medSAM2_2d_3d.ipynb

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  "metadata": {
    "colab": {
      "provenance": [],
      "gpuType": "T4",
      "authorship_tag": "ABX9TyPKnauqX2euhxPrdeOonted",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    },
    "accelerator": "GPU"
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/ayyucedemirbas/Medical_Img_Seg/blob/main/mesSAM2_2d_3d.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "id": "GRPPOQxAAnh2"
      },
      "outputs": [],
      "source": [
        "!pip install -q condacolab"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import condacolab\n",
        "condacolab.install()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "GGRvtG46AoiU",
        "outputId": "11fe8cd6-0f67-4ce0-a908-283427f182be"
      },
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "⏬ Downloading https://github.com/conda-forge/miniforge/releases/download/23.11.0-0/Mambaforge-23.11.0-0-Linux-x86_64.sh...\n",
            "📦 Installing...\n",
            "📌 Adjusting configuration...\n",
            "🩹 Patching environment...\n",
            "⏲ Done in 0:00:13\n",
            "🔁 Restarting kernel...\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!git clone https://github.com/MedicineToken/Medical-SAM2.git"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "uSDXbeliAqwG",
        "outputId": "ab6c9c05-3824-4b8d-f013-4b7c506324ad"
      },
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Cloning into 'Medical-SAM2'...\n",
            "remote: Enumerating objects: 191, done.\u001b[K\n",
            "remote: Counting objects: 100% (55/55), done.\u001b[K\n",
            "remote: Compressing objects: 100% (19/19), done.\u001b[K\n",
            "remote: Total 191 (delta 43), reused 36 (delta 36), pack-reused 136 (from 1)\u001b[K\n",
            "Receiving objects: 100% (191/191), 2.20 MiB | 5.10 MiB/s, done.\n",
            "Resolving deltas: 100% (81/81), done.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "%cd Medical-SAM2"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "7QPj3RbkAxrm",
        "outputId": "679dd396-9d21-4d58-812a-099ddff0ded6"
      },
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "/content/Medical-SAM2\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!conda env list | grep 'medsam2' || conda env create -f environment.yml"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "VrDH7JjlA3g0",
        "outputId": "5827b019-2c84-4ea5-9d2e-7f65f971d5d6"
      },
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Channels:\n",
            " - conda-forge\n",
            " - defaults\n",
            "Platform: linux-64\n",
            "Collecting package metadata (repodata.json): - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\bdone\n",
            "Solving environment: \\ \b\b| \b\bdone\n",
            "\n",
            "\n",
            "==> WARNING: A newer version of conda exists. <==\n",
            "    current version: 23.11.0\n",
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            "\n",
            "Please update conda by running\n",
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            "    $ conda update -n base -c conda-forge conda\n",
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            "\n",
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            "libgomp-11.2.0       | 474 KB    | :   3% 0.03377134671077719/1 [00:00<00:18, 19.64s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "\n",
            "\n",
            "\n",
            "\n",
            "psutil-5.9.0         | 449 KB    | :   4% 0.035650251536198586/1 [00:00<00:18, 18.77s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "\n",
            "\n",
            "\n",
            "ipython-8.26.0       | 585 KB    | :   3% 0.027339519656120106/1 [00:00<00:23, 24.51s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "\n",
            "\n",
            "\n",
            "python-3.12.4        | 34.8 MB   | :  91% 0.905246381126689/1 [00:00<00:00,  1.24it/s] \n",
            "\n",
            "\n",
            "libstdcxx-ng-11.2.0  | 4.7 MB    | : 100% 1.0/1 [00:00<00:00,  3.73it/s]               \u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "tk-8.6.14            | 3.4 MB    | : 100% 1.0/1 [00:01<00:00,  1.31s/it]                 \u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "\n",
            "tk-8.6.14            | 3.4 MB    | : 100% 1.0/1 [00:01<00:00,  1.31s/it]\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "openssl-3.0.14       | 5.2 MB    | : 100% 1.0/1 [00:01<00:00,  1.57s/it]                \u001b[A\u001b[A\n",
            "\n",
            "openssl-3.0.14       | 5.2 MB    | : 100% 1.0/1 [00:01<00:00,  1.57s/it]\u001b[A\u001b[A\n",
            "libgcc-ng-11.2.0     | 5.3 MB    | : 100% 1.0/1 [00:01<00:00,  1.92s/it]              \u001b[A\n",
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            "\n",
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            "debugpy-1.6.7        | 2.0 MB    | : 100% 1.0/1 [00:02<00:00,  2.10s/it]                 \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "debugpy-1.6.7        | 2.0 MB    | : 100% 1.0/1 [00:02<00:00,  2.10s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "pip-24.0             | 3.3 MB    | : 100% 1.0/1 [00:02<00:00,  2.19s/it]                 \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "pip-24.0             | 3.3 MB    | : 100% 1.0/1 [00:02<00:00,  2.19s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "\n",
            "sqlite-3.45.3        | 1.2 MB    | : 100% 1.0/1 [00:02<00:00,  2.21s/it]                 \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "sqlite-3.45.3        | 1.2 MB    | : 100% 1.0/1 [00:02<00:00,  2.21s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "setuptools-69.5.1    | 1.3 MB    | : 100% 1.0/1 [00:02<00:00,  2.57s/it]                \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "\n",
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            "tornado-6.4.1        | 849 KB    | : 100% 1.0/1 [00:02<00:00,  2.74s/it]                \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "ld_impl_linux-64-2.3 | 654 KB    | : 100% 1.0/1 [00:02<00:00,  2.81s/it]                 \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "xz-5.4.6             | 643 KB    | : 100% 1.0/1 [00:03<00:00,  3.07s/it]                \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
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            "libgomp-11.2.0       | 474 KB    | : 100% 1.0/1 [00:04<00:00,  4.07s/it]                \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
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            "psutil-5.9.0         | 449 KB    | : 100% 1.0/1 [00:04<00:00,  4.17s/it]                 \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
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            "psutil-5.9.0         | 449 KB    | : 100% 1.0/1 [00:04<00:00,  4.17s/it]\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
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            " ... (more hidden) ...\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
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            "ipython-8.26.0       | 585 KB    | : 100% 1.0/1 [00:04<00:00,  4.61s/it]                 \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
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            "jedi-0.19.1          | 822 KB    | : 100% 1.0/1 [00:05<00:00,  5.12s/it]                \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
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            "python-3.12.4        | 34.8 MB   | : 100% 1.0/1 [00:07<00:00,  1.24it/s]              \n",
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            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "                                                                        \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "                                                                        \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "                                                                        \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "                                                                        \u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\u001b[A\n",
            "\n",
            "\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
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            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
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            "\n",
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            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\u001b[A\n",
            "\n",
            "\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
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            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
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            "\n",
            "\n",
            "\n",
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            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
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            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
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            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
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            "\n",
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            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\n",
            "\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\u001b[A\n",
            "\u001b[A\n",
            "Preparing transaction: - \b\b\\ \b\b| \b\b/ \b\b- \b\bdone\n",
            "Verifying transaction: | \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\bdone\n",
            "Executing transaction: / \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\bdone\n",
            "Installing pip dependencies: - \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ 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\b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| \b\b/ \b\b- \b\b\\ \b\b| Ran pip subprocess with arguments:\n",
            "['/usr/local/envs/medsam2/bin/python', '-m', 'pip', 'install', '-U', '-r', '/content/Medical-SAM2/condaenv.adbl428p.requirements.txt', '--exists-action=b']\n",
            "Pip subprocess output:\n",
            "Collecting acvl-utils==0.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 1))\n",
            "  Downloading acvl_utils-0.2.tar.gz (18 kB)\n",
            "  Preparing metadata (setup.py): started\n",
            "  Preparing metadata (setup.py): finished with status 'done'\n",
            "Collecting antlr4-python3-runtime==4.9.3 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 2))\n",
            "  Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB)\n",
            "     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.0/117.0 kB 4.3 MB/s eta 0:00:00\n",
            "  Preparing metadata (setup.py): started\n",
            "  Preparing metadata (setup.py): finished with status 'done'\n",
            "Collecting anyio==4.4.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 3))\n",
            "  Downloading anyio-4.4.0-py3-none-any.whl.metadata (4.6 kB)\n",
            "Collecting argon2-cffi==23.1.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 4))\n",
            "  Using cached argon2_cffi-23.1.0-py3-none-any.whl.metadata (5.2 kB)\n",
            "Collecting argon2-cffi-bindings==21.2.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 5))\n",
            "  Using cached argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.7 kB)\n",
            "Collecting argparse==1.4.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 6))\n",
            "  Downloading argparse-1.4.0-py2.py3-none-any.whl.metadata (2.8 kB)\n",
            "Collecting arrow==1.3.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 7))\n",
            "  Downloading arrow-1.3.0-py3-none-any.whl.metadata (7.5 kB)\n",
            "Collecting async-lru==2.0.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 8))\n",
            "  Downloading async_lru-2.0.4-py3-none-any.whl.metadata (4.5 kB)\n",
            "Collecting asyncio-atexit==1.0.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 9))\n",
            "  Downloading asyncio_atexit-1.0.1-py3-none-any.whl.metadata (1.5 kB)\n",
            "Collecting attrs==23.2.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 10))\n",
            "  Downloading attrs-23.2.0-py3-none-any.whl.metadata (9.5 kB)\n",
            "Collecting babel==2.15.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 11))\n",
            "  Downloading Babel-2.15.0-py3-none-any.whl.metadata (1.5 kB)\n",
            "Collecting backoff==2.2.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 12))\n",
            "  Downloading backoff-2.2.1-py3-none-any.whl.metadata (14 kB)\n",
            "Collecting batchgenerators==0.25 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 13))\n",
            "  Downloading batchgenerators-0.25.tar.gz (61 kB)\n",
            "     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.7/61.7 kB 5.6 MB/s eta 0:00:00\n",
            "  Preparing metadata (setup.py): started\n",
            "  Preparing metadata (setup.py): finished with status 'done'\n",
            "Collecting batchgeneratorsv2==0.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 14))\n",
            "  Downloading batchgeneratorsv2-0.2.tar.gz (33 kB)\n",
            "  Installing build dependencies: started\n",
            "  Installing build dependencies: finished with status 'done'\n",
            "  Getting requirements to build wheel: started\n",
            "  Getting requirements to build wheel: finished with status 'done'\n",
            "  Preparing metadata (pyproject.toml): started\n",
            "  Preparing metadata (pyproject.toml): finished with status 'done'\n",
            "Collecting beautifulsoup4==4.12.3 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 15))\n",
            "  Using cached beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB)\n",
            "Collecting bleach==6.1.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 16))\n",
            "  Using cached bleach-6.1.0-py3-none-any.whl.metadata (30 kB)\n",
            "Collecting certifi==2024.7.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 17))\n",
            "  Downloading certifi-2024.7.4-py3-none-any.whl.metadata (2.2 kB)\n",
            "Collecting cffi==1.16.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 18))\n",
            "  Downloading cffi-1.16.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB)\n",
            "Collecting charset-normalizer==3.3.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 19))\n",
            "  Downloading charset_normalizer-3.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)\n",
            "Collecting connected-components-3d==3.18.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 20))\n",
            "  Downloading connected_components_3d-3.18.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (31 kB)\n",
            "Collecting contourpy==1.2.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 21))\n",
            "  Downloading contourpy-1.2.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)\n",
            "Collecting cycler==0.12.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 22))\n",
            "  Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)\n",
            "Collecting defusedxml==0.7.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 23))\n",
            "  Using cached defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB)\n",
            "Collecting deprecated==1.2.14 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 24))\n",
            "  Downloading Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB)\n",
            "Collecting dicom2nifti==2.4.11 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 25))\n",
            "  Downloading dicom2nifti-2.4.11-py3-none-any.whl.metadata (1.3 kB)\n",
            "Collecting dynamic-network-architectures==0.3.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 26))\n",
            "  Downloading dynamic_network_architectures-0.3.1.tar.gz (20 kB)\n",
            "  Preparing metadata (setup.py): started\n",
            "  Preparing metadata (setup.py): finished with status 'done'\n",
            "Collecting einops==0.8.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 27))\n",
            "  Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB)\n",
            "Collecting fastjsonschema==2.20.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 28))\n",
            "  Using cached fastjsonschema-2.20.0-py3-none-any.whl.metadata (2.1 kB)\n",
            "Collecting fft-conv-pytorch==1.2.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 29))\n",
            "  Downloading fft_conv_pytorch-1.2.0-py3-none-any.whl.metadata (2.8 kB)\n",
            "Collecting filelock==3.15.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 30))\n",
            "  Downloading filelock-3.15.4-py3-none-any.whl.metadata (2.9 kB)\n",
            "Collecting fonttools==4.53.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 31))\n",
            "  Downloading fonttools-4.53.1-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (162 kB)\n",
            "     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.6/162.6 kB 6.9 MB/s eta 0:00:00\n",
            "Collecting fqdn==1.5.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 32))\n",
            "  Downloading fqdn-1.5.1-py3-none-any.whl.metadata (1.4 kB)\n",
            "Collecting fsspec==2024.6.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 33))\n",
            "  Using cached fsspec-2024.6.1-py3-none-any.whl.metadata (11 kB)\n",
            "Collecting future==1.0.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 34))\n",
            "  Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)\n",
            "Collecting googleapis-common-protos==1.63.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 35))\n",
            "  Downloading googleapis_common_protos-1.63.2-py2.py3-none-any.whl.metadata (1.5 kB)\n",
            "Collecting h11==0.14.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 36))\n",
            "  Downloading h11-0.14.0-py3-none-any.whl.metadata (8.2 kB)\n",
            "Collecting httpcore==1.0.5 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 37))\n",
            "  Downloading httpcore-1.0.5-py3-none-any.whl.metadata (20 kB)\n",
            "Collecting httpx==0.27.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 38))\n",
            "  Downloading httpx-0.27.0-py3-none-any.whl.metadata (7.2 kB)\n",
            "Collecting hydra-core==1.3.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 39))\n",
            "  Downloading hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)\n",
            "Collecting idna==3.7 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 40))\n",
            "  Downloading idna-3.7-py3-none-any.whl.metadata (9.9 kB)\n",
            "Collecting imagecodecs==2024.6.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 41))\n",
            "  Downloading imagecodecs-2024.6.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)\n",
            "Collecting imageio==2.34.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 42))\n",
            "  Downloading imageio-2.34.2-py3-none-any.whl.metadata (4.9 kB)\n",
            "Collecting importlib-metadata==6.11.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 43))\n",
            "  Downloading importlib_metadata-6.11.0-py3-none-any.whl.metadata (4.9 kB)\n",
            "Collecting iopath==0.1.10 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 44))\n",
            "  Downloading iopath-0.1.10.tar.gz (42 kB)\n",
            "     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.2/42.2 kB 3.7 MB/s eta 0:00:00\n",
            "  Preparing metadata (setup.py): started\n",
            "  Preparing metadata (setup.py): finished with status 'done'\n",
            "Collecting ipympl==0.9.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 45))\n",
            "  Downloading ipympl-0.9.4-py3-none-any.whl.metadata (8.7 kB)\n",
            "Collecting ipython-genutils==0.2.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 46))\n",
            "  Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl.metadata (755 bytes)\n",
            "Collecting ipywidgets==8.1.3 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 47))\n",
            "  Downloading ipywidgets-8.1.3-py3-none-any.whl.metadata (2.4 kB)\n",
            "Collecting isoduration==20.11.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 48))\n",
            "  Downloading isoduration-20.11.0-py3-none-any.whl.metadata (5.7 kB)\n",
            "Collecting jinja2==3.1.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 49))\n",
            "  Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)\n",
            "Collecting joblib==1.4.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 50))\n",
            "  Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)\n",
            "Collecting json5==0.9.25 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 51))\n",
            "  Downloading json5-0.9.25-py3-none-any.whl.metadata (30 kB)\n",
            "Collecting jsonpointer==3.0.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 52))\n",
            "  Downloading jsonpointer-3.0.0-py2.py3-none-any.whl.metadata (2.3 kB)\n",
            "Collecting jsonschema==4.23.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 53))\n",
            "  Using cached jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB)\n",
            "Collecting jsonschema-specifications==2023.12.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 54))\n",
            "  Using cached jsonschema_specifications-2023.12.1-py3-none-any.whl.metadata (3.0 kB)\n",
            "Collecting jupyter-events==0.10.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 55))\n",
            "  Downloading jupyter_events-0.10.0-py3-none-any.whl.metadata (5.9 kB)\n",
            "Collecting jupyter-lsp==2.2.5 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 56))\n",
            "  Downloading jupyter_lsp-2.2.5-py3-none-any.whl.metadata (1.8 kB)\n",
            "Collecting jupyter-server==2.14.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 57))\n",
            "  Downloading jupyter_server-2.14.2-py3-none-any.whl.metadata (8.4 kB)\n",
            "Collecting jupyter-server-terminals==0.5.3 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 58))\n",
            "  Downloading jupyter_server_terminals-0.5.3-py3-none-any.whl.metadata (5.6 kB)\n",
            "Collecting jupyterlab==4.2.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 59))\n",
            "  Downloading jupyterlab-4.2.4-py3-none-any.whl.metadata (16 kB)\n",
            "Collecting jupyterlab-pygments==0.3.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 60))\n",
            "  Using cached jupyterlab_pygments-0.3.0-py3-none-any.whl.metadata (4.4 kB)\n",
            "Collecting jupyterlab-server==2.27.3 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 61))\n",
            "  Downloading jupyterlab_server-2.27.3-py3-none-any.whl.metadata (5.9 kB)\n",
            "Collecting jupyterlab-widgets==3.0.11 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 62))\n",
            "  Downloading jupyterlab_widgets-3.0.11-py3-none-any.whl.metadata (4.1 kB)\n",
            "Collecting kiwisolver==1.4.5 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 63))\n",
            "  Downloading kiwisolver-1.4.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB)\n",
            "Collecting lazy-loader==0.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 64))\n",
            "  Using cached lazy_loader-0.4-py3-none-any.whl.metadata (7.6 kB)\n",
            "Collecting linecache2==1.0.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 65))\n",
            "  Downloading linecache2-1.0.0-py2.py3-none-any.whl.metadata (1000 bytes)\n",
            "Collecting markupsafe==2.1.5 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 66))\n",
            "  Downloading MarkupSafe-2.1.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)\n",
            "Collecting matplotlib==3.9.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 67))\n",
            "  Downloading matplotlib-3.9.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)\n",
            "Collecting mistune==3.0.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 68))\n",
            "  Downloading mistune-3.0.2-py3-none-any.whl.metadata (1.7 kB)\n",
            "Collecting monai==1.3.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 69))\n",
            "  Downloading monai-1.3.2-py3-none-any.whl.metadata (10 kB)\n",
            "Collecting mpmath==1.3.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 70))\n",
            "  Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)\n",
            "Collecting nbclient==0.10.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 71))\n",
            "  Using cached nbclient-0.10.0-py3-none-any.whl.metadata (7.8 kB)\n",
            "Collecting nbconvert==7.16.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 72))\n",
            "  Downloading nbconvert-7.16.4-py3-none-any.whl.metadata (8.5 kB)\n",
            "Collecting nbformat==5.10.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 73))\n",
            "  Using cached nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB)\n",
            "Collecting networkx==3.3 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 74))\n",
            "  Using cached networkx-3.3-py3-none-any.whl.metadata (5.1 kB)\n",
            "Collecting nibabel==5.2.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 75))\n",
            "  Using cached nibabel-5.2.1-py3-none-any.whl.metadata (8.8 kB)\n",
            "Collecting nnunetv2==2.5.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 76))\n",
            "  Downloading nnunetv2-2.5.1.tar.gz (196 kB)\n",
            "     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 197.0/197.0 kB 3.0 MB/s eta 0:00:00\n",
            "  Installing build dependencies: started\n",
            "  Installing build dependencies: finished with status 'done'\n",
            "  Getting requirements to build wheel: started\n",
            "  Getting requirements to build wheel: finished with status 'done'\n",
            "  Preparing metadata (pyproject.toml): started\n",
            "  Preparing metadata (pyproject.toml): finished with status 'done'\n",
            "Collecting notebook-shim==0.2.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 77))\n",
            "  Using cached notebook_shim-0.2.4-py3-none-any.whl.metadata (4.0 kB)\n",
            "Collecting numpy==2.0.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 78))\n",
            "  Downloading numpy-2.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)\n",
            "     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.9/60.9 kB 4.3 MB/s eta 0:00:00\n",
            "Collecting nvidia-cublas-cu12==12.1.3.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 79))\n",
            "  Downloading nvidia_cublas_cu12-12.1.3.1-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n",
            "Collecting nvidia-cuda-cupti-cu12==12.1.105 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 80))\n",
            "  Downloading nvidia_cuda_cupti_cu12-12.1.105-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n",
            "Collecting nvidia-cuda-nvrtc-cu12==12.1.105 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 81))\n",
            "  Downloading nvidia_cuda_nvrtc_cu12-12.1.105-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n",
            "Collecting nvidia-cuda-runtime-cu12==12.1.105 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 82))\n",
            "  Downloading nvidia_cuda_runtime_cu12-12.1.105-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n",
            "Collecting nvidia-cudnn-cu12==9.1.0.70 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 83))\n",
            "  Downloading nvidia_cudnn_cu12-9.1.0.70-py3-none-manylinux2014_x86_64.whl.metadata (1.6 kB)\n",
            "Collecting nvidia-cufft-cu12==11.0.2.54 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 84))\n",
            "  Downloading nvidia_cufft_cu12-11.0.2.54-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n",
            "Collecting nvidia-curand-cu12==10.3.2.106 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 85))\n",
            "  Downloading nvidia_curand_cu12-10.3.2.106-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n",
            "Collecting nvidia-cusolver-cu12==11.4.5.107 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 86))\n",
            "  Downloading nvidia_cusolver_cu12-11.4.5.107-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n",
            "Collecting nvidia-cusparse-cu12==12.1.0.106 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 87))\n",
            "  Downloading nvidia_cusparse_cu12-12.1.0.106-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n",
            "Collecting nvidia-nccl-cu12==2.20.5 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 88))\n",
            "  Downloading nvidia_nccl_cu12-2.20.5-py3-none-manylinux2014_x86_64.whl.metadata (1.8 kB)\n",
            "Collecting nvidia-nvjitlink-cu12==12.5.82 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 89))\n",
            "  Downloading nvidia_nvjitlink_cu12-12.5.82-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)\n",
            "Collecting nvidia-nvtx-cu12==12.1.105 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 90))\n",
            "  Downloading nvidia_nvtx_cu12-12.1.105-py3-none-manylinux1_x86_64.whl.metadata (1.7 kB)\n",
            "Collecting omegaconf==2.3.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 91))\n",
            "  Downloading omegaconf-2.3.0-py3-none-any.whl.metadata (3.9 kB)\n",
            "Collecting opencv-python==4.10.0.84 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 92))\n",
            "  Using cached opencv_python-4.10.0.84-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (20 kB)\n",
            "Collecting opentelemetry-api==1.21.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 93))\n",
            "  Downloading opentelemetry_api-1.21.0-py3-none-any.whl.metadata (1.4 kB)\n",
            "Collecting opentelemetry-exporter-otlp-proto-common==1.21.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 94))\n",
            "  Downloading opentelemetry_exporter_otlp_proto_common-1.21.0-py3-none-any.whl.metadata (1.8 kB)\n",
            "Collecting opentelemetry-exporter-otlp-proto-http==1.21.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 95))\n",
            "  Downloading opentelemetry_exporter_otlp_proto_http-1.21.0-py3-none-any.whl.metadata (2.4 kB)\n",
            "Collecting opentelemetry-proto==1.21.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 96))\n",
            "  Downloading opentelemetry_proto-1.21.0-py3-none-any.whl.metadata (2.3 kB)\n",
            "Collecting opentelemetry-sdk==1.21.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 97))\n",
            "  Downloading opentelemetry_sdk-1.21.0-py3-none-any.whl.metadata (1.5 kB)\n",
            "Collecting opentelemetry-semantic-conventions==0.42b0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 98))\n",
            "  Downloading opentelemetry_semantic_conventions-0.42b0-py3-none-any.whl.metadata (2.3 kB)\n",
            "Collecting overrides==7.7.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 99))\n",
            "  Downloading overrides-7.7.0-py3-none-any.whl.metadata (5.8 kB)\n",
            "Collecting pandas==2.2.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 100))\n",
            "  Downloading pandas-2.2.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)\n",
            "Collecting pandocfilters==1.5.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 101))\n",
            "  Using cached pandocfilters-1.5.1-py2.py3-none-any.whl.metadata (9.0 kB)\n",
            "Collecting pillow==10.4.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 102))\n",
            "  Downloading pillow-10.4.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (9.2 kB)\n",
            "Collecting portalocker==2.10.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 103))\n",
            "  Downloading portalocker-2.10.1-py3-none-any.whl.metadata (8.5 kB)\n",
            "Collecting prometheus-client==0.20.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 104))\n",
            "  Downloading prometheus_client-0.20.0-py3-none-any.whl.metadata (1.8 kB)\n",
            "Collecting protobuf==4.25.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 105))\n",
            "  Downloading protobuf-4.25.4-cp37-abi3-manylinux2014_x86_64.whl.metadata (541 bytes)\n",
            "Collecting psutil==5.9.8 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 106))\n",
            "  Downloading psutil-5.9.8-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)\n",
            "Collecting pycparser==2.22 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 107))\n",
            "  Using cached pycparser-2.22-py3-none-any.whl.metadata (943 bytes)\n",
            "Collecting pydicom==2.4.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 108))\n",
            "  Downloading pydicom-2.4.4-py3-none-any.whl.metadata (7.8 kB)\n",
            "Collecting pyparsing==3.1.2 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 109))\n",
            "  Downloading pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB)\n",
            "Collecting python-dateutil==2.9.0.post0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 110))\n",
            "  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)\n",
            "Collecting python-gdcm==3.0.24.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 111))\n",
            "  Downloading python_gdcm-3.0.24.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.7 kB)\n",
            "Collecting graphviz==0.20.3 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 112))\n",
            "  Using cached graphviz-0.20.3-py3-none-any.whl.metadata (12 kB)\n",
            "Collecting python-json-logger==2.0.7 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 113))\n",
            "  Downloading python_json_logger-2.0.7-py3-none-any.whl.metadata (6.5 kB)\n",
            "Collecting pytz==2024.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 114))\n",
            "  Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)\n",
            "Collecting pyyaml==6.0.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 115))\n",
            "  Downloading PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)\n",
            "Collecting referencing==0.35.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 116))\n",
            "  Using cached referencing-0.35.1-py3-none-any.whl.metadata (2.8 kB)\n",
            "Collecting requests==2.32.3 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 117))\n",
            "  Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)\n",
            "Collecting rfc3339-validator==0.1.4 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 118))\n",
            "  Downloading rfc3339_validator-0.1.4-py2.py3-none-any.whl.metadata (1.5 kB)\n",
            "Collecting rfc3986-validator==0.1.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 119))\n",
            "  Downloading rfc3986_validator-0.1.1-py2.py3-none-any.whl.metadata (1.7 kB)\n",
            "Collecting rpds-py==0.19.1 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 120))\n",
            "  Downloading rpds_py-0.19.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.2 kB)\n",
            "Collecting scikit-image==0.24.0 (from -r /content/Medical-SAM2/condaenv.adbl428p.requirements.txt (line 121))\n",
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            "  Using cached Send2Trash-1.8.3-py3-none-any.whl.metadata (4.0 kB)\n",
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            "Installing collected packages: webencodings, torchsummary, simpleitk, pytz, mpmath, linecache2, ipython-genutils, fastjsonschema, argparse, antlr4-python3-runtime, wrapt, widgetsnbextension, websocket-client, webcolors, urllib3, uri-template, tzdata, types-python-dateutil, traceback2, tqdm, tinycss2, threadpoolctl, terminado, sympy, soupsieve, sniffio, send2trash, rpds-py, rfc3986-validator, rfc3339-validator, pyyaml, python-json-logger, python-gdcm, python-dateutil, pyparsing, pydicom, pycparser, psutil, protobuf, prometheus-client, portalocker, pillow, pandocfilters, overrides, opentelemetry-semantic-conventions, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, numpy, networkx, mistune, markupsafe, lazy-loader, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, json5, joblib, importlib-metadata, idna, h11, graphviz, future, fsspec, fqdn, fonttools, filelock, einops, defusedxml, cycler, charset-normalizer, certifi, bleach, backoff, babel, attrs, asyncio-atexit, async-lru, yacs, unittest2, triton, tifffile, tensorboardx, scipy, requests, referencing, pandas, opentelemetry-proto, opencv-python, omegaconf, nvidia-cusparse-cu12, nvidia-cudnn-cu12, nibabel, jupyter-server-terminals, jinja2, iopath, imageio, imagecodecs, httpcore, googleapis-common-protos, deprecated, contourpy, connected-components-3d, cffi, beautifulsoup4, arrow, anyio, scikit-learn, scikit-image, opentelemetry-exporter-otlp-proto-common, opentelemetry-api, nvidia-cusolver-cu12, matplotlib, jsonschema-specifications, isoduration, hydra-core, httpx, dicom2nifti, argon2-cffi-bindings, torch, seaborn, opentelemetry-sdk, jsonschema, ipywidgets, batchgenerators, argon2-cffi, torchvision, torchaudio, opentelemetry-exporter-otlp-proto-http, nbformat, monai, ipympl, fft-conv-pytorch, dynamic-network-architectures, acvl-utils, synapseclient, nbclient, jupyter-events, batchgeneratorsv2, nnunetv2, nbconvert, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab\n",
            "  Attempting uninstall: python-dateutil\n",
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            "    Uninstalling importlib_metadata-8.2.0:\n",
            "      Successfully uninstalled importlib_metadata-8.2.0\n",
            "Successfully installed acvl-utils-0.2 antlr4-python3-runtime-4.9.3 anyio-4.4.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 argparse-1.4.0 arrow-1.3.0 async-lru-2.0.4 asyncio-atexit-1.0.1 attrs-23.2.0 babel-2.15.0 backoff-2.2.1 batchgenerators-0.25 batchgeneratorsv2-0.2 beautifulsoup4-4.12.3 bleach-6.1.0 certifi-2024.7.4 cffi-1.16.0 charset-normalizer-3.3.2 connected-components-3d-3.18.0 contourpy-1.2.1 cycler-0.12.1 defusedxml-0.7.1 deprecated-1.2.14 dicom2nifti-2.4.11 dynamic-network-architectures-0.3.1 einops-0.8.0 fastjsonschema-2.20.0 fft-conv-pytorch-1.2.0 filelock-3.15.4 fonttools-4.53.1 fqdn-1.5.1 fsspec-2024.6.1 future-1.0.0 googleapis-common-protos-1.63.2 graphviz-0.20.3 h11-0.14.0 httpcore-1.0.5 httpx-0.27.0 hydra-core-1.3.2 idna-3.7 imagecodecs-2024.6.1 imageio-2.34.2 importlib-metadata-6.11.0 iopath-0.1.10 ipympl-0.9.4 ipython-genutils-0.2.0 ipywidgets-8.1.3 isoduration-20.11.0 jinja2-3.1.4 joblib-1.4.2 json5-0.9.25 jsonpointer-3.0.0 jsonschema-4.23.0 jsonschema-specifications-2023.12.1 jupyter-events-0.10.0 jupyter-lsp-2.2.5 jupyter-server-2.14.2 jupyter-server-terminals-0.5.3 jupyterlab-4.2.4 jupyterlab-pygments-0.3.0 jupyterlab-server-2.27.3 jupyterlab-widgets-3.0.11 kiwisolver-1.4.5 lazy-loader-0.4 linecache2-1.0.0 markupsafe-2.1.5 matplotlib-3.9.1 mistune-3.0.2 monai-1.3.2 mpmath-1.3.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 networkx-3.3 nibabel-5.2.1 nnunetv2-2.5.1 notebook-shim-0.2.4 numpy-2.0.1 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-9.1.0.70 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.20.5 nvidia-nvjitlink-cu12-12.5.82 nvidia-nvtx-cu12-12.1.105 omegaconf-2.3.0 opencv-python-4.10.0.84 opentelemetry-api-1.21.0 opentelemetry-exporter-otlp-proto-common-1.21.0 opentelemetry-exporter-otlp-proto-http-1.21.0 opentelemetry-proto-1.21.0 opentelemetry-sdk-1.21.0 opentelemetry-semantic-conventions-0.42b0 overrides-7.7.0 pandas-2.2.2 pandocfilters-1.5.1 pillow-10.4.0 portalocker-2.10.1 prometheus-client-0.20.0 protobuf-4.25.4 psutil-5.9.8 pycparser-2.22 pydicom-2.4.4 pyparsing-3.1.2 python-dateutil-2.9.0.post0 python-gdcm-3.0.24.1 python-json-logger-2.0.7 pytz-2024.1 pyyaml-6.0.1 referencing-0.35.1 requests-2.32.3 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.19.1 scikit-image-0.24.0 scikit-learn-1.5.1 scipy-1.14.0 seaborn-0.13.2 send2trash-1.8.3 simpleitk-2.3.1 sniffio-1.3.1 soupsieve-2.5 sympy-1.13.1 synapseclient-4.4.0 tensorboardx-2.6.2.2 terminado-0.18.1 threadpoolctl-3.5.0 tifffile-2024.7.24 tinycss2-1.3.0 torch-2.4.0 torchaudio-2.4.0 torchsummary-1.5.1 torchvision-0.19.0 tqdm-4.66.4 traceback2-1.4.0 triton-3.0.0 types-python-dateutil-2.9.0.20240316 tzdata-2024.1 unittest2-1.1.0 uri-template-1.3.0 urllib3-1.26.19 webcolors-24.6.0 webencodings-0.5.1 websocket-client-1.8.0 widgetsnbextension-4.0.11 wrapt-1.16.0 yacs-0.1.8\n",
            "\n",
            "\b\b/ \b\bdone\n",
            "#\n",
            "# To activate this environment, use\n",
            "#\n",
            "#     $ conda activate medsam2\n",
            "#\n",
            "# To deactivate an active environment, use\n",
            "#\n",
            "#     $ conda deactivate\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!source activate medsam2"
      ],
      "metadata": {
        "id": "KWx46cw3A5Dv"
      },
      "execution_count": 2,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!conda run -n medsam2 --no-capture-output conda list"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "QCSR_NS2BCjE",
        "outputId": "4598357f-482d-4891-9c79-997b1e9d6044"
      },
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "# packages in environment at /usr/local/envs/medsam2:\n",
            "#\n",
            "# Name                    Version                   Build  Channel\n",
            "_libgcc_mutex             0.1                        main    conda-forge\n",
            "_openmp_mutex             5.1                       1_gnu  \n",
            "acvl-utils                0.2                      pypi_0    pypi\n",
            "antlr4-python3-runtime    4.9.3                    pypi_0    pypi\n",
            "anyio                     4.4.0                    pypi_0    pypi\n",
            "argon2-cffi               23.1.0                   pypi_0    pypi\n",
            "argon2-cffi-bindings      21.2.0                   pypi_0    pypi\n",
            "argparse                  1.4.0                    pypi_0    pypi\n",
            "arrow                     1.3.0                    pypi_0    pypi\n",
            "asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge\n",
            "async-lru                 2.0.4                    pypi_0    pypi\n",
            "asyncio-atexit            1.0.1                    pypi_0    pypi\n",
            "attrs                     23.2.0                   pypi_0    pypi\n",
            "babel                     2.15.0                   pypi_0    pypi\n",
            "backoff                   2.2.1                    pypi_0    pypi\n",
            "batchgenerators           0.25                     pypi_0    pypi\n",
            "batchgeneratorsv2         0.2                      pypi_0    pypi\n",
            "beautifulsoup4            4.12.3                   pypi_0    pypi\n",
            "bleach                    6.1.0                    pypi_0    pypi\n",
            "bzip2                     1.0.8                h5eee18b_6  \n",
            "ca-certificates           2024.7.4             hbcca054_0    conda-forge\n",
            "certifi                   2024.7.4                 pypi_0    pypi\n",
            "cffi                      1.16.0                   pypi_0    pypi\n",
            "charset-normalizer        3.3.2                    pypi_0    pypi\n",
            "comm                      0.2.2              pyhd8ed1ab_0    conda-forge\n",
            "connected-components-3d   3.18.0                   pypi_0    pypi\n",
            "contourpy                 1.2.1                    pypi_0    pypi\n",
            "cycler                    0.12.1                   pypi_0    pypi\n",
            "debugpy                   1.6.7           py312h6a678d5_0  \n",
            "decorator                 5.1.1              pyhd8ed1ab_0    conda-forge\n",
            "defusedxml                0.7.1                    pypi_0    pypi\n",
            "deprecated                1.2.14                   pypi_0    pypi\n",
            "dicom2nifti               2.4.11                   pypi_0    pypi\n",
            "dynamic-network-architectures 0.3.1                    pypi_0    pypi\n",
            "einops                    0.8.0                    pypi_0    pypi\n",
            "exceptiongroup            1.2.2              pyhd8ed1ab_0    conda-forge\n",
            "executing                 2.0.1              pyhd8ed1ab_0    conda-forge\n",
            "expat                     2.6.2                h6a678d5_0  \n",
            "fastjsonschema            2.20.0                   pypi_0    pypi\n",
            "fft-conv-pytorch          1.2.0                    pypi_0    pypi\n",
            "filelock                  3.15.4                   pypi_0    pypi\n",
            "fonttools                 4.53.1                   pypi_0    pypi\n",
            "fqdn                      1.5.1                    pypi_0    pypi\n",
            "fsspec                    2024.6.1                 pypi_0    pypi\n",
            "future                    1.0.0                    pypi_0    pypi\n",
            "googleapis-common-protos  1.63.2                   pypi_0    pypi\n",
            "h11                       0.14.0                   pypi_0    pypi\n",
            "httpcore                  1.0.5                    pypi_0    pypi\n",
            "httpx                     0.27.0                   pypi_0    pypi\n",
            "hydra-core                1.3.2                    pypi_0    pypi\n",
            "idna                      3.7                      pypi_0    pypi\n",
            "imagecodecs               2024.6.1                 pypi_0    pypi\n",
            "imageio                   2.34.2                   pypi_0    pypi\n",
            "importlib-metadata        6.11.0                   pypi_0    pypi\n",
            "importlib_metadata        8.2.0                hd8ed1ab_0    conda-forge\n",
            "iopath                    0.1.10                   pypi_0    pypi\n",
            "ipykernel                 6.29.5             pyh3099207_0    conda-forge\n",
            "ipympl                    0.9.4                    pypi_0    pypi\n",
            "ipython                   8.26.0             pyh707e725_0    conda-forge\n",
            "ipython-genutils          0.2.0                    pypi_0    pypi\n",
            "ipywidgets                8.1.3                    pypi_0    pypi\n",
            "isoduration               20.11.0                  pypi_0    pypi\n",
            "jedi                      0.19.1             pyhd8ed1ab_0    conda-forge\n",
            "jinja2                    3.1.4                    pypi_0    pypi\n",
            "joblib                    1.4.2                    pypi_0    pypi\n",
            "json5                     0.9.25                   pypi_0    pypi\n",
            "jsonpointer               3.0.0                    pypi_0    pypi\n",
            "jsonschema                4.23.0                   pypi_0    pypi\n",
            "jsonschema-specifications 2023.12.1                pypi_0    pypi\n",
            "jupyter-events            0.10.0                   pypi_0    pypi\n",
            "jupyter-lsp               2.2.5                    pypi_0    pypi\n",
            "jupyter-server            2.14.2                   pypi_0    pypi\n",
            "jupyter-server-terminals  0.5.3                    pypi_0    pypi\n",
            "jupyter_client            8.6.2              pyhd8ed1ab_0    conda-forge\n",
            "jupyter_core              5.7.2           py312h06a4308_0  \n",
            "jupyterlab                4.2.4                    pypi_0    pypi\n",
            "jupyterlab-pygments       0.3.0                    pypi_0    pypi\n",
            "jupyterlab-server         2.27.3                   pypi_0    pypi\n",
            "jupyterlab-widgets        3.0.11                   pypi_0    pypi\n",
            "kiwisolver                1.4.5                    pypi_0    pypi\n",
            "lazy-loader               0.4                      pypi_0    pypi\n",
            "ld_impl_linux-64          2.38                 h1181459_1  \n",
            "libffi                    3.4.4                h6a678d5_1  \n",
            "libgcc-ng                 11.2.0               h1234567_1  \n",
            "libgomp                   11.2.0               h1234567_1  \n",
            "libsodium                 1.0.18               h36c2ea0_1    conda-forge\n",
            "libstdcxx-ng              11.2.0               h1234567_1  \n",
            "libuuid                   1.41.5               h5eee18b_0  \n",
            "linecache2                1.0.0                    pypi_0    pypi\n",
            "markupsafe                2.1.5                    pypi_0    pypi\n",
            "matplotlib                3.9.1                    pypi_0    pypi\n",
            "matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge\n",
            "mistune                   3.0.2                    pypi_0    pypi\n",
            "monai                     1.3.2                    pypi_0    pypi\n",
            "mpmath                    1.3.0                    pypi_0    pypi\n",
            "nbclient                  0.10.0                   pypi_0    pypi\n",
            "nbconvert                 7.16.4                   pypi_0    pypi\n",
            "nbformat                  5.10.4                   pypi_0    pypi\n",
            "ncurses                   6.4                  h6a678d5_0  \n",
            "nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge\n",
            "networkx                  3.3                      pypi_0    pypi\n",
            "nibabel                   5.2.1                    pypi_0    pypi\n",
            "nnunetv2                  2.5.1                    pypi_0    pypi\n",
            "notebook-shim             0.2.4                    pypi_0    pypi\n",
            "numpy                     2.0.1                    pypi_0    pypi\n",
            "nvidia-cublas-cu12        12.1.3.1                 pypi_0    pypi\n",
            "nvidia-cuda-cupti-cu12    12.1.105                 pypi_0    pypi\n",
            "nvidia-cuda-nvrtc-cu12    12.1.105                 pypi_0    pypi\n",
            "nvidia-cuda-runtime-cu12  12.1.105                 pypi_0    pypi\n",
            "nvidia-cudnn-cu12         9.1.0.70                 pypi_0    pypi\n",
            "nvidia-cufft-cu12         11.0.2.54                pypi_0    pypi\n",
            "nvidia-curand-cu12        10.3.2.106               pypi_0    pypi\n",
            "nvidia-cusolver-cu12      11.4.5.107               pypi_0    pypi\n",
            "nvidia-cusparse-cu12      12.1.0.106               pypi_0    pypi\n",
            "nvidia-nccl-cu12          2.20.5                   pypi_0    pypi\n",
            "nvidia-nvjitlink-cu12     12.5.82                  pypi_0    pypi\n",
            "nvidia-nvtx-cu12          12.1.105                 pypi_0    pypi\n",
            "omegaconf                 2.3.0                    pypi_0    pypi\n",
            "opencv-python             4.10.0.84                pypi_0    pypi\n",
            "openssl                   3.0.14               h5eee18b_0  \n",
            "opentelemetry-api         1.21.0                   pypi_0    pypi\n",
            "opentelemetry-exporter-otlp-proto-common 1.21.0                   pypi_0    pypi\n",
            "opentelemetry-exporter-otlp-proto-http 1.21.0                   pypi_0    pypi\n",
            "opentelemetry-proto       1.21.0                   pypi_0    pypi\n",
            "opentelemetry-sdk         1.21.0                   pypi_0    pypi\n",
            "opentelemetry-semantic-conventions 0.42b0                   pypi_0    pypi\n",
            "overrides                 7.7.0                    pypi_0    pypi\n",
            "packaging                 24.1               pyhd8ed1ab_0    conda-forge\n",
            "pandas                    2.2.2                    pypi_0    pypi\n",
            "pandocfilters             1.5.1                    pypi_0    pypi\n",
            "parso                     0.8.4              pyhd8ed1ab_0    conda-forge\n",
            "pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge\n",
            "pickleshare               0.7.5                   py_1003    conda-forge\n",
            "pillow                    10.4.0                   pypi_0    pypi\n",
            "pip                       24.0            py312h06a4308_0  \n",
            "platformdirs              4.2.2              pyhd8ed1ab_0    conda-forge\n",
            "portalocker               2.10.1                   pypi_0    pypi\n",
            "prometheus-client         0.20.0                   pypi_0    pypi\n",
            "prompt-toolkit            3.0.47             pyha770c72_0    conda-forge\n",
            "protobuf                  4.25.4                   pypi_0    pypi\n",
            "psutil                    5.9.8                    pypi_0    pypi\n",
            "ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge\n",
            "pure_eval                 0.2.3              pyhd8ed1ab_0    conda-forge\n",
            "pycparser                 2.22                     pypi_0    pypi\n",
            "pydicom                   2.4.4                    pypi_0    pypi\n",
            "pygments                  2.18.0             pyhd8ed1ab_0    conda-forge\n",
            "pyparsing                 3.1.2                    pypi_0    pypi\n",
            "python                    3.12.4               h5148396_1  \n",
            "python-dateutil           2.9.0.post0              pypi_0    pypi\n",
            "python-gdcm               3.0.24.1                 pypi_0    pypi\n",
            "python-graphviz           0.20.3                   pypi_0    pypi\n",
            "python-json-logger        2.0.7                    pypi_0    pypi\n",
            "pytz                      2024.1                   pypi_0    pypi\n",
            "pyyaml                    6.0.1                    pypi_0    pypi\n",
            "pyzmq                     25.1.2          py312h6a678d5_0  \n",
            "readline                  8.2                  h5eee18b_0  \n",
            "referencing               0.35.1                   pypi_0    pypi\n",
            "requests                  2.32.3                   pypi_0    pypi\n",
            "rfc3339-validator         0.1.4                    pypi_0    pypi\n",
            "rfc3986-validator         0.1.1                    pypi_0    pypi\n",
            "rpds-py                   0.19.1                   pypi_0    pypi\n",
            "scikit-image              0.24.0                   pypi_0    pypi\n",
            "scikit-learn              1.5.1                    pypi_0    pypi\n",
            "scipy                     1.14.0                   pypi_0    pypi\n",
            "seaborn                   0.13.2                   pypi_0    pypi\n",
            "send2trash                1.8.3                    pypi_0    pypi\n",
            "setuptools                69.5.1          py312h06a4308_0  \n",
            "simpleitk                 2.3.1                    pypi_0    pypi\n",
            "six                       1.16.0             pyh6c4a22f_0    conda-forge\n",
            "sniffio                   1.3.1                    pypi_0    pypi\n",
            "soupsieve                 2.5                      pypi_0    pypi\n",
            "sqlite                    3.45.3               h5eee18b_0  \n",
            "stack_data                0.6.2              pyhd8ed1ab_0    conda-forge\n",
            "sympy                     1.13.1                   pypi_0    pypi\n",
            "synapseclient             4.4.0                    pypi_0    pypi\n",
            "tensorboardx              2.6.2.2                  pypi_0    pypi\n",
            "terminado                 0.18.1                   pypi_0    pypi\n",
            "threadpoolctl             3.5.0                    pypi_0    pypi\n",
            "tifffile                  2024.7.24                pypi_0    pypi\n",
            "tinycss2                  1.3.0                    pypi_0    pypi\n",
            "tk                        8.6.14               h39e8969_0  \n",
            "torch                     2.4.0                    pypi_0    pypi\n",
            "torchaudio                2.4.0                    pypi_0    pypi\n",
            "torchsummary              1.5.1                    pypi_0    pypi\n",
            "torchvision               0.19.0                   pypi_0    pypi\n",
            "tornado                   6.4.1           py312h5eee18b_0  \n",
            "tqdm                      4.66.4                   pypi_0    pypi\n",
            "traceback2                1.4.0                    pypi_0    pypi\n",
            "traitlets                 5.14.3             pyhd8ed1ab_0    conda-forge\n",
            "triton                    3.0.0                    pypi_0    pypi\n",
            "types-python-dateutil     2.9.0.20240316           pypi_0    pypi\n",
            "typing_extensions         4.12.2             pyha770c72_0    conda-forge\n",
            "tzdata                    2024.1                   pypi_0    pypi\n",
            "unittest2                 1.1.0                    pypi_0    pypi\n",
            "uri-template              1.3.0                    pypi_0    pypi\n",
            "urllib3                   1.26.19                  pypi_0    pypi\n",
            "wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge\n",
            "webcolors                 24.6.0                   pypi_0    pypi\n",
            "webencodings              0.5.1                    pypi_0    pypi\n",
            "websocket-client          1.8.0                    pypi_0    pypi\n",
            "wheel                     0.43.0          py312h06a4308_0  \n",
            "widgetsnbextension        4.0.11                   pypi_0    pypi\n",
            "wrapt                     1.16.0                   pypi_0    pypi\n",
            "xz                        5.4.6                h5eee18b_1  \n",
            "yacs                      0.1.8                    pypi_0    pypi\n",
            "zeromq                    4.3.5                h6a678d5_0  \n",
            "zipp                      3.19.2             pyhd8ed1ab_0    conda-forge\n",
            "zlib                      1.2.13               h5eee18b_1  \n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!bash checkpoints/download_ckpts.sh"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "6xbEAdcFBHJf",
        "outputId": "9c916ecf-b80f-4226-bd69-41b988121b45"
      },
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Downloading sam2_hiera_tiny.pt checkpoint...\n",
            "--2024-09-30 13:07:53--  https://dl.fbaipublicfiles.com/segment_anything_2/072824/sam2_hiera_tiny.pt\n",
            "Resolving dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)... 13.226.210.78, 13.226.210.111, 13.226.210.15, ...\n",
            "Connecting to dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)|13.226.210.78|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 155906050 (149M) [application/vnd.snesdev-page-table]\n",
            "Saving to: ‘sam2_hiera_tiny.pt’\n",
            "\n",
            "sam2_hiera_tiny.pt  100%[===================>] 148.68M   186MB/s    in 0.8s    \n",
            "\n",
            "2024-09-30 13:07:54 (186 MB/s) - ‘sam2_hiera_tiny.pt’ saved [155906050/155906050]\n",
            "\n",
            "Downloading sam2_hiera_small.pt checkpoint...\n",
            "--2024-09-30 13:07:54--  https://dl.fbaipublicfiles.com/segment_anything_2/072824/sam2_hiera_small.pt\n",
            "Resolving dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)... 13.226.210.78, 13.226.210.111, 13.226.210.15, ...\n",
            "Connecting to dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)|13.226.210.78|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 184309650 (176M) [application/vnd.snesdev-page-table]\n",
            "Saving to: ‘sam2_hiera_small.pt’\n",
            "\n",
            "sam2_hiera_small.pt 100%[===================>] 175.77M   116MB/s    in 1.5s    \n",
            "\n",
            "2024-09-30 13:07:56 (116 MB/s) - ‘sam2_hiera_small.pt’ saved [184309650/184309650]\n",
            "\n",
            "Downloading sam2_hiera_base_plus.pt checkpoint...\n",
            "--2024-09-30 13:07:56--  https://dl.fbaipublicfiles.com/segment_anything_2/072824/sam2_hiera_base_plus.pt\n",
            "Resolving dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)... 13.226.210.78, 13.226.210.111, 13.226.210.15, ...\n",
            "Connecting to dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)|13.226.210.78|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 323493298 (309M) [application/vnd.snesdev-page-table]\n",
            "Saving to: ‘sam2_hiera_base_plus.pt’\n",
            "\n",
            "sam2_hiera_base_plu 100%[===================>] 308.51M  28.1MB/s    in 4.8s    \n",
            "\n",
            "2024-09-30 13:08:01 (64.2 MB/s) - ‘sam2_hiera_base_plus.pt’ saved [323493298/323493298]\n",
            "\n",
            "Downloading sam2_hiera_large.pt checkpoint...\n",
            "--2024-09-30 13:08:01--  https://dl.fbaipublicfiles.com/segment_anything_2/072824/sam2_hiera_large.pt\n",
            "Resolving dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)... 13.226.210.78, 13.226.210.111, 13.226.210.15, ...\n",
            "Connecting to dl.fbaipublicfiles.com (dl.fbaipublicfiles.com)|13.226.210.78|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 897952466 (856M) [application/vnd.snesdev-page-table]\n",
            "Saving to: ‘sam2_hiera_large.pt’\n",
            "\n",
            "sam2_hiera_large.pt 100%[===================>] 856.35M   197MB/s    in 4.5s    \n",
            "\n",
            "2024-09-30 13:08:05 (191 MB/s) - ‘sam2_hiera_large.pt’ saved [897952466/897952466]\n",
            "\n",
            "All checkpoints are downloaded successfully.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!pwd"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "Z69o1i8NBHp6",
        "outputId": "ff8fda41-2a74-4ab8-f492-462dcd6ae9aa"
      },
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "/content/Medical-SAM2\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!wget https://huggingface.co/datasets/jiayuanz3/REFUGE/resolve/main/REFUGE.zip"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "8z3G17OyBJjC",
        "outputId": "08ec1a60-3c20-461c-e706-aa71ba4104a9"
      },
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2024-09-30 13:08:07--  https://huggingface.co/datasets/jiayuanz3/REFUGE/resolve/main/REFUGE.zip\n",
            "Resolving huggingface.co (huggingface.co)... 18.164.174.55, 18.164.174.23, 18.164.174.17, ...\n",
            "Connecting to huggingface.co (huggingface.co)|18.164.174.55|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://cdn-lfs-us-1.hf.co/repos/d3/e2/d3e23fd77fa1bf9f571514adc7af3c50c8eb28518483cf73251c4da4521c037e/6048ef7afbb7e783c4db673f0689305ea68d182865bc6b9a0838e022e893cdbb?response-content-disposition=inline%3B+filename*%3DUTF-8%27%27REFUGE.zip%3B+filename%3D%22REFUGE.zip%22%3B&response-content-type=application%2Fzip&Expires=1727960887&Policy=eyJTdGF0ZW1lbnQiOlt7IkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTcyNzk2MDg4N319LCJSZXNvdXJjZSI6Imh0dHBzOi8vY2RuLWxmcy11cy0xLmhmLmNvL3JlcG9zL2QzL2UyL2QzZTIzZmQ3N2ZhMWJmOWY1NzE1MTRhZGM3YWYzYzUwYzhlYjI4NTE4NDgzY2Y3MzI1MWM0ZGE0NTIxYzAzN2UvNjA0OGVmN2FmYmI3ZTc4M2M0ZGI2NzNmMDY4OTMwNWVhNjhkMTgyODY1YmM2YjlhMDgzOGUwMjJlODkzY2RiYj9yZXNwb25zZS1jb250ZW50LWRpc3Bvc2l0aW9uPSomcmVzcG9uc2UtY29udGVudC10eXBlPSoifV19&Signature=iTZFHpngV8a%7EjSOQ-AHXVklG9pNnfSq2uWxX0wqWT0amVYk1YSQpFzapvWipPifmxhBp75KCPdHpD1RTWm0wvnOHxlx5GoRfZ2HgbToG5RrPBjTeZq7vKSA-3L1zcwPwIhSHwOEFPvBW26wUTocmOFq-MrEzeiXiRsxrQ75skwARPu4w%7E3DBI4MDwqKatWFW3uYeblG21n5qX6wNVoA7Wq6bH1HHwYGjLPamMo6bt40-8Z1CYO4S%7EeXQYAxum5JGzhREIqG2w2lTTIU3YkObyx8GZ3na3HgKxckTaNPYlThkeF4WFPaAnjfSX-A%7ER6pQw8WJf4t8BV-YSoDmjlVeiw__&Key-Pair-Id=K24J24Z295AEI9 [following]\n",
            "--2024-09-30 13:08:07--  https://cdn-lfs-us-1.hf.co/repos/d3/e2/d3e23fd77fa1bf9f571514adc7af3c50c8eb28518483cf73251c4da4521c037e/6048ef7afbb7e783c4db673f0689305ea68d182865bc6b9a0838e022e893cdbb?response-content-disposition=inline%3B+filename*%3DUTF-8%27%27REFUGE.zip%3B+filename%3D%22REFUGE.zip%22%3B&response-content-type=application%2Fzip&Expires=1727960887&Policy=eyJTdGF0ZW1lbnQiOlt7IkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTcyNzk2MDg4N319LCJSZXNvdXJjZSI6Imh0dHBzOi8vY2RuLWxmcy11cy0xLmhmLmNvL3JlcG9zL2QzL2UyL2QzZTIzZmQ3N2ZhMWJmOWY1NzE1MTRhZGM3YWYzYzUwYzhlYjI4NTE4NDgzY2Y3MzI1MWM0ZGE0NTIxYzAzN2UvNjA0OGVmN2FmYmI3ZTc4M2M0ZGI2NzNmMDY4OTMwNWVhNjhkMTgyODY1YmM2YjlhMDgzOGUwMjJlODkzY2RiYj9yZXNwb25zZS1jb250ZW50LWRpc3Bvc2l0aW9uPSomcmVzcG9uc2UtY29udGVudC10eXBlPSoifV19&Signature=iTZFHpngV8a%7EjSOQ-AHXVklG9pNnfSq2uWxX0wqWT0amVYk1YSQpFzapvWipPifmxhBp75KCPdHpD1RTWm0wvnOHxlx5GoRfZ2HgbToG5RrPBjTeZq7vKSA-3L1zcwPwIhSHwOEFPvBW26wUTocmOFq-MrEzeiXiRsxrQ75skwARPu4w%7E3DBI4MDwqKatWFW3uYeblG21n5qX6wNVoA7Wq6bH1HHwYGjLPamMo6bt40-8Z1CYO4S%7EeXQYAxum5JGzhREIqG2w2lTTIU3YkObyx8GZ3na3HgKxckTaNPYlThkeF4WFPaAnjfSX-A%7ER6pQw8WJf4t8BV-YSoDmjlVeiw__&Key-Pair-Id=K24J24Z295AEI9\n",
            "Resolving cdn-lfs-us-1.hf.co (cdn-lfs-us-1.hf.co)... 18.164.174.52, 18.164.174.97, 18.164.174.98, ...\n",
            "Connecting to cdn-lfs-us-1.hf.co (cdn-lfs-us-1.hf.co)|18.164.174.52|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 1790407034 (1.7G) [application/zip]\n",
            "Saving to: ‘REFUGE.zip’\n",
            "\n",
            "REFUGE.zip          100%[===================>]   1.67G   228MB/s    in 9.4s    \n",
            "\n",
            "2024-09-30 13:08:17 (181 MB/s) - ‘REFUGE.zip’ saved [1790407034/1790407034]\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!unzip -qq REFUGE.zip"
      ],
      "metadata": {
        "id": "iRGn9uOsBOM5"
      },
      "execution_count": 7,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!pwd"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "1U3IoQ2VGoT9",
        "outputId": "7d0a2701-ffe1-44a2-9a0d-e55083b8a9f9"
      },
      "execution_count": 8,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "/content/Medical-SAM2\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "%%writefile conf/global_settings.py\n",
        "\"\"\" configurations for this project\n",
        "\n",
        "author Yunli\n",
        "\"\"\"\n",
        "import os\n",
        "from datetime import datetime\n",
        "\n",
        "CHECKPOINT_PATH = 'checkpoint'\n",
        "\n",
        "#total training epoches\n",
        "EPOCH = 1\n",
        "step_size = 10\n",
        "i = 1\n",
        "MILESTONES = []\n",
        "while i * 5 <= EPOCH:\n",
        "    MILESTONES.append(i* step_size)\n",
        "    i += 1\n",
        "\n",
        "#initial learning rate\n",
        "#INIT_LR = 0.1\n",
        "\n",
        "#time of we run the script\n",
        "TIME_NOW = datetime.now().strftime(\"%F_%H-%M-%S.%f\")\n",
        "\n",
        "#tensorboard log dir\n",
        "LOG_DIR = 'runs'\n",
        "\n",
        "#save weights file per SAVE_EPOCH epoch\n",
        "SAVE_EPOCH = 10"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "Hee4IyA_C7Bg",
        "outputId": "35e175a3-6157-4585-f41f-53c91550190c"
      },
      "execution_count": 9,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Overwriting conf/global_settings.py\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!conda run -n medsam2 --no-capture-output bash -c \"python train_2d.py -net sam2 -exp_name REFUGE_MedSAM2 -vis 1 -sam_ckpt sam2_hiera_tiny.pt -sam_config sam2_hiera_t -image_size 1024 -out_size 1024 -b 2 -val_freq 1 -dataset REFUGE -data_path ./REFUGE\""
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "mQ6FydR9GxV_",
        "outputId": "ba3aa106-7ba8-4f4c-afc8-e8391d29258e"
      },
      "execution_count": 11,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "/content/Medical-SAM2/sam2_train/modeling/sam/transformer.py:22: UserWarning: Flash Attention is disabled as it requires a GPU with Ampere (8.0) CUDA capability.\n",
            "  OLD_GPU, USE_FLASH_ATTN, MATH_KERNEL_ON = get_sdpa_settings()\n",
            "INFO:root:Namespace(net='sam2', encoder='vit_b', exp_name='REFUGE_MedSAM2', vis=True, train_vis=False, prompt='bbox', prompt_freq=2, pretrain=None, val_freq=1, gpu=True, gpu_device=0, image_size=1024, out_size=1024, distributed='none', dataset='REFUGE', sam_ckpt='sam2_hiera_tiny.pt', sam_config='sam2_hiera_t', video_length=2, b=2, lr=0.0001, weights=0, multimask_output=1, memory_bank_size=16, data_path='./REFUGE', path_helper={'prefix': 'logs/REFUGE_MedSAM2_2024_09_30_13_26_32', 'ckpt_path': 'logs/REFUGE_MedSAM2_2024_09_30_13_26_32/Model', 'log_path': 'logs/REFUGE_MedSAM2_2024_09_30_13_26_32/Log', 'sample_path': 'logs/REFUGE_MedSAM2_2024_09_30_13_26_32/Samples'})\n",
            "Namespace(net='sam2', encoder='vit_b', exp_name='REFUGE_MedSAM2', vis=True, train_vis=False, prompt='bbox', prompt_freq=2, pretrain=None, val_freq=1, gpu=True, gpu_device=0, image_size=1024, out_size=1024, distributed='none', dataset='REFUGE', sam_ckpt='sam2_hiera_tiny.pt', sam_config='sam2_hiera_t', video_length=2, b=2, lr=0.0001, weights=0, multimask_output=1, memory_bank_size=16, data_path='./REFUGE', path_helper={'prefix': 'logs/REFUGE_MedSAM2_2024_09_30_13_26_32', 'ckpt_path': 'logs/REFUGE_MedSAM2_2024_09_30_13_26_32/Model', 'log_path': 'logs/REFUGE_MedSAM2_2024_09_30_13_26_32/Log', 'sample_path': 'logs/REFUGE_MedSAM2_2024_09_30_13_26_32/Samples'})\n",
            "Traceback (most recent call last):\n",
            "  File \"/content/Medical-SAM2/train_2d.py\", line 124, in <module>\n",
            "    main()\n",
            "  File \"/content/Medical-SAM2/train_2d.py\", line 97, in main\n",
            "    tol, (eiou, edice) = function.validation_sam(args, nice_test_loader, epoch, net, writer)\n",
            "                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
            "  File \"/content/Medical-SAM2/func_2d/function.py\", line 335, in validation_sam\n",
            "    vision_feats_temp = vision_feats[-1].permute(1, 0, 2).view(B, -1, 64, 64) \n",
            "                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
            "RuntimeError: view size is not compatible with input tensor's size and stride (at least one dimension spans across two contiguous subspaces). Use .reshape(...) instead.\n",
            "ERROR conda.cli.main_run:execute(124): `conda run bash -c python train_2d.py -net sam2 -exp_name REFUGE_MedSAM2 -vis 1 -sam_ckpt sam2_hiera_tiny.pt -sam_config sam2_hiera_t -image_size 1024 -out_size 1024 -b 2 -val_freq 1 -dataset REFUGE -data_path ./REFUGE` failed. (See above for error)\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!wget https://huggingface.co/datasets/jiayuanz3/btcv/resolve/main/btcv.zip"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "zrkPqrdJHQCC",
        "outputId": "d5440df3-d804-4f18-ba14-712ca225d9c8"
      },
      "execution_count": 12,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2024-09-30 13:28:42--  https://huggingface.co/datasets/jiayuanz3/btcv/resolve/main/btcv.zip\n",
            "Resolving huggingface.co (huggingface.co)... 18.164.174.23, 18.164.174.55, 18.164.174.17, ...\n",
            "Connecting to huggingface.co (huggingface.co)|18.164.174.23|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://cdn-lfs-us-1.hf.co/repos/9a/a1/9aa1348038139e9ecc691d85b686965cb1e7fb62df85f63d62abd69af1ed1f44/20326300cde6cc8279457ac0f0c9ffede3412a4c4d206d0d4dc2685203d88a1a?response-content-disposition=inline%3B+filename*%3DUTF-8%27%27btcv.zip%3B+filename%3D%22btcv.zip%22%3B&response-content-type=application%2Fzip&Expires=1727962122&Policy=eyJTdGF0ZW1lbnQiOlt7IkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTcyNzk2MjEyMn19LCJSZXNvdXJjZSI6Imh0dHBzOi8vY2RuLWxmcy11cy0xLmhmLmNvL3JlcG9zLzlhL2ExLzlhYTEzNDgwMzgxMzllOWVjYzY5MWQ4NWI2ODY5NjVjYjFlN2ZiNjJkZjg1ZjYzZDYyYWJkNjlhZjFlZDFmNDQvMjAzMjYzMDBjZGU2Y2M4Mjc5NDU3YWMwZjBjOWZmZWRlMzQxMmE0YzRkMjA2ZDBkNGRjMjY4NTIwM2Q4OGExYT9yZXNwb25zZS1jb250ZW50LWRpc3Bvc2l0aW9uPSomcmVzcG9uc2UtY29udGVudC10eXBlPSoifV19&Signature=e6soLtW433gy%7Ek8dmrOG-hIG9l6zIF0othl0PqWfFRFEH4s0NDiVhY8c3MxUNtD0U6QX%7EudzJAkfuHuBGASbzY%7EsQcY9LsaDh0l9NydDLrmMlYRYdPQP25Xc8ZZOiXHZYrEeDlIkZZumMVUgIBj1K9H%7Eq7ubgbrWkkIxLTGb05LsjYXynisp52wJUmYsYDl2KBkX7mGlQGKL-aKY7aPVZa9I2NjBZDIUFRyA-p3KWRiatuoWU0LzFMg6hvVoWHkMPs0IB7oS2AYvGtzAf1oadb4QD47WMkB%7EegrsZ2MiWJCSkdLe5TZrTPr26wDDVtr%7E8QX-M5z8wXogTweg1d8btg__&Key-Pair-Id=K24J24Z295AEI9 [following]\n",
            "--2024-09-30 13:28:42--  https://cdn-lfs-us-1.hf.co/repos/9a/a1/9aa1348038139e9ecc691d85b686965cb1e7fb62df85f63d62abd69af1ed1f44/20326300cde6cc8279457ac0f0c9ffede3412a4c4d206d0d4dc2685203d88a1a?response-content-disposition=inline%3B+filename*%3DUTF-8%27%27btcv.zip%3B+filename%3D%22btcv.zip%22%3B&response-content-type=application%2Fzip&Expires=1727962122&Policy=eyJTdGF0ZW1lbnQiOlt7IkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTcyNzk2MjEyMn19LCJSZXNvdXJjZSI6Imh0dHBzOi8vY2RuLWxmcy11cy0xLmhmLmNvL3JlcG9zLzlhL2ExLzlhYTEzNDgwMzgxMzllOWVjYzY5MWQ4NWI2ODY5NjVjYjFlN2ZiNjJkZjg1ZjYzZDYyYWJkNjlhZjFlZDFmNDQvMjAzMjYzMDBjZGU2Y2M4Mjc5NDU3YWMwZjBjOWZmZWRlMzQxMmE0YzRkMjA2ZDBkNGRjMjY4NTIwM2Q4OGExYT9yZXNwb25zZS1jb250ZW50LWRpc3Bvc2l0aW9uPSomcmVzcG9uc2UtY29udGVudC10eXBlPSoifV19&Signature=e6soLtW433gy%7Ek8dmrOG-hIG9l6zIF0othl0PqWfFRFEH4s0NDiVhY8c3MxUNtD0U6QX%7EudzJAkfuHuBGASbzY%7EsQcY9LsaDh0l9NydDLrmMlYRYdPQP25Xc8ZZOiXHZYrEeDlIkZZumMVUgIBj1K9H%7Eq7ubgbrWkkIxLTGb05LsjYXynisp52wJUmYsYDl2KBkX7mGlQGKL-aKY7aPVZa9I2NjBZDIUFRyA-p3KWRiatuoWU0LzFMg6hvVoWHkMPs0IB7oS2AYvGtzAf1oadb4QD47WMkB%7EegrsZ2MiWJCSkdLe5TZrTPr26wDDVtr%7E8QX-M5z8wXogTweg1d8btg__&Key-Pair-Id=K24J24Z295AEI9\n",
            "Resolving cdn-lfs-us-1.hf.co (cdn-lfs-us-1.hf.co)... 18.164.174.98, 18.164.174.52, 18.164.174.97, ...\n",
            "Connecting to cdn-lfs-us-1.hf.co (cdn-lfs-us-1.hf.co)|18.164.174.98|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 50973696 (49M) [application/zip]\n",
            "Saving to: ‘btcv.zip’\n",
            "\n",
            "btcv.zip            100%[===================>]  48.61M  62.9MB/s    in 0.8s    \n",
            "\n",
            "2024-09-30 13:28:43 (62.9 MB/s) - ‘btcv.zip’ saved [50973696/50973696]\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!unzip -qq btcv.zip"
      ],
      "metadata": {
        "id": "zgvPk-iWHptn"
      },
      "execution_count": 13,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!conda run -n medsam2 --no-capture-output bash -c \"python train_3d.py -net sam2 -exp_name BTCV_MedSAM2 -sam_ckpt sam2_hiera_small.pt -sam_config sam2_hiera_s -image_size 1024 -val_freq 1 -prompt bbox -prompt_freq 2 -dataset btcv -data_path ./btcv\""
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "AEwt5kcSHxW8",
        "outputId": "25c4829e-394d-4c66-e0bf-1a607aa09655"
      },
      "execution_count": 14,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "/content/Medical-SAM2/func_3d/function.py:41: FutureWarning: `torch.cuda.amp.GradScaler(args...)` is deprecated. Please use `torch.amp.GradScaler('cuda', args...)` instead.\n",
            "  scaler = torch.cuda.amp.GradScaler()\n",
            "/content/Medical-SAM2/sam2_train/modeling/sam/transformer.py:22: UserWarning: Flash Attention is disabled as it requires a GPU with Ampere (8.0) CUDA capability.\n",
            "  OLD_GPU, USE_FLASH_ATTN, MATH_KERNEL_ON = get_sdpa_settings()\n",
            "INFO:root:Namespace(net='sam2', encoder='vit_b', exp_name='BTCV_MedSAM2', vis=False, train_vis=False, prompt='bbox', prompt_freq=2, pretrain=None, val_freq=1, gpu=True, gpu_device=0, image_size=1024, out_size=1024, distributed='none', dataset='btcv', sam_ckpt='sam2_hiera_small.pt', sam_config='sam2_hiera_s', video_length=2, b=1, lr=0.0001, weights=0, multimask_output=1, memory_bank_size=16, data_path='./btcv', path_helper={'prefix': 'logs/BTCV_MedSAM2_2024_09_30_13_30_22', 'ckpt_path': 'logs/BTCV_MedSAM2_2024_09_30_13_30_22/Model', 'log_path': 'logs/BTCV_MedSAM2_2024_09_30_13_30_22/Log', 'sample_path': 'logs/BTCV_MedSAM2_2024_09_30_13_30_22/Samples'})\n",
            "Namespace(net='sam2', encoder='vit_b', exp_name='BTCV_MedSAM2', vis=False, train_vis=False, prompt='bbox', prompt_freq=2, pretrain=None, val_freq=1, gpu=True, gpu_device=0, image_size=1024, out_size=1024, distributed='none', dataset='btcv', sam_ckpt='sam2_hiera_small.pt', sam_config='sam2_hiera_s', video_length=2, b=1, lr=0.0001, weights=0, multimask_output=1, memory_bank_size=16, data_path='./btcv', path_helper={'prefix': 'logs/BTCV_MedSAM2_2024_09_30_13_30_22', 'ckpt_path': 'logs/BTCV_MedSAM2_2024_09_30_13_30_22/Model', 'log_path': 'logs/BTCV_MedSAM2_2024_09_30_13_30_22/Log', 'sample_path': 'logs/BTCV_MedSAM2_2024_09_30_13_30_22/Samples'})\n",
            "/usr/local/envs/medsam2/lib/python3.12/site-packages/torch/utils/data/dataloader.py:557: UserWarning: This DataLoader will create 8 worker processes in total. Our suggested max number of worker in current system is 2, which is smaller than what this DataLoader is going to create. Please be aware that excessive worker creation might get DataLoader running slow or even freeze, lower the worker number to avoid potential slowness/freeze if necessary.\n",
            "  warnings.warn(_create_warning_msg(\n",
            "Epoch 0:   0% 0/24 [00:42<?, ?img/s]\n",
            "Traceback (most recent call last):\n",
            "  File \"/content/Medical-SAM2/train_3d.py\", line 112, in <module>\n",
            "    main()\n",
            "  File \"/content/Medical-SAM2/train_3d.py\", line 95, in main\n",
            "    loss, prompt_loss, non_prompt_loss = function.train_sam(args, net, optimizer1, optimizer2, nice_train_loader, epoch)\n",
            "                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
            "  File \"/content/Medical-SAM2/func_3d/function.py\", line 114, in train_sam\n",
            "    _, _, _ = net.train_add_new_bbox(\n",
            "              ^^^^^^^^^^^^^^^^^^^^^^^\n",
            "  File \"/content/Medical-SAM2/sam2_train/sam2_video_predictor.py\", line 439, in train_add_new_bbox\n",
            "    out_frame_idx, out_obj_ids, out_mask_logits = self.train_add_new_points(\n",
            "                                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
            "  File \"/content/Medical-SAM2/sam2_train/sam2_video_predictor.py\", line 523, in train_add_new_points\n",
            "    current_out, _ = self._run_single_frame_inference(\n",
            "                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
            "  File \"/content/Medical-SAM2/sam2_train/sam2_video_predictor.py\", line 1351, in _run_single_frame_inference\n",
            "    pred_masks_gpu = fill_holes_in_mask_scores(\n",
            "                     ^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
            "  File \"/content/Medical-SAM2/sam2_train/utils/misc.py\", line 255, in fill_holes_in_mask_scores\n",
            "    is_hole = (labels > 0) & (areas <= max_area)\n",
            "               ^^^^^^^^^^\n",
            "RuntimeError: CUDA error: no kernel image is available for execution on the device\n",
            "CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect.\n",
            "For debugging consider passing CUDA_LAUNCH_BLOCKING=1\n",
            "Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.\n",
            "\n",
            "ERROR conda.cli.main_run:execute(124): `conda run bash -c python train_3d.py -net sam2 -exp_name BTCV_MedSAM2 -sam_ckpt sam2_hiera_small.pt -sam_config sam2_hiera_s -image_size 1024 -val_freq 1 -prompt bbox -prompt_freq 2 -dataset btcv -data_path ./btcv` failed. (See above for error)\n"
          ]
        }
      ]
    }
  ]
}