/
processing.py
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/
processing.py
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from particles import BeachingParticles, Density
from ocean_utilities import get_global_grid
from utilities import get_dir, convert_time_to_datetime, convert_datetime_to_time
from datetime import datetime,timedelta
from netCDF4 import Dataset
import numpy as np
import log
# -----------------------------------------------
# Sensitivity parameters
# -----------------------------------------------
def get_dx():
dx = [2,4,8,16]
return dx
def get_probabilities():
p = [0.05,0.275,0.50,0.725,0.95]
return p
def get_defaults():
dx = 8
p = 0.5
return dx,p
# -----------------------------------------------
# Write to netcdf functions
# -----------------------------------------------
def _write_density_to_netcdf(density,output_path):
log.info(None,f'Writing density to netcdf: {output_path}')
nc = Dataset(output_path,'w',format='NETCDF4')
# define dimensions
nc.createDimension('time',len(density.time))
nc.createDimension('lat',len(density.grid.lat))
nc.createDimension('lon',len(density.grid.lon))
# define variables
nc_time = nc.createVariable('time',float,'time',zlib=True)
nc_lon = nc.createVariable('lon',float,'lon',zlib=True)
nc_lat = nc.createVariable('lat',float,'lat',zlib=True)
nc_density = nc.createVariable('density',float,('time','lat','lon'),zlib=True)
nc_tp = nc.createVariable('total_particles',float,'time',zlib=True)
# write variables
time, time_units = convert_datetime_to_time(density.time)
nc_time[:] = time
nc_time.units = time_units
nc_lon[:] = density.grid.lon
nc_lat[:] = density.grid.lat
nc_density[:] = density.density
nc_tp[:] = density.total_particles
nc.close()
def _write_to_netcdf(particles,output_path):
log.info(None,f'Writing particle data to: {output_path}')
nc = Dataset(output_path,'w',format='NETCDF4')
# define dimensions
nc.createDimension('pid',len(particles.pid))
nc.createDimension('time',len(particles.time))
# define variables
nc_pid = nc.createVariable('pid',float,'pid',zlib=True)
nc_time = nc.createVariable('time',float,'time',zlib=True)
nc_lon = nc.createVariable('lon',float,('pid','time'),zlib=True)
nc_lat = nc.createVariable('lat',float,('pid','time'),zlib=True)
nc_beached = nc.createVariable('beached',float,('pid','time'),zlib=True)
# write variables
nc_pid[:] = particles.pid
time, time_units = convert_datetime_to_time(particles.time)
nc_time[:] = time
nc_time.units = time_units
nc_lon[:] = particles.lon
nc_lat[:] = particles.lat
nc_beached[:] = particles.beached
nc.close()
# -----------------------------------------------
# Processing
# -----------------------------------------------
def _get_parcels_particles_path(file_description,year=None,
dir_description='pts_output'):
parcels_dir = get_dir(dir_description)
if year is None:
parcels_path = f'{parcels_dir}{file_description}.nc'
return parcels_path
parcels_path = f'{parcels_dir}{file_description}{year}.nc'
return parcels_path
def _get_non_beaching_path(basin_name,description,extra_description=None,
dir_description='pts_processed'):
processed_dir = get_dir(dir_description)
if extra_description is None:
non_beached_path = f'{processed_dir}{basin_name}_{description}.nc'
else:
non_beached_path = f'{processed_dir}{basin_name}_{extra_description}_{description}.nc'
return non_beached_path
def _get_beaching_path(basin_name,dx,p,description,
extra_description=None,
dir_description='pts_processed'):
processed_dir = get_dir(dir_description)
p_str = str(p).replace('.','')
if extra_description is None:
beached_path = f'{processed_dir}{basin_name}_{description}_{dx}km_p{p_str}.nc'
else:
beached_path = f'{processed_dir}{basin_name}_{description}_{dx}km_p{p_str}_{extra_description}.nc'
return beached_path
def get_particles_path(basin_name,extra_description=None,
dir_description='pts_processed'):
particles_path = _get_non_beaching_path(basin_name,'particles',
extra_description=extra_description,
dir_description=dir_description)
return particles_path
def get_beached_particles_path(basin_name,dx,p,
extra_description=None,
dir_description='pts_processed'):
beached_particles_path = _get_beaching_path(basin_name,dx,p,'beached',
extra_description=extra_description,
dir_description=dir_description)
return beached_particles_path
def get_density_path(basin_name,extra_description=None,
dir_description='pts_processed'):
density_path = _get_non_beaching_path(basin_name,'density',
extra_description=extra_description,
dir_description=dir_description)
return density_path
def get_beached_density_path(basin_name,dx,p,extra_description=None,
dir_description='pts_processed'):
beached_density_path = _get_beaching_path(basin_name,dx,p,'density',
extra_description=extra_description,
dir_description=dir_description)
return beached_density_path
def process_beached_density(particles,dx,p,basin_name='io_nh',dx_grid=0.5,
output_description=None):
grid = get_global_grid(dx=dx_grid)
output_path = get_beached_density_path(basin_name,dx,p,extra_description=output_description)
density = Density.create_from_particles(grid,particles)
_write_density_to_netcdf(density,output_path)
def process_density(particles,basin_name='io_nh',dx_grid=0.5,output_description=None):
grid = get_global_grid(dx=dx_grid)
output_path = get_density_path(basin_name,extra_description=output_description)
density = Density.create_from_particles(grid,particles)
_write_density_to_netcdf(density,output_path)
def process_beached_particles(particles,dx,p,basin_name='io_nh',output_description=None):
beached_particles = particles.get_beachingparticles_at_distance_dx_with_probability(dx,p)
output_path = get_beached_particles_path(basin_name,dx,p,extra_description=output_description)
_write_to_netcdf(beached_particles,output_path)
return beached_particles
def process_particles(input_description='io_river_sources_',
basin_name='io_nh',
years=np.arange(1995,2016,1),
output_description=None):
if years is not None:
input_path = _get_parcels_particles_path(input_description,year=years[0])
particles = BeachingParticles.read_from_parcels_netcdf(input_path)
for year in years[1:]:
input_path = _get_parcels_particles_path(input_description,year=year)
particles.add_particles_from_parcels_netcdf(input_path)
else:
input_path = _get_parcels_particles_path(input_description)
particles = BeachingParticles.read_from_parcels_netcdf(input_path)
log.info(None,f'Extracting particles from initial basin only: {basin_name}')
basin_particles = particles.get_particles_from_initial_basin(basin_name)
# write to netcdf
output_path = get_particles_path(basin_name,extra_description=output_description)
_write_to_netcdf(basin_particles,output_path)
return basin_particles
def process_specific_file_density(input_path, output_path, dx_grid=0.5):
particles = BeachingParticles.read_from_netcdf(input_path)
grid = get_global_grid(dx=dx_grid)
density = Density.create_from_particles(grid, particles)
_write_density_to_netcdf(density, output_path)
def process_specific_file_particles_in_lon_lat_range(input_path, output_path, lon_range=None, lat_range=None, t_interval=1):
if type(input_path) == list:
particles = BeachingParticles.read_from_parcels_netcdf(input_path[0], t_interval=t_interval)
for i in range(len(input_path)-1):
particles.add_particles_from_parcels_netcdf(input_path[i+1])
elif type(input_path) == str:
particles = BeachingParticles.read_from_parcels_netcdf(input_path, t_interval=t_interval)
if lon_range is not None and lat_range is not None:
particles_in_range = particles.get_particles_from_initial_lon_lat_range(lon_range, lat_range)
_write_to_netcdf(particles_in_range, output_path)
else:
_write_to_netcdf(particles, output_path)
if __name__ == '__main__':
basin_names = ['io_nh','io_sh', 'io']
dx,_ = get_defaults()
ps = get_probabilities()
for basin_name in basin_names:
particles = process_particles(basin_name=basin_name)
process_density(particles,basin_name=basin_name)
for p in ps:
beached_particles = process_beached_particles(particles,dx,p,basin_name=basin_name)
process_beached_density(beached_particles,dx,p,basin_name=basin_name)
beached_particles = None
particles = None