def Kernel(self, pyfunc, c_include=""):
"""Wrapper method to convert a `pyfunc` into a :class:`parcels.kernel.Kernel` object
based on `fieldset` and `ptype` of the ParticleSet"""
return Kernel(self.fieldset,
self.ptype,
pyfunc=pyfunc,
c_include=c_include)
def Kernel(self, pyfunc, c_include="", delete_cfiles=True):
"""Wrapper method to convert a `pyfunc` into a :class:`parcels.kernel.Kernel` object
based on `fieldset` and `ptype` of the ParticleSet
:param delete_cfiles: Boolean whether to delete the C-files after compilation in JIT mode (default is True)
"""
return Kernel(self.fieldset, self.ptype, pyfunc=pyfunc, c_include=c_include,
delete_cfiles=delete_cfiles)
def density(self, field_name=None, particle_val=None, relative=False, area_scale=False):
"""Method to calculate the density of particles in a ParticleSet from their locations,
through a 2D histogram.
:param field: Optional :mod:`parcels.field.Field` object to calculate the histogram
on. Default is `fieldset.U`
:param particle_val: Optional numpy-array of values to weigh each particle with,
or string name of particle variable to use weigh particles with.
Default is None, resulting in a value of 1 for each particle
:param relative: Boolean to control whether the density is scaled by the total
weight of all particles. Default is False
:param area_scale: Boolean to control whether the density is scaled by the area
(in m^2) of each grid cell. Default is False
"""
field_name = field_name if field_name else "U"
field = getattr(self.fieldset, field_name)
f_str = """
def search_kernel(particle, fieldset, time):
x = fieldset.{}[time, particle.depth, particle.lat, particle.lon]
""".format(field_name)
k = Kernel(
self.fieldset,
self.ptype,
funcname="search_kernel",
funcvars=["particle", "fieldset", "time", "x"],
funccode=f_str,
)
self.execute(k, runtime=0)
if isinstance(particle_val, str):
particle_val = self.particle_data[particle_val]
else:
particle_val = particle_val if particle_val else np.ones(self.size)
density = np.zeros((field.grid.lat.size, field.grid.lon.size), dtype=np.float32)
p = self.data_accessor()
for i in range(self.size):
p.set_index(i)
try: # breaks if either p.xi, p.yi, p.zi, p.ti do not exist (in scipy) or field not in fieldset
if p.ti[field.igrid] < 0: # xi, yi, zi, ti, not initialised
raise('error')
xi = p.xi[field.igrid]
yi = p.yi[field.igrid]
except:
_, _, _, xi, yi, _ = field.search_indices(p.lon, p.lat, p.depth, 0, 0, search2D=True)
density[yi, xi] += particle_val[i]
if relative:
density /= np.sum(particle_val)
if area_scale:
density /= field.cell_areas()
return density
def Kernel(self, pyfunc):
"""Wrapper method to convert a `pyfunc` into a :class:`parcels.kernel.Kernel` object
based on `grid` and `ptype` of the ParticleSet"""
return Kernel(self.grid, self.ptype, pyfunc=pyfunc)
