read_viirs_and_list_sds.ipynb

{
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  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "read_viirs_and_list_sds.ipynb",
      "provenance": [],
      "collapsed_sections": []
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "zNr7Vg4ABG-G"
      },
      "source": [
        "**Module**: read_viirs_and_list_sds.ipynb\n",
        "\n",
        "**Disclaimer**: The code is for demonstration purposes only. Users are responsible to check for accuracy and revise to fit their objective.\n",
        "\n",
        "**Organization**: NASA ARSET\n",
        "\n",
        "**Author**: Justin Roberts-Pierel, 2015 \n",
        "\n",
        "**Updated**: Pawan Gupta, May 10 2019 to read netcdf data\n",
        "\n",
        "**Updated**: Aavash Thapa, June 2020 to read VIIRS data\n",
        "\n",
        "**Purpose**: To print all SDS from a VIIRS netcdf4 file"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "rWF9DENEn-1Q"
      },
      "source": [
        "#Mount drive to save files there\n",
        "#clone the repository to access files from there\n",
        "#pull the latest\n",
        "from google.colab import drive\n",
        "drive.mount('/content/drive', force_remount=True)\n",
        "! git clone https://github.com/NASAARSET/VIIRS_NASA.git\n",
        "! git -C VIIRS_NASA/ pull"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "xerBYvZDA6kL"
      },
      "source": [
        "! pip install netCDF4\n",
        "import netCDF4\n",
        "from netCDF4 import Dataset"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "9-Ms7cHMBFHW"
      },
      "source": [
        "#!/usr/bin/python\n",
        "  \n",
        "#-------------------------------------------------\n",
        "# This section of the code is adopted from colorstate univ.\n",
        "#http://schubert.atmos.colostate.edu/~cslocum/netcdf_example.html\n",
        "#-------------------------------------------------\n",
        "def ncdump(nc_fid, verb=True):\n",
        "    '''\n",
        "    ncdump outputs dimensions, variables and their attribute information.\n",
        "    The information is similar to that of NCAR's ncdump utility.\n",
        "    ncdump requires a valid instance of Dataset.\n",
        "\n",
        "    Parameters\n",
        "    ----------\n",
        "    nc_fid : netCDF4.Dataset\n",
        "        A netCDF4 dateset object\n",
        "    verb : Boolean\n",
        "        whether or not nc_attrs, nc_dims, and nc_vars are printed\n",
        "\n",
        "    Returns\n",
        "    -------\n",
        "    1) nc_attrs : list\n",
        "        A Python list of the NetCDF file global attributes\n",
        "    2) nc_dims : list\n",
        "        A Python list of the NetCDF file dimensions\n",
        "    3) nc_vars : list\n",
        "        A Python list of the NetCDF file variables\n",
        "    '''\n",
        "\n",
        "    '''\n",
        "    This function is currently not being used.\n",
        "    To see the attributes by using this function, \n",
        "    comment out the lines that says print_ncattr for each section.\n",
        "    '''\n",
        "    def print_ncattr(key):\n",
        "        \"\"\"\n",
        "        Prints the NetCDF file attributes for a given key\n",
        "\n",
        "        Parameters\n",
        "        ----------\n",
        "        key : unicode\n",
        "            a valid netCDF4.Dataset.variables key\n",
        "        \"\"\"\n",
        "        try:\n",
        "            print (\"\\t\\ttype:\", repr(nc_fid.variables[key].dtype))\n",
        "            for ncattr in nc_fid.variables[key].ncattrs():\n",
        "                print ('\\t\\t%s:' % ncattr,\\\n",
        "                      repr(nc_fid.variables[key].getncattr(ncattr)))\n",
        "        except KeyError:\n",
        "            print (\"\\t\\tWARNING: %s does not contain variable attributes\" % key)\n",
        "\n",
        "\n",
        "    #1)  NetCDF global attributes\n",
        "    #The next block of code has the global attributes and has been commented out.\n",
        "    #Remove ''' to view the global attributes.\n",
        "    #---------------------------------------------------------------------------\n",
        "    '''\n",
        "    nc_attrs = nc_fid.ncattrs()\n",
        "    if verb:\n",
        "      print (\"NetCDF Global Attributes: \\n\")\n",
        "      for nc_attr in nc_attrs:\n",
        "        print ('\\t%s:' % nc_attr, repr(nc_fid.getncattr(nc_attr)))\n",
        "    print('\\n')\n",
        "    '''\n",
        "    #---------------------------------------------------------------------------\n",
        "    \n",
        "    # 2) Dimension shape information.\n",
        "    nc_dims = [dim for dim in nc_fid.dimensions]  # list of nc dimensions\n",
        "    if verb:\n",
        "        print (\"NetCDF dimension information: \\n\")\n",
        "        for dim in nc_dims:\n",
        "            print ('\\t', dim)\n",
        "            #print (\"\\t\\tsize:\", len(nc_fid.dimensions[dim]))\n",
        "            #print_ncattr(dim)\n",
        "    print('\\n')\n",
        "\n",
        "    # 3)  Variable information.\n",
        "    nc_vars = [var for var in nc_fid.variables]  # list of nc variables\n",
        "    if verb:\n",
        "        print (\"NetCDF variable information: \\n\")\n",
        "        for var in nc_vars:\n",
        "            if var not in nc_dims:\n",
        "                print('\\t', var)\n",
        "\n",
        "                #Next few lines print the attributes of each variable\n",
        "                #Remove ''' to view in detail\n",
        "                '''\n",
        "                print (\"\\t\\tdimensions:\", nc_fid.variables[var].dimensions)\n",
        "                print (\"\\t\\tsize:\", nc_fid.variables[var].size)\n",
        "                print_ncattr(var)\n",
        "                '''\n",
        "    #return nc_attrs as well for section 1\n",
        "    return nc_dims, nc_vars\n",
        "\n",
        "\n",
        "#This finds the user's current path so that all nc files can be found\n",
        "try:\n",
        "    fileList = open('VIIRS_NASA/fileList.txt', 'r')\n",
        "except:\n",
        "    print('Did not find a text file containing file names (perhaps name does not match)')\n",
        "    sys.exit()\n",
        "\n",
        "#loops through all files listed in the text file\n",
        "for FILE_NAME in fileList:\n",
        "    FILE_NAME=FILE_NAME.strip()\n",
        "    user_input=input('\\nWould you like to process\\n' + FILE_NAME + '\\n\\n(Y/N)')\n",
        "    if(user_input == 'N' or user_input == 'n'):\n",
        "        print('Skipping...')\n",
        "        continue\n",
        "    else:\n",
        "        nc_file = Dataset('VIIRS_NASA/'+ FILE_NAME, 'r')   # 'r' means that nc file is open in read-only mode    \n",
        "        \n",
        "        #Add nc_attrs below along with nc_dims,nc_vars if you want to see the\n",
        "        #global attributes and comment out section 1 above. \n",
        "        nc_dims,nc_vars = ncdump(nc_file)\n",
        "    nc_file.close()    \n"
      ],
      "execution_count": null,
      "outputs": []
    }
  ]
}