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create_box.py
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create_box.py
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#!/usr/bin/env python
from __future__ import print_function
from __future__ import division
import os, sys
from os.path import join as pjoin
from argparse import ArgumentParser, ArgumentTypeError
import datetime
import numpy as np
import numpy.ma as ma
import netCDF4
from netCDF4 import Dataset
from shapely.geometry import Point
from shapely.geometry.polygon import Polygon
from traj_movie import get_circles
def create_initial_positions(xdivide=10, ydivide=10,lon0=55.,lon1=56.,lat0=-21.5, lat1=-20.5
,start=147, kdepth=-1.5, crop=False,
outfile='initial_positions.txt', domain_dir='/Users/agn/Data/NEMO0083'):
lons = np.linspace(lon0, lon1, xdivide+1)
lats = np.linspace(lat0, lat1, ydivide+1)
path = pjoin(domain_dir,'mask.nc')
print('path for mask file', path)
with Dataset(path) as f:
Ndlat = f.variables['nav_lat']
meridional = Ndlat[:,0]
jeq = meridional.searchsorted(0.)
Ndlon = f.variables['nav_lon']
zonal = Ndlon[jeq,:]
ibreak = np.argmax(zonal) + 1
if lon0 > zonal[0] and lon1 < zonal[ibreak-1]:
zonal_part = zonal[:ibreak]
iadd = 0
elif lon0 > zonal[ibreak] and lon1 < zonal[-1]:
zonal_part = zonal[ibreak:]
iadd = ibreal
else:
sys.exit('lon0 and lon1 bracket dateline; not implemented yet')
i0 = zonal_part.searchsorted(lon0) - 1 + iadd
i1 = zonal_part.searchsorted(lon1) + 1 + iadd
imid = (i0 + i1)//2
meridional = Ndlat[:,imid]
j0 = meridional.searchsorted(lat0) - 1
j1 = meridional.searchsorted(lat1) + 1
jmid = (j0 + j1)//2
zonal = Ndlon[jmid,:]
dlon = np.diff(zonal)
ibreak = np.argmin(dlon)
ri = np.interp(lons, zonal[i0:i1], np.arange(i0,i1,dtype=zonal.dtype))
rj = np.interp(lats, meridional[j0:j1], np.arange(j0,j1,dtype=meridional.dtype))
print('specified longitudes are','\n',lons)
print('i values are','\n',ri + 1. -.5)
print('specified latitudes are','\n',lats)
print('j values are','\n',rj + 1. -.5)
i00, i11 = i0 - 1, i1 + 1
j00, j11 = j0 - 1, j1 + 1
tmask = ~(f.variables['tmaskutil'][0,j00:j11,i00:i11].astype(np.bool))
uvmask = tmask[1:-1,1:-1] + tmask[:-2,1:-1] + tmask[2:,1:-1] \
+ tmask[1:-1,:-2] + tmask[1:-1,2:]
if crop:
inner_circle, outer_circle, fuel_circle, box = get_circles()
polygon = Polygon( zip(*box) )
npoints = 0
with open(outfile, 'w') as f:
for y, lat in zip(rj, lats):
for x, lon in zip(ri, lons):
if (not crop) or (crop and polygon.contains(Point(lon, lat))):
i, j = int(x), int(y)
if not uvmask[j-j0, i-i0]:
# ri and rj are c-indices relative to T-cells
# subtract .5 to produce u v indices as required by ariane
# ... and add 1 to convert from C to fortran numbering
f.write('%10g%10g%10g%10g%5g\n' %(x + 1. -.5, y + 1. -.5 , kdepth, start, 1))
npoints +=1
print('# of sea points started is %g out of %g' % (npoints, len(rj)*len(ri)))
def create_initial_positions3(xdivide=10, ydivide=10,lon0=55.,lon1=56.,lat0=-21.5, lat1=-20.5
,start=1, zdivide=10, k0=56., k1=60., crop=False,
outfile='initial_positions.txt', domain_dir='/Users/agn/Data/NEMO0083'):
lons = np.linspace(lon0, lon1, xdivide+1)
lats = np.linspace(lat0, lat1, ydivide+1)
kdepths = np.linspace(k0, k1, zdivide+1)
path = pjoin(domain_dir,'mask.nc')
print('path for mask file', path)
with Dataset(path) as f:
Ndlat = f.variables['nav_lat']
meridional = Ndlat[:,0]
jeq = meridional.searchsorted(0.)
Ndlon = f.variables['nav_lon']
zonal = Ndlon[jeq,:]
ibreak = np.argmax(zonal) + 1
if lon0 > zonal[0] and lon1 < zonal[ibreak-1]:
zonal_part = zonal[:ibreak]
iadd = 0
elif lon0 > zonal[ibreak] and lon1 < zonal[-1]:
zonal_part = zonal[ibreak:]
iadd = ibreak
else:
sys.exit('lon0 and lon1 bracket dateline; not implemented yet')
i0 = zonal_part.searchsorted(lon0) - 1 + iadd
i1 = zonal_part.searchsorted(lon1) + 1 + iadd
imid = (i0 + i1)//2
meridional = Ndlat[:,imid]
j0 = meridional.searchsorted(lat0) - 1
j1 = meridional.searchsorted(lat1) + 1
jmid = (j0 + j1)//2
zonal = Ndlon[jmid,:]
dlon = np.diff(zonal)
ibreak = np.argmin(dlon)
ri = np.interp(lons, zonal[i0:i1], np.arange(i0,i1,dtype=zonal.dtype))
rj = np.interp(lats, meridional[j0:j1], np.arange(j0,j1,dtype=meridional.dtype))
print('specified longitudes are','\n',lons)
print('i values are','\n',ri + 1. -.5)
print('specified latitudes are','\n',lats)
print('j values are','\n',rj + 1. -.5)
print('k values are','\n',kdepths)
i00, i11 = i0 - 1, i1 + 1
j00, j11 = j0 - 1, j1 + 1
tmask = ~(f.variables['tmask'][0,:,j00:j11,i00:i11].astype(np.bool))
uvmask = tmask[:,1:-1,1:-1] + tmask[:,:-2,1:-1] + tmask[:,2:,1:-1] \
+ tmask[:,1:-1,:-2] + tmask[:,1:-1,2:]
if crop:
inner_circle, outer_circle, fuel_circle, box = get_circles()
polygon = Polygon( zip(*box) )
npoints = 0
with open(outfile, 'w') as f:
for kdepth in kdepths:
for y, lat in zip(rj, lats):
for x, lon in zip(ri, lons):
if (not crop) or (crop and polygon.contains(Point(lon, lat))):
i, j, k = int(x), int(y), int(kdepth)
if not uvmask[k-1,j-j0, i-i0]:
# ri and rj are c-indices relative to T-cells
# subtract .5 to produce u v indices as required by ariane
# ... and add 1 to convert from C to fortran numbering
f.write('%10g%10g%10g%10g%5g\n' %(x + 1. -.5, y + 1. -.5 , kdepth, start, 1))
npoints +=1
print('# of sea points started is %g out of %g' % (npoints, len(rj)*len(ri)*len(kdepths)))
if __name__ == '__main__':
parser = ArgumentParser(description=
"""
produce movie of particle positions
""")
parser.add_argument('--nx',dest='xdivide',
help="x divisions ",type=int, default=100)
parser.add_argument('--ny',dest='ydivide',
help="y divisions ",type=int, default=100)
parser.add_argument('--nz',dest='zdivide',
help="z divisions ",type=int, default=100)
parser.add_argument('--lon0',dest='lon0',
help="W bdry ",type=float, default=55.)
parser.add_argument('--lon1',dest='lon1',
help="E bdry ",type=float, default=56.)
parser.add_argument('--lat0',dest='lat0',
help="S bdry ",type=float, default=-21.5)
parser.add_argument('--lat1',dest='lat1',
help="N bdry ",type=float, default=-20.5)
parser.add_argument('--time_index',dest='time_index',
help="time index when particles at initial positions ",type=int, default=1)
parser.add_argument('--kdepth',dest='kdepth',
help="depth in terms of k (k=1 is ths surface) ",type=float, default=-1.5)
parser.add_argument('--k0',dest='k0',
help="min depth in terms of k (k=1 is ths surface) ",type=float, default=None)
parser.add_argument('--k1',dest='k1',
help="max depth in terms of k (k=1 is ths surface) ",type=float, default=None)
parser.add_argument('--start',dest='start',
help="starting time index",type=int, default=None)
parser.add_argument('--outfile', '-o', dest='outfile',
help="output file of points ",default='initial_positions.txt')
parser.add_argument('-d', '--domain_dir', dest='domain_dir',
help="domain containing mesh files", default='/Users/Data/NEMO/0083')
parser.add_argument('--crop', '-c',dest='crop', action='store_true',
help="crop by satellite zone ",default=False)
args = parser.parse_args()
if (args.k0 is None) or (args.k1 is None):
create_initial_positions(xdivide=args.xdivide, ydivide=args.ydivide,
lon0=args.lon0,lon1=args.lon1,lat0=args.lat0, lat1=args.lat1,
start=args.start, kdepth=args.kdepth, crop=args.crop,
domain_dir = args.domain_dir, outfile=args.outfile)
else:
create_initial_positions3(xdivide=args.xdivide, ydivide=args.ydivide, zdivide=args.zdivide,
lon0=args.lon0,lon1=args.lon1,lat0=args.lat0, lat1=args.lat1,
start=args.start, k0=args.k0, k1=args.k1, crop=args.crop,
domain_dir = args.domain_dir, outfile=args.outfile)