{
  "id": 343795,
  "title": "pylibjpeg problem",
  "url": "/competitions/rsna-2022-cervical-spine-fracture-detection/discussion/343795",
  "author_name": "Aleksandr Kruchinin",
  "post_date": "2022-08-12T14:52:21.468000",
  "votes": 8,
  "comment_count": 5,
  "views": 0,
  "content": "<p>Has anyone encountered such a problem?</p>\n<blockquote>\n  <p>RuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg (req. )</p>\n</blockquote>\n<p>When I add</p>\n<p><code>!pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg</code></p>\n<p>Then:</p>\n<blockquote>\n  <p>RuntimeError: Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed</p>\n</blockquote>\n<p>But:<br>\nIf I am after this do</p>\n<blockquote>\n  <p>Run -&gt; Restart and clear cell outputs</p>\n</blockquote>\n<p>That everything works!!!!!!!!!!!</p>\n<p>I think the plugin is being installed, but a restart is required to load it into memory. But how to update this plugin information without notebook restart?</p>",
  "messages": [
    {
      "id": 1896059,
      "postDate": "2022-08-12T14:52:21.470Z",
      "content": "<p>Has anyone encountered such a problem?</p>\n<blockquote>\n  <p>RuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg (req. )</p>\n</blockquote>\n<p>When I add</p>\n<p><code>!pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg</code></p>\n<p>Then:</p>\n<blockquote>\n  <p>RuntimeError: Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed</p>\n</blockquote>\n<p>But:<br>\nIf I am after this do</p>\n<blockquote>\n  <p>Run -&gt; Restart and clear cell outputs</p>\n</blockquote>\n<p>That everything works!!!!!!!!!!!</p>\n<p>I think the plugin is being installed, but a restart is required to load it into memory. But how to update this plugin information without notebook restart?</p>",
      "rawMarkdown": "Has anyone encountered such a problem?\n\n> RuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg (req. )\n\nWhen I add\n\n`!pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg`\n\nThen:\n\n> RuntimeError: Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed\n\nBut:\nIf I am after this do\n> Run -> Restart and clear cell outputs\n\nThat everything works!!!!!!!!!!!\n\nI think the plugin is being installed, but a restart is required to load it into memory. But how to update this plugin information without notebook restart?",
      "votes": 8
    },
    {
      "id": 1896119,
      "postDate": "2022-08-12T15:42:20.200Z",
      "content": "<p>you can add <a href=\"https://www.kaggle.com/code/awsaf49/pydicom-conda-helper\" target=\"_blank\">this</a> and <a href=\"https://www.kaggle.com/datasets/ronaldokun/gdcm-conda-install\" target=\"_blank\">this</a> <br>\nthen run this at 1st cell</p>\n<pre><code>%load_ext autoreload\n%autoreload 2\n!conda install '/kaggle/input/pydicom-conda-helper/libjpeg-turbo-2.1.0-h7f98852_0.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/libgcc-ng-9.3.0-h2828fa1_19.tar.bz2' --offline -y\n#!conda install '/kaggle/input/pydicom-conda-helper/gdcm-2.8.9-py37h500ead1_1.Truetar.bz2' --offline -y \n!cp ../input/gdcm-conda-install/gdcm.tar .\n!tar -xvzf gdcm.tar\n!conda install --offline ./gdcm/gdcm-2.8.9-py37h71b2a6d_0.tar.bz2\n!conda install '/kaggle/input/pydicom-conda-helper/conda-4.10.1-py37h89c1867_0.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/certifi-2020.12.5-py37h89c1867_1.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/openssl-1.1.1k-h7f98852_0.tar.bz2' --offline -y\n</code></pre>",
      "rawMarkdown": "you can add [this](https://www.kaggle.com/code/awsaf49/pydicom-conda-helper) and [this](https://www.kaggle.com/datasets/ronaldokun/gdcm-conda-install) \nthen run this at 1st cell\n```\n%load_ext autoreload\n%autoreload 2\n!conda install '/kaggle/input/pydicom-conda-helper/libjpeg-turbo-2.1.0-h7f98852_0.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/libgcc-ng-9.3.0-h2828fa1_19.tar.bz2' --offline -y\n#!conda install '/kaggle/input/pydicom-conda-helper/gdcm-2.8.9-py37h500ead1_1.Truetar.bz2' --offline -y \n!cp ../input/gdcm-conda-install/gdcm.tar .\n!tar -xvzf gdcm.tar\n!conda install --offline ./gdcm/gdcm-2.8.9-py37h71b2a6d_0.tar.bz2\n!conda install '/kaggle/input/pydicom-conda-helper/conda-4.10.1-py37h89c1867_0.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/certifi-2020.12.5-py37h89c1867_1.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/openssl-1.1.1k-h7f98852_0.tar.bz2' --offline -y\n```\n\n\n",
      "votes": 5,
      "replies": [
        {
          "id": 1897277,
          "postDate": "2022-08-13T15:56:10.410Z",
          "content": "<p>it works</p>\n<pre><code>%load_ext autoreload\n%autoreload 2\n!cp /kaggle/input/gdcm-conda-install/gdcm.tar .\n!tar -xvzf gdcm.tar\n!conda install --offline ./gdcm/gdcm-2.8.9-py37h71b2a6d_0.tar.bz2\n</code></pre>",
          "rawMarkdown": "it works\n```\n%load_ext autoreload\n%autoreload 2\n!cp /kaggle/input/gdcm-conda-install/gdcm.tar .\n!tar -xvzf gdcm.tar\n!conda install --offline ./gdcm/gdcm-2.8.9-py37h71b2a6d_0.tar.bz2\n```",
          "votes": 1
        },
        {
          "id": 1901659,
          "postDate": "2022-08-16T19:47:24.513Z",
          "content": "<p><a href=\"https://www.kaggle.com/abebe9849\" target=\"_blank\">@abebe9849</a> how do you add the first link? It is a notebook with some output files</p>",
          "rawMarkdown": "@abebe9849 how do you add the first link? It is a notebook with some output files"
        },
        {
          "id": 1907631,
          "postDate": "2022-08-21T00:11:06.203Z",
          "content": "<p>[add data]→[notebook output files]→search \"pydicom-conda-helper\"<br>\nor <br>\ncreate new datasets from <a href=\"https://www.kaggle.com/code/awsaf49/pydicom-conda-helper/data\" target=\"_blank\">output</a></p>",
          "rawMarkdown": "[add data]→[notebook output files]→search \"pydicom-conda-helper\"\nor \ncreate new datasets from [output](https://www.kaggle.com/code/awsaf49/pydicom-conda-helper/data)",
          "votes": 2
        }
      ]
    },
    {
      "id": 1906520,
      "postDate": "2022-08-20T00:25:32.623Z",
      "content": "<p>You can use this <a href=\"https://www.kaggle.com/code/hey24sheep/frozen-packages-for-offline-use\" target=\"_blank\">notebook</a>. It will help with offline installation of a lot of packages.</p>",
      "rawMarkdown": "You can use this [notebook](https://www.kaggle.com/code/hey24sheep/frozen-packages-for-offline-use). It will help with offline installation of a lot of packages."
    }
  ],
  "comments": [
    {
      "id": 1896119,
      "author_name": "patriot",
      "author_url": "",
      "post_date": "2022-08-12T15:42:20.200000",
      "content": "<p>you can add <a href=\"https://www.kaggle.com/code/awsaf49/pydicom-conda-helper\" target=\"_blank\">this</a> and <a href=\"https://www.kaggle.com/datasets/ronaldokun/gdcm-conda-install\" target=\"_blank\">this</a> <br>\nthen run this at 1st cell</p>\n<pre><code>%load_ext autoreload\n%autoreload 2\n!conda install '/kaggle/input/pydicom-conda-helper/libjpeg-turbo-2.1.0-h7f98852_0.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/libgcc-ng-9.3.0-h2828fa1_19.tar.bz2' --offline -y\n#!conda install '/kaggle/input/pydicom-conda-helper/gdcm-2.8.9-py37h500ead1_1.Truetar.bz2' --offline -y \n!cp ../input/gdcm-conda-install/gdcm.tar .\n!tar -xvzf gdcm.tar\n!conda install --offline ./gdcm/gdcm-2.8.9-py37h71b2a6d_0.tar.bz2\n!conda install '/kaggle/input/pydicom-conda-helper/conda-4.10.1-py37h89c1867_0.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/certifi-2020.12.5-py37h89c1867_1.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/openssl-1.1.1k-h7f98852_0.tar.bz2' --offline -y\n</code></pre>",
      "votes": 5,
      "replies": [
        {
          "id": 1897277,
          "author_name": "Aleksandr Kruchinin",
          "author_url": "",
          "post_date": "2022-08-13T15:56:10.410000",
          "content": "<p>it works</p>\n<pre><code>%load_ext autoreload\n%autoreload 2\n!cp /kaggle/input/gdcm-conda-install/gdcm.tar .\n!tar -xvzf gdcm.tar\n!conda install --offline ./gdcm/gdcm-2.8.9-py37h71b2a6d_0.tar.bz2\n</code></pre>",
          "votes": 1,
          "replies": []
        },
        {
          "id": 1901659,
          "author_name": "Samuel Cortinhas",
          "author_url": "",
          "post_date": "2022-08-16T19:47:24.513000",
          "content": "<p><a href=\"https://www.kaggle.com/abebe9849\" target=\"_blank\">@abebe9849</a> how do you add the first link? It is a notebook with some output files</p>",
          "votes": 0,
          "replies": []
        },
        {
          "id": 1907631,
          "author_name": "patriot",
          "author_url": "",
          "post_date": "2022-08-21T00:11:06.203000",
          "content": "<p>[add data]→[notebook output files]→search \"pydicom-conda-helper\"<br>\nor <br>\ncreate new datasets from <a href=\"https://www.kaggle.com/code/awsaf49/pydicom-conda-helper/data\" target=\"_blank\">output</a></p>",
          "votes": 2,
          "replies": []
        }
      ]
    },
    {
      "id": 1906520,
      "author_name": "Hey24sheep",
      "author_url": "",
      "post_date": "2022-08-20T00:25:32.623000",
      "content": "<p>You can use this <a href=\"https://www.kaggle.com/code/hey24sheep/frozen-packages-for-offline-use\" target=\"_blank\">notebook</a>. It will help with offline installation of a lot of packages.</p>",
      "votes": 0,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "1896059": "Has anyone encountered such a problem?\n\n> RuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. GDCM), pylibjpeg (req. )\n\nWhen I add\n\n`!pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg`\n\nThen:\n\n> RuntimeError: Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' plugin is not installed\n\nBut:\nIf I am after this do\n> Run -> Restart and clear cell outputs\n\nThat everything works!!!!!!!!!!!\n\nI think the plugin is being installed, but a restart is required to load it into memory. But how to update this plugin information without notebook restart?",
    "1896119": "you can add [this](https://www.kaggle.com/code/awsaf49/pydicom-conda-helper) and [this](https://www.kaggle.com/datasets/ronaldokun/gdcm-conda-install) \nthen run this at 1st cell\n```\n%load_ext autoreload\n%autoreload 2\n!conda install '/kaggle/input/pydicom-conda-helper/libjpeg-turbo-2.1.0-h7f98852_0.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/libgcc-ng-9.3.0-h2828fa1_19.tar.bz2' --offline -y\n#!conda install '/kaggle/input/pydicom-conda-helper/gdcm-2.8.9-py37h500ead1_1.Truetar.bz2' --offline -y \n!cp ../input/gdcm-conda-install/gdcm.tar .\n!tar -xvzf gdcm.tar\n!conda install --offline ./gdcm/gdcm-2.8.9-py37h71b2a6d_0.tar.bz2\n!conda install '/kaggle/input/pydicom-conda-helper/conda-4.10.1-py37h89c1867_0.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/certifi-2020.12.5-py37h89c1867_1.tar.bz2' --offline -y\n!conda install '/kaggle/input/pydicom-conda-helper/openssl-1.1.1k-h7f98852_0.tar.bz2' --offline -y\n```\n\n\n",
    "1906520": "You can use this [notebook](https://www.kaggle.com/code/hey24sheep/frozen-packages-for-offline-use). It will help with offline installation of a lot of packages."
  }
}