python_notebooks/jsonToCsv.ipynb

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      "source": [
        "#Table of Content "
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      "metadata": {
        "id": "2LdsatksTstB"
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      "source": [
        "import json, csv, os\n",
        "import pandas as pd\n",
        "from re import search"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "PosFilPath=\"\"\n",
        "while PosFilPath.startswith('y') == False:\n",
        "  workDir = input(\"Input parent directory path: \\n\")\n",
        "  PosFilPath = input(\"Does this look correct? \" + workDir + \"\\n\")\n",
        "\n",
        "  if PosFilPath.lower().startswith('y') == True: \n",
        "\n",
        "    parentDirExit = os.path.exists(workDir)\n",
        "    #print(envVarsExist)\n",
        "\n",
        "    if parentDirExit != False:\n",
        "        print(\"Working directory has been set to \" + workDir + \".\\n\")\n",
        "    else: \n",
        "      print(\"The path \" + workDir + \" is an invalid , try again\\n\")\n",
        "      PosFilPath = \"no\""
      ],
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          "text": [
            "Input parent directory path: \n",
            "/content\n",
            "Does this look correct? /content\n",
            "yes\n",
            "Working directory has been set to /content.\n",
            "\n"
          ]
        }
      ]
    },
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      "cell_type": "code",
      "source": [
        "cats = [\"images\", \"annotations\", \"categories\"] #catagories of intrest\n",
        "\n",
        "os.makedirs(workDir + '/CSVfiles', exist_ok=True)  \n",
        "\n",
        "for name in cats:\n",
        "  with open(workDir + \"/channel_islands_camera_traps.json\", \"r\") as f: #insert path to channel_islands_camera_traps.json file\n",
        "    data = json.load(f)\n",
        "    names = data[name]\n",
        "\n",
        "  with open(workDir + \"/CSVfiles/channel_islands_camera_traps_\" + name + \".csv\", \"w\") as p: \n",
        "    fieldnames = names[0].keys()\n",
        "    writer = csv.DictWriter(p,fieldnames=fieldnames)\n",
        "    writer.writeheader()\n",
        "    for i in names:\n",
        "      writer.writerow(i)"
      ],
      "metadata": {
        "id": "3YsNn5cQUPvE"
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      "execution_count": null,
      "outputs": []
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      "source": [
        "annotations = pd.read_csv(workDir + \"/CSVfiles/channel_islands_camera_traps_annotations.csv\")\n",
        "images = pd.read_csv(workDir + \"/CSVfiles/channel_islands_camera_traps_images.csv\")\n",
        "catagories = pd.read_csv(workDir + '/CSVfiles/channel_islands_camera_traps_categories.csv')"
      ],
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              "Index(['id', 'file_name', 'seq_id', 'seq_num_frames', 'frame_num',\n",
              "       'original_relative_path', 'location', 'temperature', 'width', 'height'],\n",
              "      dtype='object')"
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          "execution_count": 16
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              "Index(['id', 'image_id', 'category_id', 'sequence_level_annotation', 'bbox'], dtype='object')"
            ]
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          "metadata": {},
          "execution_count": 18
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      ]
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              "(264321, 5)"
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      "source": [
        "annotations.rename(columns={\"id\":\"annotation_id\",\n",
        "                            \"image_id\":\"id\"}, inplace = True)\n",
        "parentTable = pd.merge(images, annotations,\n",
        "         how='inner', on='id')"
      ],
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      "source": [
        "sanity check "
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              "Index(['id', 'file_name', 'seq_id', 'seq_num_frames', 'frame_num',\n",
              "       'original_relative_path', 'location', 'temperature', 'width', 'height',\n",
              "       'annotation_id', 'category_id', 'sequence_level_annotation', 'bbox'],\n",
              "      dtype='object')"
            ]
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          "execution_count": 21
        }
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              "Index(['id', 'file_name', 'seq_id', 'seq_num_frames', 'frame_num',\n",
              "       'original_relative_path', 'location', 'temperature', 'width', 'height',\n",
              "       'annotation_id', 'category_id', 'sequence_level_annotation', 'bbox'],\n",
              "      dtype='object')"
            ]
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          "metadata": {},
          "execution_count": 22
        }
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      "cell_type": "code",
      "source": [
        "parentTable.head()"
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              "                                     id                       file_name  \\\n",
              "0  dd8b68e9-360b-429e-a43b-892c2e036455  loc-h500ee07133376/000/000.jpg   \n",
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              "\n",
              "                                 seq_id  seq_num_frames  frame_num  \\\n",
              "0  836f6487-50fd-42f5-8dcc-336fc538b7a8               6          0   \n",
              "1  836f6487-50fd-42f5-8dcc-336fc538b7a8               6          1   \n",
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              "4  836f6487-50fd-42f5-8dcc-336fc538b7a8               6          4   \n",
              "\n",
              "                              original_relative_path        location  \\\n",
              "0  2011_09_Set/Station%201/2011/2011-09-13/IMG_00...  h500ee07133376   \n",
              "1  2011_09_Set/Station%201/2011/2011-09-13/IMG_00...  h500ee07133376   \n",
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              "4  2011_09_Set/Station%201/2011/2011-09-13/IMG_00...  h500ee07133376   \n",
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              "  temperature  width  height                         annotation_id  \\\n",
              "0        21 c   1920    1080  16e360cc-4a53-11eb-b9b3-000d3a74c7de   \n",
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              "2        21 c   1920    1080  16e360ce-4a53-11eb-832e-000d3a74c7de   \n",
              "3        21 c   1920    1080  16e360cf-4a53-11eb-9447-000d3a74c7de   \n",
              "4        21 c   1920    1080  16e360d0-4a53-11eb-90ec-000d3a74c7de   \n",
              "\n",
              "   category_id  sequence_level_annotation                 bbox  \n",
              "0            0                      False   [0, 0, 1919, 1079]  \n",
              "1            0                      False   [0, 0, 1919, 1079]  \n",
              "2            0                      False   [0, 0, 1919, 1079]  \n",
              "3            1                      False  [0, 657, 1919, 391]  \n",
              "4            0                      False   [0, 0, 1919, 1079]  "
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              "          dataTable['output_type'] = 'display_data';\n",
              "          await google.colab.output.renderOutput(dataTable, element);\n",
              "          const docLink = document.createElement('div');\n",
              "          docLink.innerHTML = docLinkHtml;\n",
              "          element.appendChild(docLink);\n",
              "        }\n",
              "      </script>\n",
              "    </div>\n",
              "  </div>\n",
              "  "
            ]
          },
          "metadata": {},
          "execution_count": 27
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "os.makedirs(workDir + '/fileByCat', exist_ok=True)  "
      ],
      "metadata": {
        "id": "vySZhagcM_ZE"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "empty = parentTable.loc[parentTable['category_id'] == 0].file_name\n",
        "emptyID = parentTable.loc[parentTable['category_id'] == 0].id\n",
        "\n",
        "emptyID.to_csv(workDir + \"/fileByCat/emptyID.txt\", header=False, index = False)\n",
        "empty.to_csv(workDir + \"/fileByCat/emptyPath.txt\", header=False, index = False)\n",
        "\n",
        "\n",
        "human = parentTable.loc[parentTable['category_id'] == 1].file_name\n",
        "humanID = parentTable.loc[parentTable['category_id'] == 1].id\n",
        "\n",
        "human.to_csv(workDir + \"/fileByCat/humanPath.txt\", header=False, index = False)\n",
        "humanID.to_csv(workDir + \"/fileByCat/humanID.txt\", header=False, index = False)\n",
        "\n",
        "fox = parentTable.loc[parentTable['category_id'] == 2].file_name\n",
        "foxID = parentTable.loc[parentTable['category_id'] == 2].id\n",
        "\n",
        "fox.to_csv(workDir + \"/fileByCat/foxPath.txt\", header=False, index = False)\n",
        "foxID.to_csv(workDir + \"/fileByCat/foxID.txt\", header=False, index = False)\n",
        "\n",
        "\n",
        "skunk = parentTable.loc[parentTable['category_id'] == 3].file_name\n",
        "skunkID = parentTable.loc[parentTable['category_id'] == 3].id\n",
        "\n",
        "skunk.to_csv(workDir + \"/fileByCat/skunkPath.txt\", header=False, index = False)\n",
        "skunkID.to_csv(workDir + \"/fileByCat/skunkID.txt\", header=False, index = False)\n",
        "\n",
        "\n",
        "rodent = parentTable.loc[parentTable['category_id'] == 4].file_name\n",
        "rodentID = parentTable.loc[parentTable['category_id'] == 4].id\n",
        "\n",
        "rodent.to_csv(workDir + \"/fileByCat/rodentPath.txt\", header=False, index = False)\n",
        "rodentID.to_csv(workDir + \"/fileByCat/rodentID.txt\", header=False, index = False)\n",
        "\n",
        "\n",
        "bird = parentTable.loc[parentTable['category_id'] == 5].file_name\n",
        "birdID = parentTable.loc[parentTable['category_id'] == 5].id\n",
        "\n",
        "bird.to_csv(workDir + \"/fileByCat/birdPath.txt\", header=False, index = False)\n",
        "birdID.to_csv(workDir + \"/fileByCat/birdID.txt\", header=False, index = False)\n",
        "\n",
        "other = parentTable.loc[parentTable['category_id'] == 6].file_name\n",
        "otherID = parentTable.loc[parentTable['category_id'] == 6].id\n",
        "\n",
        "other.to_csv(workDir + \"/fileByCat/otherPath.txt\", header=False, index = False)\n",
        "otherID.to_csv(workDir + \"/fileByCat/otherID.txt\", header=False, index = False)"
      ],
      "metadata": {
        "id": "DBSzvt-_GnUG"
      },
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!zip -r $workDir/fileByCat.zip $workDir/fileByCat \n",
        "\n",
        "#Manually download fileByCat.zip from within /content section"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "CIrtijRPQ75B",
        "outputId": "8a7b79dc-4068-4bcd-d4c3-581eaf847cdb"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "updating: content/fileByCat/ (stored 0%)\n",
            "updating: content/fileByCat/otherPath.txt (deflated 86%)\n",
            "updating: content/fileByCat/birdPath.txt (deflated 92%)\n",
            "updating: content/fileByCat/emptyPath.txt (deflated 91%)\n",
            "updating: content/fileByCat/humanPath.txt (deflated 91%)\n",
            "updating: content/fileByCat/foxPath.txt (deflated 91%)\n",
            "updating: content/fileByCat/skunkPath.txt (deflated 89%)\n",
            "updating: content/fileByCat/rodentPath.txt (deflated 92%)\n",
            "  adding: content/fileByCat/emptyID.txt (deflated 43%)\n",
            "  adding: content/fileByCat/humanID.txt (deflated 50%)\n",
            "  adding: content/fileByCat/otherID.txt (deflated 42%)\n",
            "  adding: content/fileByCat/birdID.txt (deflated 56%)\n",
            "  adding: content/fileByCat/foxID.txt (deflated 46%)\n",
            "  adding: content/fileByCat/skunkID.txt (deflated 42%)\n",
            "  adding: content/fileByCat/rodentID.txt (deflated 50%)\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!zip -r {workDir}/CSVfiles.zip {workDir}/CSVfiles\n",
        "print(\"\\nFiles have been saves to \" + workDir + \" as a ziped folder called CSVfiles.zip\")\n",
        "\n",
        "#Manually download CSVfiles.zip from within /content section"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "EhThITPHQy6J",
        "outputId": "b7ab5012-dd54-43c7-bce8-60a6a5bd53fa"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "updating: content/CSVfiles/ (stored 0%)\n",
            "updating: content/CSVfiles/channel_islands_camera_traps_annotations.csv (deflated 68%)\n",
            "updating: content/CSVfiles/channel_islands_camera_traps_images.csv (deflated 79%)\n",
            "updating: content/CSVfiles/channel_islands_camera_traps_categories.csv (deflated 6%)\n",
            "\n",
            "Files have been saves to /content as a ziped folder called CSVfiles.zip\n"
          ]
        }
      ]
    }
  ]
}