LANCE_NRT_AMSR2_SurfacePrecip_Quickview.ipynb

{"cells":[{"cell_type":"markdown","metadata":{},"source":["<br>\n","LANCE NRT AMSR2 Ocean Rain Data Quickview<br>\n","<br>\n","Description: This code reads latitudes, longitudes, and surface<br>\n","precipitation rates from a LANCE NRT AMSR2 Ocean Rain Data file (*.he5)<br>\n","and generate a CSV file with these info. The CSV file will be used to<br>\n","plot surface precipitation rates in ESRI ArcMap.<br>\n","<br>\n","Authors: Lucy Wang, Leigh Sinclair,<br>\n","Information and Technology Systems Center (ITSC)<br>\n","University of Alabama in Huntsville<br>\n","<br>\n","Last Edit Date: 31 January 2019<br>\n","<br>"]},{"cell_type":"code","execution_count":1,"metadata":{},"outputs":[{"name":"stdout","output_type":"stream","text":["Requirement already satisfied: numpy in /home/davis_dev/anaconda3/lib/python3.9/site-packages (1.21.5)\n","Requirement already satisfied: tables in /home/davis_dev/anaconda3/lib/python3.9/site-packages (3.6.1)\n","Requirement already satisfied: numexpr>=2.6.2 in /home/davis_dev/anaconda3/lib/python3.9/site-packages (from tables) (2.8.1)\n","Requirement already satisfied: numpy>=1.9.3 in /home/davis_dev/anaconda3/lib/python3.9/site-packages (from tables) (1.21.5)\n","Requirement already satisfied: packaging in /home/davis_dev/anaconda3/lib/python3.9/site-packages (from numexpr>=2.6.2->tables) (21.3)\n","Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/davis_dev/anaconda3/lib/python3.9/site-packages (from packaging->numexpr>=2.6.2->tables) (3.0.4)\n"]},{"ename":"NoSuchNodeError","evalue":"group ``/`` does not have a child named ``/HDFEOS/SWATHS/GPROF2010V2/Data Fields/surfacePrecipitation``","output_type":"error","traceback":["\u001b[0;31m---------------------------------------------------------------------------\u001b[0m","\u001b[0;31mNoSuchNodeError\u001b[0m                           Traceback (most recent call last)","\u001b[1;32m/home/davis_dev/github/data-recipes/LANCE_NRT_AMSR2_SurfacePrecip_Quickview.ipynb Cell 2\u001b[0m in \u001b[0;36m<cell line: 22>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     <a href='vscode-notebook-cell://wsl%2Bubuntu/home/davis_dev/github/data-recipes/LANCE_NRT_AMSR2_SurfacePrecip_Quickview.ipynb#W1sdnNjb2RlLXJlbW90ZQ%3D%3D?line=23'>24</a>\u001b[0m h5file \u001b[39m=\u001b[39m tables\u001b[39m.\u001b[39mopen_file(i)\n\u001b[1;32m     <a href='vscode-notebook-cell://wsl%2Bubuntu/home/davis_dev/github/data-recipes/LANCE_NRT_AMSR2_SurfacePrecip_Quickview.ipynb#W1sdnNjb2RlLXJlbW90ZQ%3D%3D?line=25'>26</a>\u001b[0m \u001b[39m#Read data layer(s) of interest within HDF-EOS5 file\u001b[39;00m\n\u001b[0;32m---> <a href='vscode-notebook-cell://wsl%2Bubuntu/home/davis_dev/github/data-recipes/LANCE_NRT_AMSR2_SurfacePrecip_Quickview.ipynb#W1sdnNjb2RlLXJlbW90ZQ%3D%3D?line=26'>27</a>\u001b[0m surface_precip \u001b[39m=\u001b[39m h5file\u001b[39m.\u001b[39;49mget_node(\u001b[39m'\u001b[39;49m\u001b[39m/HDFEOS/SWATHS/GPROF2010V2/Data Fields/surfacePrecipitation\u001b[39;49m\u001b[39m'\u001b[39;49m)\u001b[39m.\u001b[39mread()\n\u001b[1;32m     <a href='vscode-notebook-cell://wsl%2Bubuntu/home/davis_dev/github/data-recipes/LANCE_NRT_AMSR2_SurfacePrecip_Quickview.ipynb#W1sdnNjb2RlLXJlbW90ZQ%3D%3D?line=27'>28</a>\u001b[0m quality_flag \u001b[39m=\u001b[39m h5file\u001b[39m.\u001b[39mget_node(\u001b[39m'\u001b[39m\u001b[39m/HDFEOS/SWATHS/GPROF2010V2/Data Fields/QualityFlag\u001b[39m\u001b[39m'\u001b[39m)\u001b[39m.\u001b[39mread()\n\u001b[1;32m     <a href='vscode-notebook-cell://wsl%2Bubuntu/home/davis_dev/github/data-recipes/LANCE_NRT_AMSR2_SurfacePrecip_Quickview.ipynb#W1sdnNjb2RlLXJlbW90ZQ%3D%3D?line=28'>29</a>\u001b[0m pixel_status \u001b[39m=\u001b[39m h5file\u001b[39m.\u001b[39mget_node(\u001b[39m'\u001b[39m\u001b[39m/HDFEOS/SWATHS/GPROF2010V2/Data Fields/pixelStatus\u001b[39m\u001b[39m'\u001b[39m)\u001b[39m.\u001b[39mread()\n","File \u001b[0;32m~/anaconda3/lib/python3.9/site-packages/tables/file.py:1642\u001b[0m, in \u001b[0;36mFile.get_node\u001b[0;34m(self, where, name, classname)\u001b[0m\n\u001b[1;32m   1640\u001b[0m     basepath \u001b[39m=\u001b[39m where\n\u001b[1;32m   1641\u001b[0m     nodepath \u001b[39m=\u001b[39m join_path(basepath, name \u001b[39mor\u001b[39;00m \u001b[39m'\u001b[39m\u001b[39m'\u001b[39m) \u001b[39mor\u001b[39;00m \u001b[39m'\u001b[39m\u001b[39m/\u001b[39m\u001b[39m'\u001b[39m\n\u001b[0;32m-> 1642\u001b[0m     node \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_get_node(nodepath)\n\u001b[1;32m   1643\u001b[0m \u001b[39melse\u001b[39;00m:\n\u001b[1;32m   1644\u001b[0m     \u001b[39mraise\u001b[39;00m \u001b[39mTypeError\u001b[39;00m(\n\u001b[1;32m   1645\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39m``where`` must be a string or a node: \u001b[39m\u001b[39m%r\u001b[39;00m\u001b[39m\"\u001b[39m \u001b[39m%\u001b[39m (where,))\n","File \u001b[0;32m~/anaconda3/lib/python3.9/site-packages/tables/file.py:1590\u001b[0m, in \u001b[0;36mFile._get_node\u001b[0;34m(self, nodepath)\u001b[0m\n\u001b[1;32m   1587\u001b[0m \u001b[39mif\u001b[39;00m nodepath \u001b[39m==\u001b[39m \u001b[39m'\u001b[39m\u001b[39m/\u001b[39m\u001b[39m'\u001b[39m:\n\u001b[1;32m   1588\u001b[0m     \u001b[39mreturn\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mroot\n\u001b[0;32m-> 1590\u001b[0m node \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_node_manager\u001b[39m.\u001b[39;49mget_node(nodepath)\n\u001b[1;32m   1591\u001b[0m \u001b[39massert\u001b[39;00m node \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m, \u001b[39m\"\u001b[39m\u001b[39munable to instantiate node ``\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m``\u001b[39m\u001b[39m\"\u001b[39m \u001b[39m%\u001b[39m nodepath\n\u001b[1;32m   1593\u001b[0m \u001b[39mreturn\u001b[39;00m node\n","File \u001b[0;32m~/anaconda3/lib/python3.9/site-packages/tables/file.py:432\u001b[0m, in \u001b[0;36mNodeManager.get_node\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m    429\u001b[0m         node \u001b[39m=\u001b[39m \u001b[39mNone\u001b[39;00m\n\u001b[1;32m    431\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mnode_factory:\n\u001b[0;32m--> 432\u001b[0m     node \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mnode_factory(key)\n\u001b[1;32m    433\u001b[0m     \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mcache_node(node, key)\n\u001b[1;32m    435\u001b[0m \u001b[39mreturn\u001b[39;00m node\n","File \u001b[0;32m~/anaconda3/lib/python3.9/site-packages/tables/group.py:1178\u001b[0m, in \u001b[0;36mRootGroup._g_load_child\u001b[0;34m(self, childname)\u001b[0m\n\u001b[1;32m   1176\u001b[0m     childname \u001b[39m=\u001b[39m join_path(\u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_v_file\u001b[39m.\u001b[39mroot_uep, childname)\n\u001b[1;32m   1177\u001b[0m \u001b[39m# Is the node a group or a leaf?\u001b[39;00m\n\u001b[0;32m-> 1178\u001b[0m node_type \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49m_g_check_has_child(childname)\n\u001b[1;32m   1180\u001b[0m \u001b[39m# Nodes that HDF5 report as H5G_UNKNOWN\u001b[39;00m\n\u001b[1;32m   1181\u001b[0m \u001b[39mif\u001b[39;00m node_type \u001b[39m==\u001b[39m \u001b[39m'\u001b[39m\u001b[39mUnknown\u001b[39m\u001b[39m'\u001b[39m:\n","File \u001b[0;32m~/anaconda3/lib/python3.9/site-packages/tables/group.py:393\u001b[0m, in \u001b[0;36mGroup._g_check_has_child\u001b[0;34m(self, name)\u001b[0m\n\u001b[1;32m    391\u001b[0m node_type \u001b[39m=\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_g_get_objinfo(name)\n\u001b[1;32m    392\u001b[0m \u001b[39mif\u001b[39;00m node_type \u001b[39m==\u001b[39m \u001b[39m\"\u001b[39m\u001b[39mNoSuchNode\u001b[39m\u001b[39m\"\u001b[39m:\n\u001b[0;32m--> 393\u001b[0m     \u001b[39mraise\u001b[39;00m NoSuchNodeError(\n\u001b[1;32m    394\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mgroup ``\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m`` does not have a child named ``\u001b[39m\u001b[39m%s\u001b[39;00m\u001b[39m``\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    395\u001b[0m         \u001b[39m%\u001b[39m (\u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_v_pathname, name))\n\u001b[1;32m    396\u001b[0m \u001b[39mreturn\u001b[39;00m node_type\n","\u001b[0;31mNoSuchNodeError\u001b[0m: group ``/`` does not have a child named ``/HDFEOS/SWATHS/GPROF2010V2/Data Fields/surfacePrecipitation``"]}],"source":["! pip install numpy\n","! pip install tables\n","\n","import numpy as np\n","import tables\n","import csv\n","\n","# Define the file directories\n","\n","dataDir = 'test_files/'\n","files = ['AMSR_U2_L2_Rain_R02_202208100047_A.he5']\n","datafiles = [dataDir + x for x in files]\n","\n","# Create a list of dictionaries 'dict_list'; each dictionary has three keys 'lon', 'lat', 'sfc_precip'\n","\n","dict_list = []\n","fieldnames = ['lon','lat','sfc_precip']\n","\n","# Loop through list of HDF-EOS5 files, for each file, extract the surface precipitation\n","# and correspoinding latitude and longitude \n","\n","for i in datafiles:\n","    #Open HDF5 file\n","    h5file = tables.open_file(i)\n","\n","    #Read data layer(s) of interest within HDF-EOS5 file\n","    surface_precip = h5file.get_node('/HDFEOS/SWATHS/GPROF2010V2/Data Fields/surfacePrecipitation').read()\n","    quality_flag = h5file.get_node('/HDFEOS/SWATHS/GPROF2010V2/Data Fields/QualityFlag').read()\n","    pixel_status = h5file.get_node('/HDFEOS/SWATHS/GPROF2010V2/Data Fields/pixelStatus').read()\n","    lat = h5file.get_node('/HDFEOS/SWATHS/GPROF2010V2/Geolocation Fields/Latitude').read()\n","    lon = h5file.get_node('/HDFEOS/SWATHS/GPROF2010V2/Geolocation Fields/Longitude').read()\n","\n","    #Close HDF5 file\n","    h5file.close()\n","    n_track = surface_precip.shape[0]\n","    n_xtrack = surface_precip.shape[1]\n","    for ii in range(0,n_track):\n","        for jj in range(0,n_xtrack):\n","            if pixel_status[ii,jj] == 0 and quality_flag[ii,jj] == 0 and surface_precip[ii,jj] > 0:\n","               #Create a new dictionary with the three keys 'lon', 'lat', 'sfc_precip'\n","               row_dict = {}\n","               row_dict.update({'lon':lon[ii,jj],'lat':lat[ii,jj],'sfc_precip':surface_precip[ii,jj]})\n","               #Add this new dictionary to the list\n","               dict_list.append(row_dict)\n","               \n","# Write lon, lat, surface_precip into a CSV file\n","\n","if len(dict_list) > 0:\n","   output_csv_file = dataDir + 'AMSR2_NRT_L2B_swath_20181231.csv'\n","   \n","   with open(output_csv_file,'wb') as csvfile:\n","        writer = csv.DictWriter(csvfile,fieldnames = fieldnames)\n","        writer.writeheader()\n","        writer.writerows(dict_list)\n","        "]}],"metadata":{"kernelspec":{"display_name":"Python 3.9.12 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