import shapely
import shapely.geometry
import shapely.wkt
import xarray
import PyOFS
from PyOFS import (
CRS_EPSG,
DATA_DIRECTORY,
LEAFLET_NODATA_VALUE,
TIFF_CREATION_OPTIONS,
get_logger,
utilities,
)
LOGGER = get_logger('PyOFS.VIIRS')
VIIRS_START_TIME = datetime.strptime('2012-03-01 00:10:00',
'%Y-%m-%d %H:%M:%S')
VIIRS_PERIOD = timedelta(days=16)
PASS_TIMES_FILENAME = DATA_DIRECTORY / 'reference' / 'viirs_pass_times.txt'
STUDY_AREA_POLYGON_FILENAME = DATA_DIRECTORY / 'reference' / 'wcofs.gpkg:study_area'
OUTPUT_CRS = fiona.crs.from_epsg(CRS_EPSG)
NRT_DELAY = timedelta(hours=2)
SOURCE_URLS = OrderedDict({
'OpenDAP':
OrderedDict({
import shapely
import shapely.geometry
import shapely.wkt
import xarray
import PyOFS
from PyOFS import (
CRS_EPSG,
DATA_DIRECTORY,
LEAFLET_NODATA_VALUE,
TIFF_CREATION_OPTIONS,
get_logger,
utilities,
)
LOGGER = get_logger('PyOFS.ABI')
STUDY_AREA_POLYGON_FILENAME = DATA_DIRECTORY / 'reference' / 'wcofs.gpkg:study_area'
OUTPUT_CRS = fiona.crs.from_epsg(CRS_EPSG)
NRT_DELAY = timedelta(hours=2)
SOURCE_URLS = OrderedDict({
'OpenDAP':
OrderedDict({
'NESDIS':
'https://www.star.nesdis.noaa.gov/thredds/dodsC',
'JPL':
'https://podaac-opendap.jpl.nasa.gov:443/opendap/allData/ghrsst/data/GDS2/L3C',
'NODC':
from os import PathLike
from pathlib import Path
import re
import fiona
import fiona.crs
import numpy
import requests
import shapely
import shapely.geometry
import xarray
import PyOFS
from PyOFS import CRS_EPSG, DATA_DIRECTORY, get_logger, utilities
LOGGER = get_logger('PyOFS.NDBC')
MEASUREMENT_VARIABLES = [
'water_temperature',
'conductivity',
'salinity',
'o2_saturation',
'dissolved_oxygen',
'chlorophyll_concentration',
'turbidity',
'water_ph',
'water_eh',
]
OUTPUT_CRS = fiona.crs.from_epsg(CRS_EPSG)
import os
from os import PathLike
from pathlib import Path
from datetime import datetime, timedelta
import boto3
from botocore.exceptions import NoCredentialsError
from PyOFS import get_logger
LOGGER = get_logger('PyOFS.azure')
def upload_to_azure(
local_path: PathLike,
remote_path: PathLike,
credentials: str,
overwrite: bool = False,
azcopy_path: PathLike = None,
**kwargs,
):
if not isinstance(azcopy_path, Path):
azcopy_path = Path(azcopy_path)
LOGGER.info(f'Uploading {local_path} to {remote_path}')
os.environ['AZCOPY_CRED_TYPE'] = 'Anonymous'
if azcopy_path is not None:
azcopy_dir = azcopy_path.parent
azcopy_filename = azcopy_path.name
os.chdir(azcopy_dir)
else:
from concurrent import futures
from datetime import datetime, timedelta
import os
from os import PathLike
from pathlib import Path
import numpy
import xarray
from PyOFS import DATA_DIRECTORY, get_logger
from PyOFS.model import wcofs
from PyOFS.observation import hf_radar, viirs
LOGGER = get_logger('PyOFS.valid')
WORKSPACE_DIR = DATA_DIRECTORY / 'validation'
# UTC offset of study area
UTC_OFFSET = 8
def to_netcdf(start_time: datetime, end_time: datetime, output_dir: PathLike):
"""
Writes HFR, VIIRS, and WCOFS data to NetCDF files at the given filenames.
:param start_time: Start of time interval.
:param end_time: End of time interval.
:param output_dir: Output directory.
"""
if not isinstance(output_dir, Path):
from os import PathLike
from pathlib import Path
from typing import Collection
import fiona
import fiona.crs
import numpy
import rasterio
from rasterio.enums import Resampling
import scipy.interpolate
import xarray
import PyOFS
from PyOFS import CRS_EPSG, LEAFLET_NODATA_VALUE, TIFF_CREATION_OPTIONS, get_logger
LOGGER = get_logger('PyOFS.HFR')
DATA_VARIABLES = {'ssu': 'u', 'ssv': 'v', 'dopx': 'dopx', 'dopy': 'dopy'}
OUTPUT_CRS = fiona.crs.from_epsg(CRS_EPSG)
NRT_DELAY = timedelta(hours=1)
# either UCSD (University of California San Diego) or NDBC (National Data Buoy Center); NDBC has larger extent but only for the past 4 days
SOURCE_URLS = {
'NDBC': 'https://dods.ndbc.noaa.gov/thredds/dodsC',
'UCSD': 'http://hfrnet-tds.ucsd.edu/thredds/dodsC/HFR/USWC',
}
class HFRadarRange:
import rasterio.mask
import rasterio.warp
from shapely import geometry
import xarray
import PyOFS
from PyOFS import (
CRS_EPSG,
DATA_DIRECTORY,
LEAFLET_NODATA_VALUE,
TIFF_CREATION_OPTIONS,
get_logger,
utilities,
)
LOGGER = get_logger('PyOFS.RTOFS')
OUTPUT_CRS = fiona.crs.from_epsg(CRS_EPSG)
COORDINATE_VARIABLES = ['time', 'lev', 'lat', 'lon']
DATASET_STRUCTURE = {
'2ds': {
'nowcast': {
'prog': ['sss', 'sst', 'u_velocity', 'v_velocity'],
'diag': ['ssh', 'ice_coverage', 'ice_thickness'],
},
'forecast': {
'prog': ['sss', 'sst', 'u_velocity', 'v_velocity'],
'diag': ['ssh', 'ice_coverage', 'ice_thickness'],
},
import shapely.geometry
import shapely.wkt
import xarray
import PyOFS
from PyOFS import (
CRS_EPSG,
DATA_DIRECTORY,
LEAFLET_NODATA_VALUE,
NoDataError,
TIFF_CREATION_OPTIONS,
get_logger,
utilities,
)
LOGGER = get_logger('PyOFS.SMAP')
STUDY_AREA_POLYGON_FILENAME = DATA_DIRECTORY / 'reference' / 'wcofs.gpkg:study_area'
OUTPUT_CRS = fiona.crs.from_epsg(CRS_EPSG)
SOURCE_URLS = OrderedDict({
'OpenDAP':
OrderedDict({
'JPL':
'https://thredds.jpl.nasa.gov/thredds/dodsC/ncml_aggregation/SalinityDensity/smap/aggregate__SMAP_JPL_L3_SSS_CAP_MONTHLY_V42.ncml',
})
})
class SMAPDataset:
from datetime import datetime, timedelta
from os import PathLike
from pathlib import Path
from PyOFS import DATA_DIRECTORY, get_logger
from main.leaflet import write_json
LOGGER = get_logger('PyOFS.check')
observations = {'hfr': ['dir', 'mag'], 'viirs': ['sst']}
models = {
'wcofs': ['dir', 'mag', 'sst', 'ssh', 'sss'],
'rtofs': ['dir', 'mag', 'sst', 'ssh', 'sss'],
}
time_deltas = ['n001', 'f001', 'f002', 'f003']
def check_files(input_dir: PathLike) -> dict:
if not isinstance(input_dir, Path):
input_dir = Path(input_dir)
missing_files = {}
structure = write_json.get_directory_structure(input_dir)
for day, filenames in structure['output']['daily_averages'].items():
for observation, variables in observations.items():
for variable in variables:
if variable in ['dir', 'mag']:
extension = 'asc'
else:
avg_dir,
fwd_dir,
obs_dir,
mod_dir,
] + list(day_directories.values()): # experimental_dir]:
if not directory.exists():
os.makedirs(directory, exist_ok=True)
# define log filename
log_path = LOG_DIRECTORY / f'{datetime.now():%Y%m%d}_download.log'
# check whether logfile exists
log_exists = log_path.exists()
logger = get_logger('download',
log_path,
file_level=logging.INFO,
console_level=logging.DEBUG)
# write initial message
logger.info('Starting FTP transfer...')
# instantiate FTP connection
with ftplib.FTP(TIDEPOOL_URL) as ftp_connection:
ftp_connection.login()
path_map = {}
for input_path in ftp_connection.nlst(INPUT_DIRECTORY):
filename = os.path.basename(input_path)
if 'rtofs' in filename:
output_path = rtofs_dir / filename
LOG_DIRECTORY = DATA_DIRECTORY / 'log'
LOG_FILENAME = LOG_DIRECTORY / f'{datetime.now():%Y%m%d}_conversion.log'
OUTPUT_DIRECTORY = DATA_DIRECTORY / 'output'
REFERENCE_DIRECTORY = DATA_DIRECTORY / 'reference'
# offset from study area to UTC
STUDY_AREA_TIMEZONE = 'US/Pacific'
STUDY_AREA_TO_UTC = timedelta(
hours=-datetime.now(pytz.timezone(STUDY_AREA_TIMEZONE)).utcoffset() /
timedelta(hours=1))
# range of day deltas that models reach
MODEL_DAY_DELTAS = {'WCOFS': range(-1, 3), 'RTOFS': range(-3, 9)}
LOGGER = get_logger('PyOFS',
LOG_FILENAME,
file_level=logging.INFO,
console_level=logging.INFO)
def write_observation(output_dir: PathLike, observation_date: Union[datetime,
date],
observation: str):
"""
Writes daily average of observational data on given date.
:param output_dir: output directory to write files
:param observation_date: fate of observation
:param observation: observation to write
:raise _utilities.NoDataError: if no data found
"""
import shapely
from shapely.geometry import shape
from shapely.ops import transform
import xarray
from PyOFS import get_logger, split_layer_filename
WGS84 = pyproj.Proj('+proj=longlat +datum=WGS84 +no_defs')
WEB_MERCATOR = pyproj.Proj(
'+proj=merc +a=6378137 +b=6378137 +lat_ts=0.0 +lon_0=0.0 +x_0=0.0 +y_0=0 +k=1.0 +units=m +nadgrids=@null +wktext +no_defs'
)
GRAVITATIONAL_ACCELERATION = 9.80665 # meters per second squared
SIDEREAL_ROTATION_PERIOD = timedelta(hours=23, minutes=56, seconds=4.1)
LOGGER = get_logger('PyOFS.utili')
def copy_xarray(input_path: str, output_path: str) -> xarray.Dataset:
"""
Copy given xarray observation to a local file at the given path.
:param input_path: path to observation to copy
:param output_path: path to output file
:return: copied observation at given path
"""
LOGGER.info(f'Reading observation from {input_path}')
input_dataset = xarray.open_dataset(input_path, decode_times=False)
from datetime import datetime, timedelta
from pathlib import Path
import fiona
from matplotlib import pyplot
import numpy
import pandas
from shapely import geometry
from PyOFS import DATA_DIRECTORY, get_logger
LOGGER = get_logger('PyOFS.track')
def diffusion(polygons: [geometry.Polygon]):
for polygon in polygons:
centroid = polygon.centroid
max_radius = max(
centroid.distance(vertex)
for vertex in (geometry.Point(point) for point in zip(*polygon.exterior.xy))
)
radius_interval = 500
for radius in range(radius_interval, max_radius, step=radius_interval):
analysis_area = geometry.Polygon(
centroid.buffer(radius + radius_interval), centroid.buffer(radius)
)
polygon.intersection(analysis_area)
