096562e7c28e0bd54d00ddd4bf1d6a419c3daa20427ce\n",
            "  Stored in directory: /root/.cache/pip/wheels/36/24/3b/9baa50c4824de1cf6697ee4226ec19f07fab94a65208834234\n",
            "  Building wheel for pycurl (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
            "  Created wheel for pycurl: filename=pycurl-7.43.0.6-cp36-cp36m-linux_x86_64.whl size=284435 sha256=7ccca6aa3c767ef4772a553a6bfc6025b4e16494ffe3e125356230e19e2150cb\n",
            "  Stored in directory: /root/.cache/pip/wheels/d9/a1/7b/2894883fd5c69a3ba684a49d255466d1e924b3cf58cedc1ade\n",
            "Successfully built http.client pycurl\n",
            "Installing collected packages: pycurl, http.client\n",
            "Successfully installed http.client pycurl-7.43.0.6\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "imBX4oXr_-lL",
        "outputId": "2211aef1-7aa3-4923-f81b-92775f0d8c65"
      },
      "source": [
        "!python3 /content/NoduleNet/train.py"
      ],
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Warning: C++ module import failed! This should only happen in deployment\n",
            "Traceback (most recent call last):\n",
            "  File \"/content/NoduleNet/net/layer/rpn_nms.py\", line 8, in <module>\n",
            "    from utils.pybox import *\n",
            "  File \"/content/NoduleNet/utils/pybox.py\", line 3, in <module>\n",
            "    from box import cpu_nms, cpu_overlap\n",
            "  File \"/usr/local/lib/python3.6/dist-packages/box/__init__.py\", line 1, in <module>\n",
            "    from .client import BoxClient, \\\n",
            "  File \"/usr/local/lib/python3.6/dist-packages/box/client.py\", line 7, in <module>\n",
            "    from httplib import NOT_FOUND, PRECONDITION_FAILED, CONFLICT, UNAUTHORIZED\n",
            "ModuleNotFoundError: No module named 'httplib'\n",
            "\n",
            "During handling of the above exception, another exception occurred:\n",
            "\n",
            "Traceback (most recent call last):\n",
            "  File \"/content/NoduleNet/train.py\", line 1, in <module>\n",
            "    from net.nodule_net import NoduleNet\n",
            "  File \"/content/NoduleNet/net/nodule_net.py\", line 3, in <module>\n",
            "    from net.layer import *\n",
            "  File \"/content/NoduleNet/net/layer/__init__.py\", line 1, in <module>\n",
            "    from net.layer.rpn_nms import *\n",
            "  File \"/content/NoduleNet/net/layer/rpn_nms.py\", line 11, in <module>\n",
            "    from utils.util import py_nms as torch_nms\n",
            "  File \"/content/NoduleNet/utils/util.py\", line 5, in <module>\n",
            "    import pydicom as dicom\n",
            "ModuleNotFoundError: No module named 'pydicom'\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "hY5CvKXSD8nC"
      },
      "source": [
        ""
      ],
      "execution_count": null,
      "outputs": []
    }
  ]
}