How to process GRIB2 weather data for maritime applications (GeoJSON)
by Elliott Wobler -

How to process GRIB2 weather data for maritime applications (GeoJSON)

Learn how to work with Spire Weather’s global Numerical Weather Prediction (NWP) data in GRIB2 format using python

An alternative version using Shapefile input is also available.

Overview

This tutorial covers how to work with Spire Weather’s global Numerical Weather Prediction (NWP) data in GRIB2 format using python

If you have never worked with GRIB2 data before, it’s recommended to start with the basic tutorial, since this current one will address slightly more advanced topics.

Specifically, this tutorial demonstrates how to retrieve significant wave height (combined swell and wind waves) within the bounds of a complex polygon (e.g. a nation’s exclusive economic zone). Note that Spire Weather also offers a separate Maritime-Wave bundle which includes distinct values for swell and wind waves, rather than combining them like the standard Maritime bundle.

By the end of this tutorial, you will know how to:

  1. Load files containing GRIB2 messages into a Python program
  2. Inspect the GRIB2 data to understand which weather variables are included
  3. Crop the GRIB2 data to the area defined by a GeoJSON file input
  4. Convert the transformed GRIB2 data into a CSV output file for further analysis and visualization

Downloading the Data

The first step is downloading data from Spire Weather’s File API.

This tutorial expects the GRIB2 messages to contain NWP data from Spire’s Maritime data bundle.

For information on using Spire Weather’s File API endpoints, please see the API documentation and FAQ.

The FAQ also contains detailed examples covering how to download multiple forecast files at once using cURL.

For the purposes of this tutorial, it is assumed that the GRIB2 data has already been successfully downloaded, if not you can get a global weather forecast sample here.

Understanding filenames

Files downloaded from Spire Weather’s forecast API products all share the same file naming convention.

Just from looking at the filename, we can determine:

For more detailed information on the above, please refer to our FAQ.

Python Requirements

The following Python packages are required for this tutorial.

Although using conda is not strictly required, it is the officially recommended method for installing PyNIO (see link below).

Once a conda environment has been created and activated, the following commands can be run directly:

Inspecting the Data

After downloading the data and setting up a Python environment with the required packages, the next step is inspecting the data contents in order to determine which weather variables are available to access. Data inspection can be done purely with PyNIO, but in this tutorial we will instead use PyNIO as the engine for xarray and load the data into an xarray dataset for transformation. Note that an explicit import of PyNIO is not required, so long as it’s installed properly in the active Python environment.

First, import the xarray package:

import xarray as xr

Next, open the GRIB2 data with xarray using PyNIO as its engine (note that the GRIB2 data should be from Spire’s Maritime’s Weather data bundle):

ds = xr.open_dataset("path_to_maritime_file.grib2", engine="pynio")

Finally, for each of the variables, print the lookup key, human-readable name, and units of measurement:

for v in ds:
    print("{}, {}, {}".format(v, ds[v].attrs["long_name"], ds[v].attrs["units"]))

The output of the above should look something like this, giving a clear overview of the available data fields:

HTSGW_P0_L101_GLL0, Significant height of combined wind waves and swell, m
WWSDIR_P0_L101_GLL0, Direction of combined wind waves and swell, degree true
MWSPER_P0_L101_GLL0, Mean period of combined wind waves and swell, s
UOGRD_P0_L1_GLL0, U-component of current, m s-1
VOGRD_P0_L1_GLL0, V-component of current, m s-1
WTMP_P0_L1_GLL0, Water temperature, K

For more details, the full metadata of each variable can be inspected as well: print(ds["HTSGW_P0_L101_GLL0"])

Processing the Data

Now that we know which Numerical Weather Predition variables are included in the GRIB2 data, we can start processing our xarray dataset.

Filtering the xarray data to a specific variable

With xarray, filtering the dataset’s contents to a single variable of interest is very straightforward:

ds = ds.get("HTSGW_P0_L101_GLL0")

Selecting multiple variables is also possible by using an array of strings as the input: ds = ds.get([var1, var2])

It’s recommended to perform this step before converting the xarray dataset into a pandas DataFrame (rather than filtering the DataFrame later), since it minimizes the size of the data being converted and therefore reduces the overall runtime.

Converting the xarray data into a pandas.DataFrame

To convert the filtered xarray dataset into a pandas DataFrame, simply run the following:

df = ds.to_dataframe()

Loading a GeoJSON file with the GDAL Python package

Although the package we installed with conda was named gdal, we import it into Python as osgeo. This is an abbreviation of the Open Source Geospatial Foundation, which GDAL/OGR (a Free and Open Source Software) is licensed through.

To load GeoJSON data into GDAL, we just use GDAL’s CreateGeometryFromJSON function:

from osgeo.ogr import CreateGeometryFromJson

The GeoJSON format is a common standard in the world of geographic information systems. It is also the format used to specify geospatial filters in Spire Maritime’s AIS data APIs. Many pre-existing GeoJSON regions can be downloaded for free online (e.g. national borders, exclusive economic zones, etc.) and custom shapes can also be created in a variety of free software tools, such as geojson.io or geoman.io. For this tutorial, we use the EEZ of Australia as our complex polygon, but this could just as easily be a region containing ports of interest or any other geographical area.

When loading GeoJSON data into GDAL, only the geometry section of the Feature is needed. Here is a simple example of what the GeoJSON input file could contain:

{"type":"Polygon","coordinates":[[[5,35],[20,35],[20,50],[5,50],[5,35]]]}

The GeoJSON input file could also contain data for a MultiPolygon, starting with {"type":"MultiPolygon","coordinates": .... All of the code in this tutorial works the same way whether a Polygon or MultiPolygon geometry is being used.

The GeoJSON file can be loaded into Python using the standard json package, and should then be converted into a Python string:

import os, json

json_filepath = os.path.join("eez.json")
with open(json_filepath) as json_file:
    json_obj = json.load(json_file)
    json_str = json.dumps(json_obj)

Once we have loaded our GeoJSON definition into a Python string, we can create a GDAL geometry object like this:

area = CreateGeometryFromJson(json_str)

Getting the bounding box that contains a GeoJSON area

Eventually we will crop the data to the precise area defined by the GeoJSON file, but this is a computationally expensive process so it’s best to limit the data size first. In theory we could skip the step of cropping to a simple box altogether, but in practice it’s worth doing so to reduce the overall runtime.

GDAL makes it easy to calculate the coarse bounding box that contains a complex GeoJSON area:

bbox = area.GetEnvelope()

Coordinate values can then be accessed individually from the resulting array:

min_lon = bbox[0]
max_lon = bbox[1]
min_lat = bbox[2]
max_lat = bbox[3]

The order of geospatial coordinates is a common source of confusion, so take care to note that GDAL’s GetEnvelope function returns an array where the longitude values come before the latitude values.

Cropping the pandas.DataFrame to a geospatial bounding box

Now that the filtered data is converted into a pandas DataFrame and we have the bounds containing our area of interest, we can crop the data to a simple box.

The first step in this process is unpacking the latitude and longitude values from the DataFrame’s index, which can be accessed through the index names of lat_0 and lon_0:

latitudes = df.index.get_level_values("lat_0")
longitudes = df.index.get_level_values("lon_0")

Although latitude values are already in the standard range of -90 degress to +90 degrees, longitude values are in the range of 0 to +360.

To make the data easier to work with, we convert longitude values into the standard range of -180 degrees to +180 degrees:

map_function = lambda lon: (lon - 360) if (lon > 180) else lon
remapped_longitudes = longitudes.map(map_function)

With latitude and longitude data now in the desired value ranges, we can store them as new columns in our existing DataFrame:

df["longitude"] = remapped_longitudes
df["latitude"] = latitudes

Then, we use the bounding box values from the previous section (the components of the bbox array) to construct the DataFrame filter expressions:

lat_filter = (df["latitude"] >= min_lat) & (df["latitude"] <= max_lat)
lon_filter = (df["longitude"] >= min_lon) & (df["longitude"] <= max_lon)

Finally, we apply the filters to our existing DataFrame:

df = df.loc[lat_filter & lon_filter]

The resulting DataFrame has been cropped to the bounds of the box that contains the complex GeoJSON area.

Cropping the pandas.DataFrame to the precise bounds of a GeoJSON area

In order to crop the DataFrame to the precise bounds of the complex GeoJSON area, we will need to check every coordinate pair in our data. Similar to the previous section where we remapped every longitude value, we will perform this action with a map expression.

To pass each coordinate pair into the map function, we create a new DataFrame column called point where each value is a tuple containing both latitude and longitude:

df["point"] = list(zip(df["latitude"], df["longitude"]))

We can then pass each coordinate pair tuple value into the map function, along with the previously loaded GeoJSON area, and process them in a function called check_point_in_area which we will define below. The check_point_in_area function will return either True or False to indicate whether the provided coordinate pair is inside of the area or not. As a result, we will end up with a new DataFrame column of boolean values called inArea:

map_function = lambda latlon: check_point_in_area(latlon, area)
df["inArea"] = df["point"].map(map_function)

Once the inArea column is populated, we perform a simple filter to remove rows where the inArea value is False. This effectively removes data for all point locations that are not within the GeoJSON area:

df = df.loc[(df["inArea"] == True)]

Of course, the success of the above is dependent upon the logic inside of the check_point_in_area function, which we have not yet implemented. Since the GeoJSON area was loaded with GDAL, we can leverage a GDAL geometry method called Contains to quickly check if the area contains a specific point. In order to do this, the coordinate pair must first be converted into a wkbPoint geometry in GDAL:

from osgeo.ogr import Geometry, wkbPoint

OGR_POINT = Geometry(wkbPoint)
OGR_POINT.AddPoint(longitude, latitude)

Once we have our wkbPoint geometry, we simply pass it into the area.Contains method to check if the area contains the point:

if area.Contains(OGR_POINT):
    point_in_area = True

Putting the pieces together, here is what we get for our final check_point_in_area function:

def check_point_in_area(latlon, area):
    # Initialize the boolean
    point_in_area = False
    # Parse coordinates and convert to floats
    lat = float(latlon[0])
    lon = float(latlon[1])
    # Set the point geometry
    OGR_POINT.AddPoint(lon, lat)
    if area.Contains(OGR_POINT):
        # This point is within a feature
        point_in_area = True
    # Return flag indicating whether point is in the area
    return point_in_area

As you can see, the only variable returned by the check_point_in_area function is a boolean value indicating whether the specified point is in the area or not. These boolean values then populate the new inArea DataFrame column. This allows us to apply the filter from above and end up with the precisely cropped data we want:

df = df.loc[(df["inArea"] == True)]

Parsing the forecast time from the filename

Each individual file contains global weather forecast data for the same point in time.

Using our knowledge from the Understanding Filenames section of this tutorial, and assuming that the filename argument is in the expected format, we can write a function to parse the valid forecast time from the filename:

from datetime import datetime, timedelta

def parse_datetime_from_filename(filename):
    parts = filename.split(".")
    # Parse the forecast date from the filename
    date = parts[1]
    forecast_date = datetime.strptime(date, "%Y%m%d")
    # Strip `t` and `z` to parse the forecast issuance time (an integer representing the hour in UTC)
    issuance_time = parts[2]
    issuance_time = int(issuance_time[1:3])
    # Strip `f` to parse the forecast lead time (an integer representing the number of hours since the forecast issuance)
    lead_time = parts[-2]
    lead_time = int(lead_time[1:])
    # Combine the forecast issuance and lead times to get the valid time for this file
    hours = issuance_time + lead_time
    forecast_time = forecast_date + timedelta(hours=hours)
    # Return the datetime as a string to store it in the DataFrame
    return str(forecast_time)

Then, we can create a new DataFrame column for time which stores this value as a string in every row:

timestamp = parse_datetime_from_filename(filename)
df["time"] = timestamp

Although it may seem unnecessary to store the same exact timestamp value in every row, this is an important step if we want to eventually concatenate our DataFrame with forecast data for other times (demonstrated below in Processing Multiple Data Files).

Saving the data to a CSV output file

Perform a final filter on our DataFrame to select only the columns that we want in our output, where variable is a string like "HTSGW_P0_L101_GLL0" :

df = df.loc[:, ["latitude", "longitude", "time", variable]]

Save the processed DataFrame to an output CSV file:

df.to_csv("output_data.csv", index=False)

Setting the index=False parameter ensures that the DataFrame index columns are not included in the output. This way, we exclude the lat_0 and lon_0 values since we already have columns for latitude and remapped longitude.

Please note that converting from GRIB2 to CSV can result in very large file sizes, especially if the data is not significantly cropped or filtered.

Processing Multiple Data Files

It is often desirable to process multiple data files at once, in order to combine the results into a single unified CSV output file.

For example, let’s say that we have just used the Spire Weather API to download a full Global forecast’s worth of GRIB2 data into a local directory called forecast_data/. We can then read those filenames into a list and sort them alphabetically for good measure:

import glob

filenames = glob.glob("forecast_data/*.grib2")
filenames = sorted(filenames)

From here, we can iterate through the filenames and pass each one into a function that performs the steps outlined in the Processing the Data section of this tutorial.

Once all of our final DataFrames are ready, we can use pandas to concatenate them together like so (where final_dataframes is a list of DataFrames):

import pandas as pd

output_df = pd.DataFrame()

for df in final_dataframes:
    output_df = pd.concat([output_df, df])

We end up with a combined DataFrame called output_df which we can save to an output CSV file like we did before:

output_df.to_csv("combined_output_data.csv", index=False)

Complete Code

Below is an operational Python script which uses the techniques described in this tutorial and also includes explanatory in-line comments.

The script takes three arguments:

  1. The NWP data variable of interest
  2. The local directory where the Maritime Weather GRIB2 data is stored
  3. The path to the GeoJSON file defining the area of interest

For example, the script can be run like this:

python script.py --variable HTSGW_P0_L101_GLL0 --source-data grib_directory/ --geojson eez.json

Here is the complete code:

from osgeo.ogr import CreateGeometryFromJson, Geometry, wkbPoint
from datetime import datetime, timedelta
import xarray as xr
import pandas as pd
import argparse
import glob
import json
import sys
import os

# Only one OGR point needs to be created,
# since each call to `OGR_POINT.AddPoint`
# in the `check_point_in_area` function
# will reset the variable
OGR_POINT = Geometry(wkbPoint)

def parse_datetime_from_filename(filename):
    """
    Assuming that the filename matches Spire's naming convention,
    this function will parse the valid forecast time from the filename.
    Example filename: `sof-d.20200401.t00z.0p125.maritime.global.f006.grib2`
    """
    parts = filename.split(".")
    # Parse the forecast date from the filename
    date = parts[1]
    forecast_date = datetime.strptime(date, "%Y%m%d")
    # Strip `t` and `z` to parse the forecast issuance time (an integer representing the hour in UTC)
    issuance_time = parts[2]
    issuance_time = int(issuance_time[1:3])
    # Strip `f` to parse the forecast lead time (an integer representing the number of hours since the forecast issuance)
    lead_time = parts[-2]
    lead_time = int(lead_time[1:])
    # Combine the forecast issuance and lead times to get the valid time for this file
    hours = issuance_time + lead_time
    forecast_time = forecast_date + timedelta(hours=hours)
    # Return the datetime as a string to store it in the DataFrame
    return str(forecast_time)

def coarse_geo_filter(df, area):
    """
    Perform an initial coarse filter on the dataframe
    based on the extent (bounding box) of the specified area
    """
    # Get longitude and latitude values from the DataFrame index
    longitudes = df.index.get_level_values("lon_0")
    latitudes = df.index.get_level_values("lat_0")
    # Map longitude range from (0 to 360) into (-180 to 180)
    map_function = lambda lon: (lon - 360) if (lon > 180) else lon
    remapped_longitudes = longitudes.map(map_function)
    # Create new longitude and latitude columns in the DataFrame
    df["longitude"] = remapped_longitudes
    df["latitude"] = latitudes
    # Get the area's bounding box
    bbox = area.GetEnvelope()
    min_lon = bbox[0]
    max_lon = bbox[1]
    min_lat = bbox[2]
    max_lat = bbox[3]
    # Perform an initial coarse filter on the global dataframe
    # by limiting the data to the complex area's simple bounding box,
    # thereby reducing the total processing time of the `precise_geo_filter`
    lat_filter = (df["latitude"] >= min_lat) & (df["latitude"] <= max_lat)
    lon_filter = (df["longitude"] >= min_lon) & (df["longitude"] <= max_lon)
    # Apply filters to the dataframe
    df = df.loc[lat_filter & lon_filter]
    return df

def precise_geo_filter(df, area):
    """
    Perform a precise filter on the dataframe
    to check if each point is inside of the GeoJSON area
    """
    # Create a new tuple column in the dataframe of lat/lon points
    df["point"] = list(zip(df["latitude"], df["longitude"]))
    # Create a new boolean column in the dataframe, where each value represents
    # whether the row's lat/lon point is contained in the GeoJSON area
    map_function = lambda latlon: check_point_in_area(latlon, area)
    df["inArea"] = df["point"].map(map_function)
    # Remove point locations that are not within the GeoJSON area
    df = df.loc[(df["inArea"] == True)]
    return df

def check_point_in_area(latlon, area):
    """
    Return a boolean value indicating whether
    the specified point is inside of the GeoJSON area
    """
    # Initialize the boolean
    point_in_area = False
    # Parse coordinates and convert to floats
    lat = float(latlon[0])
    lon = float(latlon[1])
    # Set the point geometry
    OGR_POINT.AddPoint(lon, lat)
    if area.Contains(OGR_POINT):
   # This point is within a feature
   point_in_area = True
   # Return flag indicating whether point is in the area
   return point_in_area

def process_data(filepath, variable, area):
   """
   Load and process the GRIB2 data
   """
   # Load the files with GRIB2 data into an xarray dataset
   ds = xr.open_dataset(filepath, engine="pynio")
   # Retrieve only the desired values to reduce the volume of data,
   # otherwise converting to a DataFrame will take a long time.
   # To get more than 1 variable, use a list: `ds.get([var1, var2])`
   ds = ds.get(variable)
   # Convert the xarray dataset to a DataFrame
   df = ds.to_dataframe()
   # Perform an initial coarse filter on the global dataframe
   # by limiting the data to the area's bounding box,
   # thereby reducing the total processing time of the `precise_geo_filter`
   df = coarse_geo_filter(df, area)
   # Perform a precise filter to crop the remaining data to the GeoJSON area
   df = precise_geo_filter(df, area)
   # Parse the filename from the full filepath string
   filename = filepath.split("/")[1]
   # Convert the filename to a datetime string
   timestamp = parse_datetime_from_filename(filename)
   # Store the forecast time in a new DataFrame column
   df["time"] = timestamp
   # Trim the data to just the lat, lon, time, and weather variable columns
   df = df.loc[:, ["latitude", "longitude", "time", variable]]
   return df

if __name__ == "__main__":
   parser = argparse.ArgumentParser(description="Extract weather data within a region")
   parser.add_argument(
      "--variable",
      type=str,
      default="HTSGW_P0_L101_GLL0", # This combined wave height variable is in the Maritime data bundle
      help="The name of the weather data variable to extract",
   )
   parser.add_argument(
      "--source-data",
      type=str,
      help="The name of the directory containing properly formatted Spire GRIB2 data from the Maritime bundle",
      required=True,
   )
   parser.add_argument(
      "--geojson",
      type=str,
      help="The name of the directory containing the GeoJSON Polygon or MultiPolygon geometry",
      required=True,
   )
   # Parse the input arguments
   args = parser.parse_args()
   # Read all data files in the specified directory
   filepath = os.path.join(args.source_data, "*.grib2")
   filenames = glob.glob(filepath)
   # Sort the filenames alphabetically
   filenames = sorted(filenames)
   # Initialize the output DataFrame
   output_df = pd.DataFrame()
   # Load the GeoJSON area
   json_filepath = os.path.join(args.geojson)
   with open(json_filepath) as json_file:
      json_obj = json.load(json_file)
      json_str = json.dumps(json_obj)
   area = CreateGeometryFromJson(json_str)
   # For each file, process the data into a DataFrame
   # and concatenate all of the DataFrames together
   for file in filenames:
      print("Processing ", file)
      data = process_data(file, args.variable, area)
      if data is not None:
         output_df = pd.concat([output_df, data])
   # Save the final DataFrame to a CSV file
   # and do not include the index values (`lat_0` and `lon_0`)
   # since we created new `latitude` and `longitude` columns
   output_df.to_csv("output_data.csv", index=False)

Final Notes

Using the CSV data output from our final script, we can now easily visualize the processed data in a free tool such as kepler.gl. We can also set thresholds for alerts, generate statistics, or fuse with other datasets.

Spire Weather also offers pre-created visualizations for the Maritime bundle through the Web Map Service (WMS) API, which you can read more about here.

For additional code samples, check out Spire Weather’s public GitHub repository.

 

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