def test_prepareForSimulation():
"""
Test initial steps to get ready for a simulation.
"""
# Get projection object
proj = tracpy.tools.make_proj(setup="galveston", usebasemap=False)
# Read in grid
grid_filename = os.path.join(here, "input", "grid.nc")
currents_filename = os.path.join(here, "input", "ocean_his_0001.nc")
grid = tracpy.inout.readgrid(grid_filename, proj, vert_filename=currents_filename)
tp = Tracpy(currents_filename, grid)
date = datetime.datetime(2013, 12, 19, 0)
lon0 = [-123.0, -123.0]
lat0 = [48.55, 48.75]
tinds, nc, t0save, xend, yend, zend, zp, ttend, flag = tp.prepare_for_model_run(date, lon0, lat0)
assert True
assert tp.uf is not None
assert np.sum(np.isnan(tp.uf[0, :, :, :])) == tp.uf[0, :, :, :].size
def test_prepareForSimulation():
'''
Test initial steps to get ready for a simulation.
'''
# Get projection object
proj = tracpy.tools.make_proj(setup='galveston', usebasemap=False)
# Read in grid
grid_filename = os.path.join(here, 'input', 'grid.nc')
currents_filename = os.path.join(here, 'input', 'ocean_his_0001.nc')
grid = tracpy.inout.readgrid(grid_filename,
proj,
vert_filename=currents_filename)
tp = Tracpy(currents_filename, grid)
date = datetime.datetime(2013, 12, 19, 0)
lon0 = [-123., -123.]
lat0 = [48.55, 48.75]
tinds, nc, t0save, xend, yend, zend, zp, ttend, flag \
= tp.prepare_for_model_run(date, lon0, lat0)
assert True
assert tp.uf is not None
assert np.sum(np.isnan(tp.uf[0, :, :, :])) == tp.uf[0, :, :, :].size
def init(name, grid_filename, currents_filename):
'''
Initialize parameters for idealized eddy simulations.
Initialization for seeding drifters at all shelf model
grid points to be run forward.
'''
time_units = 'seconds since 0001-01-01 00:00:00'
# horizontal_diffusivity project showed that relative dispersion did not
# change between nsteps=25 and 50, but does between nsteps=5 and 25, and
# interim numbers have not been tested yet.
nsteps = 19 # to approximate the output timing of the TXLA model 25
# Number of steps to divide model output for outputting drifter location
N = 4 # to approximate the output timing of the TXLA model # 5
# Number of days
ndays = 7
# This is a forward-moving simulation
ff = 1
# Time between outputs
tseas = 10800.0 # time between output in seconds
ah = 0.
av = 0. # m^2/s
# surface drifters
z0 = 's'
zpar = 29 # 30 layers
# for 3d flag, do3d=0 makes the run 2d and do3d=1 makes the run 3d
do3d = 0
doturb = 0
# for periodic boundary conditions in the x direction
doperiodic = 1
# Flag for streamlines. All the extra steps right after this are for streamlines.
dostream = 0
# Initialize Tracpy class
tp = Tracpy(currents_filename, grid_filename, name=name, tseas=tseas, ndays=ndays, nsteps=nsteps,
N=N, ff=ff, ah=ah, av=av, doturb=doturb, do3d=do3d, z0=z0, zpar=zpar, time_units=time_units,
usespherical=False, savell=False, doperiodic=doperiodic)
# force grid reading
tp._readgrid()
# Start uniform array of drifters across domain using x,y coords
x0 = tp.grid['xr'][1:-1,1:-1]
y0 = tp.grid['yr'][1:-1,1:-1]
return tp, x0, y0
def test_readgrid():
'''
Test for initializing grid without vertical grid information.
'''
tp = Tracpy(os.path.join(here, 'input', 'grid.nc'))
tp._readgrid()
assert True
assert tp.grid
def test_readgrid():
'''
Test for initializing grid without vertical grid information.
'''
tp = Tracpy(os.path.join(here, 'input', 'grid.nc'))
tp._readgrid()
assert True
assert tp.grid
def test_readgridWithVertical():
'''
Test for initializing grid and saving vertical grid information.
'''
tp = Tracpy(os.path.join(here, 'input', 'ocean_his_0001.nc'),
os.path.join(here, 'input', 'grid.nc'))
tp._readgrid()
assert True
assert tp.grid
assert tp.grid['Vtransform'] # make sure vertical info is in there
def test_readgridWithVertical():
'''
Test for initializing grid and saving vertical grid information.
'''
tp = Tracpy(os.path.join(here, 'input', 'ocean_his_0001.nc'),
os.path.join(here, 'input', 'grid.nc'))
tp._readgrid()
assert True
assert tp.grid
assert tp.grid['Vtransform'] # make sure vertical info is in there
def __init__(
self,
currents_filename,
grid_filename=None,
nsteps=1, ndays=1, ff=1, tseas=3600.,
ah=0., av=0., z0='s', zpar=1, do3d=0, doturb=0, name='test', dostream=0, N=1,
time_units='seconds since 1970-01-01', dtFromTracmass=None, zparuv=None, tseas_use=None
**kwargs
):
"""
tracpy_mover (velocity)
create a tracpy_mover instance
:param velocity: a (u, v, w) triple -- in meters per second
Remaining kwargs are passed onto Mover's __init__ using super.
See Mover documentation for remaining valid kwargs.
"""
# self.velocity = np.asarray(velocity,
# dtype=basic_types.mover_type).reshape((3,
# )) # use this, to be compatible with whatever we are using for location
# self.uncertainty_scale = uncertainty_scale
# initializes Tracpy class
self.tp = Tracpy(currents_filename, grid_filename=grid_filename, nsteps=nsteps,
ndays=ndays, ff=ff, tseas=tseas, ah=ah, av=av, z0=z0, zpar=zpar,
do3d=do3d, doturb=doturb, name=name, dostream=dostream, N=N,
time_units=time_units, dtFromTracmass=dtFromTracmass,
zparuv=zparuv, tseas_use=tseas_use)
# calls Mover class
super(TracpyMover, self).__init__(**kwargs)
def test_prepareForSimulation():
'''
Test initial steps to get ready for a simulation.
'''
date = datetime.datetime(2013, 12, 19, 0)
lon0 = [-123., -123.]
lat0 = [48.55, 48.75]
tp = Tracpy(os.path.join(here, 'input', 'ocean_his_0001.nc'), grid_filename=os.path.join(here, 'input', 'grid.nc'))
tinds, nc, t0save, xend, yend, zend, zp, ttend, flag = tp.prepare_for_model_run(date, lon0, lat0)
assert True
assert tp.uf is not None
assert np.sum(np.isnan(tp.uf[:,:,:,0])) == tp.uf[:,:,:,0].size
def test_init():
'''
Make sure that we can initialize the class.
'''
tp = Tracpy(os.path.join(here, 'input', 'ocean_his_0001.nc'))
assert True
def test_initWithGridSource():
'''
Make sure we can initialize with a grid source location
'''
tp = Tracpy(os.path.join(here, 'input', 'ocean_his_0001.nc'),
grid_filename=os.path.join(here, 'input', 'grid.nc'))
assert True
def test_prepareForSimulation():
'''
Test initial steps to get ready for a simulation.
'''
date = datetime.datetime(2013, 12, 19, 0)
lon0 = [-123., -123.]
lat0 = [48.55, 48.75]
tp = Tracpy(os.path.join(here, 'input', 'ocean_his_0001.nc'),
grid_filename=os.path.join(here, 'input', 'grid.nc'))
tinds, nc, t0save, xend, yend, zend, zp, ttend, flag = tp.prepare_for_model_run(
date, lon0, lat0)
assert True
assert tp.uf is not None
assert np.sum(np.isnan(tp.uf[:, :, :, 0])) == tp.uf[:, :, :, 0].size
def test_readgridWithVertical():
'''
Test for initializing grid and saving vertical grid information.
'''
# Get projection object
proj = tracpy.tools.make_proj(setup='galveston', usebasemap=False)
# Read in grid
grid_filename = os.path.join(here, 'input', 'grid.nc')
currents_filename = os.path.join(here, 'input', 'ocean_his_0001.nc')
grid = tracpy.inout.readgrid(grid_filename,
proj,
vert_filename=currents_filename)
tp = Tracpy(currents_filename, grid)
assert True
assert tp.grid
# make sure there is a value for a vertical grid parameter
assert hasattr(grid, 'sc_r')
def test_init():
'''
Initialize class without vertical grid information.
Make sure that we can initialize the class with a grid and without
vertical grid information.
'''
# Get projection object
proj = tracpy.tools.make_proj(setup='galveston', usebasemap=False)
# Read in grid
grid_filename = os.path.join(here, 'input', 'grid.nc')
currents_filename = os.path.join(here, 'input', 'ocean_his_0001.nc')
grid = tracpy.inout.readgrid(grid_filename, proj)
tp = Tracpy(currents_filename, grid)
assert True
assert tp.grid
# make sure there isn't a value for a vertical grid parameter
assert not hasattr(grid, 'sc_r')
def init(name, lonsink, latsink, sinkarrows):
'''
Initialization for the simulation.
'''
time_units = 'seconds since 1970-01-01'
# horizontal_diffusivity project showed that relative dispersion did not
# change between nsteps=25 and 50, but does between nsteps=5 and 25, and
# interim numbers have not been tested yet.
nsteps = 5 # interpolation forced between model output
# Number of steps to divide model output for outputting drifter location
N = 1
# Number of days
ndays = 30
# This is a forward-moving simulation
ff = 1
# Time between outputs
tseas = 3 * 3600 # 3 hours between outputs, in seconds, time between model outputs
ah = 0. # old tracks: 5.
av = 0. # m^2/s
# surface drifters
z0 = 's'
zpar = 0
zparuv = 0
# for 3d flag, do3d=0 makes the run 2d and do3d=1 makes the run 3d
do3d = 0
doturb = 0
# Flag for streamlines.
dostream = 0
# Initialize Tracpy class
tp = Tracpy(loc,
grid=grid,
name=name,
tseas=tseas,
ndays=ndays,
nsteps=nsteps,
dostream=dostream,
savell=False,
doperiodic=0,
N=N,
ff=ff,
ah=ah,
av=av,
doturb=doturb,
do3d=do3d,
z0=z0,
zpar=zpar,
time_units=time_units,
sinkarrows=sinkarrows)
# initial separation distance of drifters, in meters, from sensitivity project
dx = 100
seedsfile = 'calcs/seeds_lon0_%2.2f_lat0_%2.2f.npz' % (abs(lonsink),
latsink)
if os.path.exists(seedsfile):
seeds = np.load(seedsfile)
lon0 = seeds['lon0']
lat0 = seeds['lat0']
seeds.close()
else:
# Initial lon/lat locations for drifters
# Start uniform array of drifters across domain using x,y coords
llcrnrlon = lonsink - 0.1
urcrnrlon = lonsink + 0.1
llcrnrlat = latsink - 0.1
urcrnrlat = latsink + 0.1
xcrnrs, ycrnrs = tp.grid.proj([llcrnrlon, urcrnrlon],
[llcrnrlat, urcrnrlat])
X, Y = np.meshgrid(np.arange(xcrnrs[0], xcrnrs[1], dx),
np.arange(ycrnrs[0], ycrnrs[1], dx))
lon0, lat0 = tp.grid.proj(X, Y, inverse=True)
# save starting locations for future use
np.savez(seedsfile, lon0=lon0, lat0=lat0)
return tp, lon0, lat0
def init(rootdir, ndrifters):
'''
Initialize simulation.
'''
name = os.path.join(rootdir, 'tracks')
# Where to find simulation information
currents_filename = os.path.join(rootdir, 'ocean_his_0001.nc')
grid_filename = os.path.join(rootdir, 'grid.nc')
time_units = 'seconds since 1970-01-01'
num_layers = 3
nsteps = 5
# Number of steps to divide model output for outputting drifter location
N = 4
# This is a forward-moving simulation
ff = 1
# Time between outputs
tseas = 4 * 3600. # 4 hours between outputs, in seconds
ah = 0.
av = 0. # m^2/s
# Number of days
ndays = tseas * 9. / (3600. * 24)
# surface drifters
z0 = 's'
zpar = num_layers - 1 # top layer
# for 3d flag, do3d=0 makes the run 2d and do3d=1 makes the run 3d
do3d = 0
doturb = 0
# for periodic boundary conditions in the x direction
doperiodic = 1
# Flag for streamlines. All the extra steps right after this are for streamlines.
dostream = 0
# Initialize Tracpy class
tp = Tracpy(currents_filename,
grid_filename,
name=name,
tseas=tseas,
ndays=ndays,
nsteps=nsteps,
N=N,
ff=ff,
ah=ah,
av=av,
doturb=doturb,
do3d=do3d,
z0=z0,
zpar=zpar,
time_units=time_units,
savell=False,
doperiodic=0,
usespherical=False)
# one particle starting position times however many drifters
x0 = np.ones(ndrifters) * 12000.
y0 = np.ones(ndrifters) * 31000.
return tp, x0, y0
def init(name):
'''Initialize tracpy simulation'''
time_units = 'seconds since 0001-01-01 00:00:00'
nsteps = 25
# Number of steps to divide model output for outputting drifter location
N = 1
# Number of days
# 165 seconds max or less as simulations step forward in time
# name accounts for start time stepping forward in time each simulation
if len(name) == 19:
startdate = datetime.strptime(name, '%Y-%m-%dT%H:%M:%S')
elif len(name) > 19:
startdate = datetime.strptime(name, '%Y-%m-%dT%H:%M:%S.%f')
starttime = netCDF.date2num(startdate, time_units)
ndays = (220. - starttime - dt) / 86400
# This is a forward-moving simulation
ff = 1
# Time between outputs
tseas = dt # time between output in seconds
ah = 0.
av = 0. # m^2/s
# surface drifters
z0 = 's'
zpar = 0 # 1 layer
# for 3d flag, do3d=0 makes the run 2d and do3d=1 makes the run 3d
do3d = 0
doturb = 0
# for periodic boundary conditions in the x direction
doperiodic = 0
# Flag for streamlines. All the extra steps right after this are for streamlines.
dostream = 0
# import pdb; pdb.set_trace()
proj = tracpy.tools.make_proj(setup='galveston')
loc = 'model/model.nc'
grid = tracpy.inout.readgrid(loc, proj, usespherical=False)
# Start uniform array of drifters across domain using x,y coords
# z0temp = tracpy.op.resize(np.linspace(-1,0,7), 0) # s_rho
# z0 = np.concatenate((z0temp, z0temp))
# x0temp = [7.435, 7.435]
# x0 = np.concatenate((x0temp[0]*np.ones(z0temp.size), x0temp[1]*np.ones(z0temp.size)))
# y0temp = [2.3945, 2.968]
# y0 = np.concatenate((y0temp[0]*np.ones(z0temp.size), y0temp[1]*np.ones(z0temp.size)))
x0 = [7.435, 7.435]
y0 = [2.3945, 2.968]
# Initialize Tracpy class
tp = Tracpy(loc,
grid,
name='tracks/tracks_' + name,
tseas=tseas,
ndays=ndays,
nsteps=nsteps,
N=N,
ff=ff,
ah=ah,
av=av,
doturb=doturb,
do3d=do3d,
z0=z0,
zpar=zpar,
time_units=time_units,
usespherical=False,
savell=True,
doperiodic=doperiodic)
# force grid reading
# tp._readgrid()
return tp, x0, y0
def init(name):
'''
Initialization for the simulation.
'''
# loc = 'http://barataria.tamu.edu:6060/thredds/dodsC/NcML/txla_nesting6.nc'
time_units = 'seconds since 1970-01-01'
# horizontal_diffusivity project showed that relative dispersion did not
# change between nsteps=25 and 50, but does between nsteps=5 and 25, and
# interim numbers have not been tested yet.
nsteps = 25 # in-between tracks: 12 # old tracks: 25
# Number of steps to divide model output for outputting drifter location
N = 5
# Number of days
ndays = 50
# This is a forward-moving simulation
ff = 1
# Time between outputs
tseas = 4*3600 # 4 hours between outputs, in seconds, time between model outputs
ah = 0. # old tracks: 5.
av = 0. # m^2/s
# surface drifters
z0 = 's'
zpar = 29
# for 3d flag, do3d=0 makes the run 2d and do3d=1 makes the run 3d
do3d = 0
doturb = 0
# Flag for streamlines.
dostream = 0
# Initialize Tracpy class
tp = Tracpy(currents_filename, name=name, tseas=tseas, ndays=ndays, nsteps=nsteps, dostream=dostream, savell=False, doperiodic=0,
N=N, ff=ff, ah=ah, av=av, doturb=doturb, do3d=do3d, z0=z0, zpar=zpar,
time_units=time_units, usebasemap=True, grid=grid)
# tp = Tracpy(currents_filename, grid_filename=grid_filename, name=name, tseas=tseas, ndays=ndays, nsteps=nsteps, dostream=dostream, savell=False, doperiodic=0,
# N=N, ff=ff, ah=ah, av=av, doturb=doturb, do3d=do3d, z0=z0, zpar=zpar,
# time_units=time_units, usebasemap=True, grid=grid, vert_filename=vert_filename)
# tp._readgrid()
if os.path.exists('calcs/seeds.npz'):
seeds = np.load('calcs/seeds.npz')
lon0 = seeds['lon0']; lat0 = seeds['lat0']
seeds.close()
else:
llcrnrlon = -93.8; urcrnrlon = -92.2; llcrnrlat = 28; urcrnrlat = 29.2; # New
xcrnrs, ycrnrs = grid['basemap']([llcrnrlon, urcrnrlon], [llcrnrlat, urcrnrlat])
X, Y = np.meshgrid(np.arange(xcrnrs[0], xcrnrs[1], 700),
np.arange(ycrnrs[0], ycrnrs[1], 700))
lon0, lat0 = grid['basemap'](X, Y, inverse=True)
# Eliminate points that are outside domain or in masked areas
lon0, lat0 = tracpy.tools.check_points(lon0, lat0, grid)
# save starting locations for future use
np.savez('calcs/seeds.npz', lon0=lon0, lat0=lat0)
# # equal weightings for drifters for transport.
# T0 = np.ones(lon0.size, order='F')
# U = np.ma.zeros(tp.grid['xu'].shape, order='F')
# V = np.ma.zeros(tp.grid['xv'].shape, order='F')
# pdb.set_trace()
return tp, lon0, lat0
def test_run_2d_ll():
"""
can we initialize and run tracpy (using rectangle example). Compare final location of drifters
with known analytic answer. Using lon/lat coords.
"""
# some simple example data
currents_filename = os.path.join('input', 'ocean_his_0001.nc')
grid_filename = os.path.join('input', 'grid.nc')
time_units = 'seconds since 1970-01-01'
num_layers = 3
name = 'test_run_2d_ll'
start = time.time()
# grd = tracpy.inout.readgrid(grid_filename, vert_filename=currents_filename)
print "building grid took:", time.time() - start
# Start date in date time formatting
date = datetime.datetime(2013, 12, 19, 0)
# Time between outputs
tseas = 4 * 3600. # 4 hours between outputs, in seconds
# Number of days to run the drifters.
ndays = tseas * 9. / (3600. * 24)
# Sets a smaller limit than between model outputs for when to force interpolation if hasn't already occurred.
nsteps = 5
# Controls the sampling frequency of the drifter tracks.
N = 4
# This allows the user to call to TRACMASS for a different period of time than between 2 model outputs
dtFromTracmass = tseas / 2. # Just testing to try new loop, should have same behavior as before
# Use ff = 1 for forward in time and ff = -1 for backward in time.
ff = 1 # will work for ff=1 or ff=-1 since checks by distance traveled
ah = 0. # m^2/s
av = 0. # m^2/s
# turbulence/diffusion flag
doturb = 0
# two particles (starting positions)
lon0 = [-123., -123.]
lat0 = [48.55, 48.75]
do3d = 0 # flag to set to 2-d
z0 = 's' #'z' #'salt' #'s'
zpar = num_layers - 1 # top layer
# Initialize Tracpy class
tp = Tracpy(currents_filename,
grid_filename,
name=name,
tseas=tseas,
ndays=ndays,
nsteps=nsteps,
N=N,
ff=ff,
ah=ah,
av=av,
doturb=doturb,
do3d=do3d,
z0=z0,
zpar=zpar,
time_units=time_units,
dtFromTracmass=dtFromTracmass)
# tp._readgrid()
lonp, yp, zp, t, T0, U, V = tracpy.run.run(tp, date, lon0, lat0)
## check the results:
print lonp.shape
print lonp
print yp
#eastward current, latitude should not change:
assert np.allclose(lat0, yp.T)
# current velocity -- 0.1 m/s
# position
distance = (ndays * 24 * 3600 * 0.1) * ff
# better to use pyproj to compute the geodesic
geod = pyproj.Geod(ellps='WGS84')
end = geod.fwd(lon0, lat0, (90, 90), (distance, distance), radians=False)
assert np.allclose(lonp[:, -1], end[0])
days = np.arange(1, 32)
for day in days:
date = datetime.datetime(year, month, day, 0)
name = '%dJuly%d' % (year, day) # 1994July5
if not os.path.exists('tracks/' + name +
'.nc') and not os.path.exists('tracks/' + name +
'gc.nc'):
print(day)
tp = Tracpy(loc,
grid,
name=name,
tseas=tseas,
ndays=ndays,
nsteps=nsteps,
N=N,
ff=ff,
ah=ah,
av=av,
doturb=doturb,
do3d=do3d,
z0=z0,
zpar=zpar,
time_units=time_units)
# evenly spaced surface drifters
dx = 1000 # in meters
lonsink, latsink = -93.72595, 27.902 # exactly in between outer boundaries of banks from fgb website
llcrnrlon = lonsink - 0.2
urcrnrlon = lonsink + 0.2
llcrnrlat = latsink - 0.12
urcrnrlat = latsink + 0.12
xcrnrs, ycrnrs = tp.grid.proj([llcrnrlon, urcrnrlon],
def init(name):
'''Initialize tracpy simulation'''
time_units = 'seconds since 0001-01-01 00:00:00'
nsteps = 25
# Number of steps to divide model output for outputting drifter location
N = 1
# Number of days
ndays = 150. / 86400 # 150 sec 0.0025 # 220 seconds
# This is a forward-moving simulation
ff = 1
# Time between outputs
tseas = 0.1 # time between output in seconds
ah = 0.
av = 0. # m^2/s
# surface drifters
z0 = 's'
zpar = 0 # 1 layer
# for 3d flag, do3d=0 makes the run 2d and do3d=1 makes the run 3d
do3d = 0
doturb = 0
# for periodic boundary conditions in the x direction
doperiodic = 0
# Flag for streamlines. All the extra steps right after this are for streamlines.
dostream = 0
# import pdb; pdb.set_trace()
proj = tracpy.tools.make_proj(setup='galveston')
loc = 'model.nc'
grid = tracpy.inout.readgrid(loc, proj, usespherical=False)
# Initialize Tracpy class
tp = Tracpy(loc,
grid,
name='tracks',
tseas=tseas,
ndays=ndays,
nsteps=nsteps,
N=N,
ff=ff,
ah=ah,
av=av,
doturb=doturb,
do3d=do3d,
z0=z0,
zpar=zpar,
time_units=time_units,
usespherical=False,
savell=True,
doperiodic=doperiodic)
# force grid reading
# tp._readgrid()
# Start uniform array of drifters across domain using x,y coords
x0 = grid.x_rho[1:-1:2, 1:-1:2]
y0 = grid.y_rho[1:-1:2, 1:-1:2]
return tp, x0, y0
def init(name, ndays, grid_filename, currents_filename):
'''
Initialization for seeding drifters at all shelf model grid points to be run
forward.
'''
# horizontal_diffusivity project showed that relative dispersion did not
# change between nsteps=25 and 50, but does between nsteps=5 and 25, and
# interim numbers have not been tested yet.
nsteps = 19 # to approximate the output timing of the TXLA model 25
# Number of steps to divide model output for outputting drifter location
N = 4 # to approximate the output timing of the TXLA model # 5
# Number of days
# ndays = 30
# This is a forward-moving simulation
ff = 1
# Time between outputs
tseas = 10800.0 # time between output in seconds
ah = 0.
av = 0. # m^2/s
# Initial lon/lat locations for drifters
# The following few lines aren't necessary because the grid cells are uniformly 1km res
# # Start uniform array of drifters across domain using x,y coords
# dx = 1000 # initial separation distance of drifters, in meters
# xcrnrs = np.array([grid['xr'][1:-1,:].min(), grid['xr'][1:-1,:].max()])
# ycrnrs = np.array([grid['yr'][1:-1,:].min(), grid['yr'][1:-1,:].max()])
# X, Y = np.meshgrid(np.arange(xcrnrs[0], xcrnrs[1], dx), np.arange(ycrnrs[0], ycrnrs[1], dx))
# lon0, lat0 = grid['basemap'](X, Y, inverse=True)
# surface drifters
z0 = 's'
zpar = 29 # 30 layers
# zpar = grid['km']-1
# for 3d flag, do3d=0 makes the run 2d and do3d=1 makes the run 3d
do3d = 0
doturb = 0
# for periodic boundary conditions in the x direction
doperiodic = 1
# Flag for streamlines. All the extra steps right after this are for streamlines.
dostream = 0
# Initialize Tracpy class
tp = Tracpy(currents_filename,
grid_filename,
name=name,
tseas=tseas,
ndays=ndays,
nsteps=nsteps,
N=N,
ff=ff,
ah=ah,
av=av,
doturb=doturb,
do3d=do3d,
z0=z0,
zpar=zpar,
time_units=time_units,
savell=False,
doperiodic=1)
# force grid reading
tp._readgrid()
# Start uniform array of drifters across domain using x,y coords
x0 = tp.grid['xr'][1:-1, 1:-1]
y0 = tp.grid['yr'][1:-1, 1:-1]
return tp, x0, y0
def test_run_2d_xy():
"""
can we initialize and run tracpy (using rectangle example). Compare final location of drifters
with known analytic answer. Using x/y coords for idealized type runs.
Made this simulation information from the other test information using:
"""
# some simple example data
currents_filename = os.path.join('input', 'ocean_his_0001.nc')
grid_filename = os.path.join('input', 'gridxy.nc')
time_units = 'seconds since 1970-01-01'
num_layers = 3
name = 'test_run_2d_xy'
start = time.time()
# grd = tracpy.inout.readgrid(grid_filename, vert_filename=currents_filename)
print "building grid took:", time.time() - start
# Start date in date time formatting
date = datetime.datetime(2013, 12, 19, 0)
# Time between outputs
tseas = 4 * 3600. # 4 hours between outputs, in seconds
# Number of days to run the drifters.
ndays = tseas * 9. / (3600. * 24)
# Sets a smaller limit than between model outputs for when to force interpolation if hasn't already occurred.
nsteps = 5
# Controls the sampling frequency of the drifter tracks.
N = 4
# This allows the user to call to TRACMASS for a different period of time than between 2 model outputs
dtFromTracmass = tseas / 2. # Just testing to try new loop, should have same behavior as before
# Use ff = 1 for forward in time and ff = -1 for backward in time.
ff = 1 # will work for ff=1 or ff=-1 since checks by distance traveled
ah = 0. # m^2/s
av = 0. # m^2/s
# turbulence/diffusion flag
doturb = 0
# two particles (starting positions)
x0 = [22065., 22065.]
y0 = [27777., 51587.]
do3d = 0 # flag to set to 2-d
z0 = 's' #'z' #'salt' #'s'
zpar = num_layers - 1 # top layer
# Initialize Tracpy class
tp = Tracpy(currents_filename,
grid_filename,
name=name,
tseas=tseas,
ndays=ndays,
nsteps=nsteps,
N=N,
ff=ff,
ah=ah,
av=av,
doturb=doturb,
do3d=do3d,
z0=z0,
zpar=zpar,
time_units=time_units,
dtFromTracmass=dtFromTracmass,
usespherical=False)
# tp._readgrid()
xp, yp, zp, t, T0, U, V = tracpy.run.run(tp, date, x0, y0)
## check the results:
print xp.shape
print xp
print yp
#eastward current, latitude should not change:
assert np.allclose(y0, yp.T)
# current velocity -- 0.1 m/s
# position
distance = (ndays * 24 * 3600 * 0.1) * ff
print distance
print xp[:, -1] - xp[:, 0]
assert np.allclose(xp[:, -1] - xp[:, 0], distance)
class TracpyMover(Mover):
"""
tracpy_mover
"""
_state = copy.deepcopy(Mover._state)
_state.add(update=['uncertainty_scale', 'velocity'],
create=['uncertainty_scale', 'velocity'])
def __init__(
self,
currents_filename,
grid_filename=None,
nsteps=1, ndays=1, ff=1, tseas=3600.,
ah=0., av=0., z0='s', zpar=1, do3d=0, doturb=0, name='test', dostream=0, N=1,
time_units='seconds since 1970-01-01', dtFromTracmass=None, zparuv=None, tseas_use=None
**kwargs
):
"""
tracpy_mover (velocity)
create a tracpy_mover instance
:param velocity: a (u, v, w) triple -- in meters per second
Remaining kwargs are passed onto Mover's __init__ using super.
See Mover documentation for remaining valid kwargs.
"""
# self.velocity = np.asarray(velocity,
# dtype=basic_types.mover_type).reshape((3,
# )) # use this, to be compatible with whatever we are using for location
# self.uncertainty_scale = uncertainty_scale
# initializes Tracpy class
self.tp = Tracpy(currents_filename, grid_filename=grid_filename, nsteps=nsteps,
ndays=ndays, ff=ff, tseas=tseas, ah=ah, av=av, z0=z0, zpar=zpar,
do3d=do3d, doturb=doturb, name=name, dostream=dostream, N=N,
time_units=time_units, dtFromTracmass=dtFromTracmass,
zparuv=zparuv, tseas_use=tseas_use)
# calls Mover class
super(TracpyMover, self).__init__(**kwargs)
def __repr__(self):
return 'TracpyMover(<%s>)' % self.id
def prepare_for_model_run(self, date, lon0, lat0):
tinds, nc, t0save, xend, yend, zend, zp, ttend, t, flag = self.tp.prepare_for_model_run(date, lon0, lat0)
return tinds, nc, t0save, xend, yend, zend, zp, ttend, t, flag
def prepare_for_model_step2(self, tind, nc, flag, xend, yend, zend, j):
xstart, ystart, zstart = self.tp.prepare_for_model_step(tind, nc, flag, xend, yend, zend, j)
# xstart, ystart, zstart = self.tp.prepare_for_model_step(tinds[j+1], nc, flag, xend, yend, zend, j)
def get_move(
self,
spill,
time_step,
model_time,
):
"""
moves the particles defined in the spill object
:param spill: spill is an instance of the gnome.spill.Spill class
:param time_step: time_step in seconds
:param model_time: current model time as a datetime object
In this case, it uses the:
positions
status_code
data arrays.
:returns delta: Nx3 numpy array of movement -- in (long, lat, meters) units
"""
# Get the data:
try:
positions = spill['positions'] # Nx3 with lon,lat,z
status_codes = spill['status_codes']
except KeyError, err:
raise ValueError('The spill does not have the required data arrays\n'
+ err.message)
# which ones should we move?
# status codes for things like off map or on beach
in_water_mask = status_codes == basic_types.oil_status.in_water
# compute the move
delta = np.zeros_like(positions)
if self.active and self.on:
# Old:
# delta[in_water_mask] = tracpy. #self.velocity * time_step
# Convert from lon/lat to grid coords
# Interpolate to get starting positions in grid space
xstart, ystart, _ = tracpy.tools.interpolate2d(positions[:,0], positions[:,1], self.tp.grid, 'd_ll2ij')
# Call TRACMASS
# Since I know I am doing 2d for now, can I essentially ignore the z positions?
# FLAG PROBABLY NEEDS TO BE UPDATED FOR STATUS CODES FOR EXITING DRIFTERS?
xend,\
yend,\
zend,\
flag,\
ttend, U, V = self.tp.step(xstart, ystart, positions[:,2])
# xend_temp,\
# yend_temp,\
# zend_temp,\
# flag[ind],\
# ttend_temp, U, V = self.tp.step(j, ttend[ind,j*self.tp.N], xstart, ystart, zstart)
# Convert back to lon/lat from grid indices and calculate change in lon/lat
lon, lat, _ = tracpy.tools.interpolate2d(xend, yend, self.tp.grid, 'm_ij2ll')
delta[in_water_mask] = np.hstack((lon-positions[:,0], lat-positions[:,1], positions[:,2]))
return delta
def test_run_2d_xy_ssh():
"""
Test initialization and running of tracpy with projected coordinates and ssh.
can we initialize and run tracpy (using rectangle example). Compare final
location of drifters with known analytic answer. Using x/y coords for
idealized type runs. Made this simulation information from the other test
information using:
"""
import xarray as xr
ds = xr.open_dataset('input/ocean_his_0001.nc')
# sine wave in x, fixed in y and t
zeta = np.sin(np.linspace(0, 2 * np.pi, ds['xr'].size))
zeta = zeta[np.newaxis, np.newaxis, :].repeat(ds['tl'].size,
axis=0).repeat(ds['yr'].size,
axis=1)
ds['zeta'] = xr.Variable(['tl', 'yr', 'xr'], data=zeta)
# ds['zeta'] = xr.Variable(['tl','yr','xr'],
# data=10*np.ones((ds['tl'].size, ds['yr'].size, ds['xr'].size)))
# ds['zeta'] = xr.Variable(['tl','yr','xr'],
# data=np.random.rand(ds['tl'].size, ds['yr'].size, ds['xr'].size))
ds.to_netcdf('input/ocean_his_0002.nc')
# some simple example data
currents_filename = os.path.join('input', 'ocean_his_0001.nc')
grid_filename = os.path.join('input', 'gridxy.nc')
time_units = 'seconds since 1970-01-01'
num_layers = 3
name = 'test_run_2d_xy_ssh'
# Start date in date time formatting
date = datetime.datetime(2013, 12, 19, 0)
# Time between outputs
tseas = 4 * 3600. # 4 hours between outputs, in seconds
# Number of days to run the drifters.
ndays = tseas * 9. / (3600. * 24)
# Sets a smaller limit than between model outputs for when to force
# interpolation if hasn't already occurred.
nsteps = 5
# Controls the sampling frequency of the drifter tracks.
N = 4
# # This allows the user to call to TRACMASS for a different period of time
# # than between 2 model outputs
# # Just testing to try new loop, should have same behavior as before
# dtFromTracmass = tseas/2.
# Use ff = 1 for forward in time and ff = -1 for backward in time.
ff = 1 # will work for ff=1 or ff=-1 since checks by distance traveled
ah = 0. # m^2/s
av = 0. # m^2/s
# turbulence/diffusion flag
doturb = 0
# two particles (starting positions)
x0 = [22065., 22065.]
y0 = [27777., 51587.]
do3d = 0 # flag to set to 2-d
z0 = 's' # 'z' 'salt' 's'
zpar = num_layers - 1 # top layer
usespherical = False
# Get projection object
proj = tracpy.tools.make_proj(setup='galveston')
# Read in grid
grid = tracpy.inout.readgrid(grid_filename,
proj,
vert_filename=currents_filename,
usespherical=usespherical)
# Initialize Tracpy class
tp = Tracpy(currents_filename,
grid,
name=name,
tseas=tseas,
ndays=ndays,
nsteps=nsteps,
N=N,
ff=ff,
ah=ah,
av=av,
doturb=doturb,
do3d=do3d,
z0=z0,
zpar=zpar,
time_units=time_units,
usespherical=usespherical)
xp, yp, zp, t, T0, U, V = tracpy.run.run(tp, date, x0, y0)
## check the results:
# print xp.shape
print(xp)
# print yp
#eastward current, latitude should not change:
assert np.allclose(y0, yp.T)
# current velocity -- 0.1 m/s
# position
distance = (ndays * 24 * 3600 * 0.1) * ff
print(distance)
print(xp[:, -1] - xp[:, 0])
assert np.allclose(xp[:, -1] - xp[:, 0], distance)