def check_divergence(self):
"""
Used to terminate the program if a blowup occurs in any segment
of the solver, resulting in the values becoming infinity or
undefined.
"""
if (af.any_true(af.isinf(self.f)) or af.any_true(af.isnan(self.f))):
raise SystemExit('Solver Diverging!')
def op_fvm_q(self, dt):
self._communicate_f()
self._apply_bcs_f()
if (self.performance_test_flag == True):
tic = af.time()
fvm_timestep_RK2(self, dt)
if (self.performance_test_flag == True):
af.sync()
toc = af.time()
self.time_fvm_solver += toc - tic
# Solving for tau = 0 systems
if (af.any_true(
self.physical_system.params.tau(self.q1_center, self.q2_center,
self.p1, self.p2, self.p3) == 0)):
if (self.performance_test_flag == True):
tic = af.time()
self.f = self._source(self.f, self.q1_center, self.q2_center, self.p1,
self.p2, self.p3, self.compute_moments,
self.physical_system.params, True)
if (self.performance_test_flag == True):
af.sync()
toc = af.time()
self.time_sourcets += toc - tic
af.eval(self.f)
return
def RK5_step(self, dt):
self.Y = integrators.RK5(dY_dt, self.Y, dt, self)
# Solving for tau = 0 systems
if (self.single_mode_evolution == False and af.any_true(
self.physical_system.params.tau(self.q1_center, self.q2_center,
self.p1, self.p2, self.p3) == 0)):
f_hat = self.Y[:, :, :, 0]
f = af.real(af.ifft2(0.5 * self.N_q2 * self.N_q1 * f_hat))
self.Y[:, :, :, 0] = 2 * af.fft2(
self._source(f, self.q1_center, self.q2_center, self.p1, self.p2,
self.p3, self.compute_moments,
self.physical_system.params,
True)) / (self.N_q2 * self.N_q1)
return
def BGK(f, q1, q2, p1, p2, p3, moments, params, flag = False):
"""Return BGK operator -(f-f0)/tau."""
n = moments('density', f)
# Floor used to avoid 0/0 limit:
eps = 1e-30
p1_bulk = moments('mom_p1_bulk', f) / (n + eps)
p2_bulk = moments('mom_p2_bulk', f) / (n + eps)
p3_bulk = moments('mom_p3_bulk', f) / (n + eps)
T = (1 / params.p_dim) * ( 2 * moments('energy', f)
- n * p1_bulk**2
- n * p2_bulk**2
- n * p3_bulk**2
) / (n + eps) + eps
if(af.any_true(params.tau(q1, q2, p1, p2, p3) == 0)):
f_MB = f0(p1, p2, p3, n, T, p1_bulk, p2_bulk, p3_bulk, params)
if(flag == False):
f_MB[:] = 0
return(f_MB)
else:
C_f = -( f
- f0(p1, p2, p3, n, T, p1_bulk, p2_bulk, p3_bulk, params)
) / params.tau(q1, q2, p1, p2, p3)
# When (f - f0) is NaN. Dividing by np.inf doesn't give 0
# Setting when tau is zero we assign f = f0 manually
# WORKAROUND:
if(isinstance(params.tau(q1, q2, p1, p2, p3), af.Array) is True):
C_f = af.select(params.tau(q1, q2, p1, p2, p3) == np.inf, 0, C_f)
af.eval(C_f)
else:
if(params.tau(q1, q2, p1, p2, p3) == np.inf):
C_f = 0
return(C_f)
def RK5_step(self, dt):
"""
Evolves the physical system defined using an RK5
integrator. This method is 5th order accurate.
Parameters
----------
dt: double
The timestep size.
"""
# For purely collisional cases:
tau = self.physical_system.params.tau(self.q1_center, self.q2_center,
self.p1, self.p2, self.p3)
if (af.any_true(tau == 0)):
f0 = self._source(
0.5 * self.N_q1 * self.N_q2 * af.real(ifft2(self.f_hat)),
self.time_elapsed, self.q1_center, self.q2_center, self.p1,
self.p2, self.p3, self.compute_moments,
self.physical_system.params, True)
self.f_hat = af.select(tau == 0,
2 * fft2(f0) / (self.N_q1 * self.N_q2),
self.f_hat)
if (self.physical_system.params.EM_fields_enabled == True
and self.physical_system.params.fields_type == 'electrodynamic'):
# Since the fields and the distribution function are coupled,
# we evolve the system by making use of a coupled integrator
# which ensures that throughout the timestepping they are
# evaluated at the same temporal locations.
self.f_hat, self.fields_solver.fields_hat = \
integrators.RK5_coupled(df_hat_dt, self.f_hat,
dfields_hat_dt, self.fields_solver.fields_hat,
dt, self
)
else:
self.f_hat = integrators.RK5(df_hat_dt, self.f_hat, dt,
self.fields_solver.fields_hat, self)
return
def op_solve_src(self, dt):
"""
Evolves the source term of the equations specified:
df/dt = source
Parameters
----------
dt : double
Time-step size to evolve the system
"""
if (self.performance_test_flag == True):
tic = af.time()
# Solving for tau = 0 systems:
tau = self.physical_system.params.tau(self.q1_center, self.q2_center,
self.p1_center, self.p2_center,
self.p3_center)
if (af.any_true(tau == 0)):
self.f = af.select(
tau == 0,
self._source(self.f, self.time_elapsed, self.q1_center,
self.q2_center, self.p1_center, self.p2_center,
self.p3_center, self.compute_moments,
self.physical_system.params, True), self.f)
self.f = integrators.RK2(self._source, self.f, dt, self.time_elapsed,
self.q1_center, self.q2_center, self.p1_center,
self.p2_center, self.p3_center,
self.compute_moments, self.physical_system.params)
if (self.performance_test_flag == True):
af.sync()
toc = af.time()
self.time_sourcets += toc - tic
return
def op_solve_src(self, dt):
if (self.performance_test_flag == True):
tic = af.time()
# Solving for tau = 0 systems
if (af.any_true(
self.physical_system.params.tau(self.q1_center, self.q2_center,
self.p1, self.p2, self.p3) == 0)):
self.f = self._source(self.f, self.q1_center, self.q2_center, self.p1,
self.p2, self.p3, self.compute_moments,
self.physical_system.params, True)
else:
self.f = integrators.RK2(self._source, self.f, dt, self.q1_center,
self.q2_center, self.p1, self.p2, self.p3,
self.compute_moments,
self.physical_system.params)
if (self.performance_test_flag == True):
af.sync()
toc = af.time()
self.time_sourcets += toc - tic
return
def simple_algorithm(verbose = False):
display_func = _util.display_func(verbose)
print_func = _util.print_func(verbose)
a = af.randu(3, 3)
print_func(af.sum(a), af.product(a), af.min(a), af.max(a),
af.count(a), af.any_true(a), af.all_true(a))
display_func(af.sum(a, 0))
display_func(af.sum(a, 1))
display_func(af.product(a, 0))
display_func(af.product(a, 1))
display_func(af.min(a, 0))
display_func(af.min(a, 1))
display_func(af.max(a, 0))
display_func(af.max(a, 1))
display_func(af.count(a, 0))
display_func(af.count(a, 1))
display_func(af.any_true(a, 0))
display_func(af.any_true(a, 1))
display_func(af.all_true(a, 0))
display_func(af.all_true(a, 1))
display_func(af.accum(a, 0))
display_func(af.accum(a, 1))
display_func(af.sort(a, is_ascending=True))
display_func(af.sort(a, is_ascending=False))
b = (a > 0.1) * a
c = (a > 0.4) * a
d = b / c
print_func(af.sum(d));
print_func(af.sum(d, nan_val=0.0));
display_func(af.sum(d, dim=0, nan_val=0.0));
val,idx = af.sort_index(a, is_ascending=True)
display_func(val)
display_func(idx)
val,idx = af.sort_index(a, is_ascending=False)
display_func(val)
display_func(idx)
b = af.randu(3,3)
keys,vals = af.sort_by_key(a, b, is_ascending=True)
display_func(keys)
display_func(vals)
keys,vals = af.sort_by_key(a, b, is_ascending=False)
display_func(keys)
display_func(vals)
c = af.randu(5,1)
d = af.randu(5,1)
cc = af.set_unique(c, is_sorted=False)
dd = af.set_unique(af.sort(d), is_sorted=True)
display_func(cc)
display_func(dd)
display_func(af.set_union(cc, dd, is_unique=True))
display_func(af.set_union(cc, dd, is_unique=False))
display_func(af.set_intersect(cc, cc, is_unique=True))
display_func(af.set_intersect(cc, cc, is_unique=False))
def transform(self, X):
"""Impute all missing values in X.
Parameters
----------
X : {array-like, sparse matrix}, shape (n_samples, n_features)
The input data to complete.
"""
check_is_fitted(self)
X = self._validate_input(X, in_fit=False)
#X = af.Array.to_ndarray(X)
X_indicator = super()._transform_indicator(X)
statistics = self.statistics_
if X.shape[1] != statistics.shape[0]:
raise ValueError(
f"X has {X.shape[1]} features per sample, expected {self.statistics_.shape[0]}"
)
# Delete the invalid columns if strategy is not constant
if self.strategy == "constant":
valid_statistics = statistics
else:
# same as af.isnan but also works for object dtypes
# invalid_mask = _get_mask(statistics, np.nan) # BUG: af runtime error
invalid_mask = af.isnan(statistics) # FIXME
valid_mask = invalid_mask.logical_not()
valid_statistics = statistics[valid_mask]
valid_statistics_indexes = np.flatnonzero(valid_mask)
if af.any_true(invalid_mask):
missing = af.arange(X.shape[1])[invalid_mask]
if self.verbose:
warnings.warn(
f"Deleting features without observed values: {missing}"
)
X = X[:, valid_statistics_indexes]
# Do actual imputation
if sp.issparse(X):
if self.missing_values == 0:
raise ValueError(
"Imputation not possible when missing_values == 0 and input is sparse."
"Provide a dense array instead.")
else:
mask = _get_mask(X.data, self.missing_values)
indexes = af.repeat(af.arange(len(X.indptr) - 1, dtype=af.int),
af.diff(X.indptr))[mask]
X.data[mask] = valid_statistics[indexes].astype(X.dtype,
copy=False)
else:
# mask = _get_mask(X, self.missing_values) # BUG
mask = af.isnan(X) # FIXME
# n_missing = af.sum(mask, axis=0) # BUG af
n_missing = af.sum(mask, dim=0)
coordinates = af.where(mask.T)[::-1] # BUG
valid_statistics = valid_statistics.to_ndarray().ravel()
n_missing = n_missing.to_ndarray().ravel()
values = np.repeat(valid_statistics, n_missing) # BUG
values = af.interop.from_ndarray(values)
odims = X.dims()
X = af.flat(X)
X[coordinates] = values
X = af.moddims(X, *odims)
return super()._concatenate_indicator(X, X_indicator)
def check_divergence(self):
if (af.any_true(af.isinf(self.f)) or af.any_true(af.isnan(self.f))):
raise SystemExit('Solver Diverging!')
#!/usr/bin/python import arrayfire as af a = af.randu(3, 3) print(af.sum(a), af.product(a), af.min(a), af.max(a), af.count(a), af.any_true(a), af.all_true(a)) af.print_array(af.sum(a, 0)) af.print_array(af.sum(a, 1)) af.print_array(af.product(a, 0)) af.print_array(af.product(a, 1)) af.print_array(af.min(a, 0)) af.print_array(af.min(a, 1)) af.print_array(af.max(a, 0)) af.print_array(af.max(a, 1)) af.print_array(af.count(a, 0)) af.print_array(af.count(a, 1)) af.print_array(af.any_true(a, 0)) af.print_array(af.any_true(a, 1)) af.print_array(af.all_true(a, 0)) af.print_array(af.all_true(a, 1)) af.print_array(af.accum(a, 0)) af.print_array(af.accum(a, 1))
def any(self, s, axis):
return arrayfire.any_true(s, dim=axis)
def any(a: ndarray,
axis: tp.Optional[int] = None,
out: tp.Optional[ndarray] = None,
keepdims: bool = False) \
-> tp.Union[bool, ndarray]:
return _wrap_af_array(af.any_true(a._af_array, dim=axis))
def r2_score(y_true, y_pred, *, sample_weight=None,
multioutput="uniform_average"):
"""R^2 (coefficient of determination) regression score function.
Best possible score is 1.0 and it can be negative (because the
model can be arbitrarily worse). A constant model that always
predicts the expected value of y, disregarding the input features,
would get a R^2 score of 0.0.
Read more in the :ref:`User Guide <r2_score>`.
Parameters
----------
y_true : array-like of shape (n_samples,) or (n_samples, n_outputs)
Ground truth (correct) target values.
y_pred : array-like of shape (n_samples,) or (n_samples, n_outputs)
Estimated target values.
sample_weight : array-like of shape (n_samples,), optional
Sample weights.
multioutput : string in ['raw_values', 'uniform_average', \
'variance_weighted'] or None or array-like of shape (n_outputs)
Defines aggregating of multiple output scores.
Array-like value defines weights used to average scores.
Default is "uniform_average".
'raw_values' :
Returns a full set of scores in case of multioutput input.
'uniform_average' :
Scores of all outputs are averaged with uniform weight.
'variance_weighted' :
Scores of all outputs are averaged, weighted by the variances
of each individual output.
.. versionchanged:: 0.19
Default value of multioutput is 'uniform_average'.
Returns
-------
z : float or ndarray of floats
The R^2 score or ndarray of scores if 'multioutput' is
'raw_values'.
Notes
-----
This is not a symmetric function.
Unlike most other scores, R^2 score may be negative (it need not actually
be the square of a quantity R).
This metric is not well-defined for single samples and will return a NaN
value if n_samples is less than two.
References
----------
.. [1] `Wikipedia entry on the Coefficient of determination
<https://en.wikipedia.org/wiki/Coefficient_of_determination>`_
Examples
--------
>>> from sklearn.metrics import r2_score
>>> y_true = [3, -0.5, 2, 7]
>>> y_pred = [2.5, 0.0, 2, 8]
>>> r2_score(y_true, y_pred)
0.948...
>>> y_true = [[0.5, 1], [-1, 1], [7, -6]]
>>> y_pred = [[0, 2], [-1, 2], [8, -5]]
>>> r2_score(y_true, y_pred,
... multioutput='variance_weighted')
0.938...
>>> y_true = [1, 2, 3]
>>> y_pred = [1, 2, 3]
>>> r2_score(y_true, y_pred)
1.0
>>> y_true = [1, 2, 3]
>>> y_pred = [2, 2, 2]
>>> r2_score(y_true, y_pred)
0.0
>>> y_true = [1, 2, 3]
>>> y_pred = [3, 2, 1]
>>> r2_score(y_true, y_pred)
-3.0
"""
y_type, y_true, y_pred, multioutput = _check_reg_targets(
y_true, y_pred, multioutput)
check_consistent_length(y_true, y_pred, sample_weight)
if _num_samples(y_pred) < 2:
msg = "R^2 score is not well-defined with less than two samples."
warnings.warn(msg, UndefinedMetricWarning)
return float('nan')
if sample_weight is not None:
sample_weight = column_or_1d(sample_weight)
weight = sample_weight[:, np.newaxis]
else:
weight = 1.
numerator = af.sum((weight * (y_true - y_pred) ** 2), dim=0)
#denominator = (weight * (y_true - np.average(
#y_true, axis=0, weights=sample_weight)) ** 2).sum(axis=0,
#dtype=np.float64)
denominator = af.sum((weight * (y_true - af.tile(af.mean(y_true, weights=sample_weight, dim=0), y_true.shape[0])) ** 2), dim=0)
nonzero_denominator = denominator != 0
nonzero_numerator = numerator != 0
valid_score = nonzero_denominator & nonzero_numerator
y_sz_1 = 1 if y_true.numdims() == 1 else y_true.shape[1]
output_scores = af.constant(0, y_sz_1)
if(af.any_true(valid_score)):
output_scores[valid_score] = (1.0 - (numerator[valid_score] /
denominator[valid_score])).as_type(output_scores.dtype())
# arbitrary set to zero to avoid -inf scores, having a constant
# y_true is not interesting for scoring a regression anyway
output_scores[nonzero_numerator & ~nonzero_denominator] = 0.
if isinstance(multioutput, str):
if multioutput == 'raw_values':
# return scores individually
return output_scores
elif multioutput == 'uniform_average':
# passing None as weights results is uniform mean
avg_weights = None
elif multioutput == 'variance_weighted':
avg_weights = denominator
# avoid fail on constant y or one-element arrays
if not af.any_true(nonzero_denominator):
if not af.any_true(nonzero_numerator):
return 1.0
else:
return 0.0
else:
avg_weights = multioutput
#return np.average(output_scores, weights=avg_weights)
return af.mean(output_scores, weights=avg_weights)
#!/usr/bin/python
#######################################################
# Copyright (c) 2015, ArrayFire
# All rights reserved.
#
# This file is distributed under 3-clause BSD license.
# The complete license agreement can be obtained at:
# http://arrayfire.com/licenses/BSD-3-Clause
########################################################
import arrayfire as af
a = af.randu(3, 3)
print(af.sum(a), af.product(a), af.min(a), af.max(a), af.count(a),
af.any_true(a), af.all_true(a))
af.display(af.sum(a, 0))
af.display(af.sum(a, 1))
af.display(af.product(a, 0))
af.display(af.product(a, 1))
af.display(af.min(a, 0))
af.display(af.min(a, 1))
af.display(af.max(a, 0))
af.display(af.max(a, 1))
af.display(af.count(a, 0))
af.display(af.count(a, 1))
def hasnan(arr):
return af.any_true(af.isnan(arr))
def any(self, s, axis):
return arrayfire.any_true(s, dim=axis)
def simple_algorithm(verbose=False):
display_func = _util.display_func(verbose)
print_func = _util.print_func(verbose)
a = af.randu(3, 3)
k = af.constant(1, 3, 3, dtype=af.Dtype.u32)
af.eval(k)
print_func(af.sum(a), af.product(a), af.min(a), af.max(a), af.count(a),
af.any_true(a), af.all_true(a))
display_func(af.sum(a, 0))
display_func(af.sum(a, 1))
rk = af.constant(1, 3, dtype=af.Dtype.u32)
rk[2] = 0
af.eval(rk)
display_func(af.sumByKey(rk, a, dim=0))
display_func(af.sumByKey(rk, a, dim=1))
display_func(af.productByKey(rk, a, dim=0))
display_func(af.productByKey(rk, a, dim=1))
display_func(af.minByKey(rk, a, dim=0))
display_func(af.minByKey(rk, a, dim=1))
display_func(af.maxByKey(rk, a, dim=0))
display_func(af.maxByKey(rk, a, dim=1))
display_func(af.anyTrueByKey(rk, a, dim=0))
display_func(af.anyTrueByKey(rk, a, dim=1))
display_func(af.allTrueByKey(rk, a, dim=0))
display_func(af.allTrueByKey(rk, a, dim=1))
display_func(af.countByKey(rk, a, dim=0))
display_func(af.countByKey(rk, a, dim=1))
display_func(af.product(a, 0))
display_func(af.product(a, 1))
display_func(af.min(a, 0))
display_func(af.min(a, 1))
display_func(af.max(a, 0))
display_func(af.max(a, 1))
display_func(af.count(a, 0))
display_func(af.count(a, 1))
display_func(af.any_true(a, 0))
display_func(af.any_true(a, 1))
display_func(af.all_true(a, 0))
display_func(af.all_true(a, 1))
display_func(af.accum(a, 0))
display_func(af.accum(a, 1))
display_func(af.scan(a, 0, af.BINARYOP.ADD))
display_func(af.scan(a, 1, af.BINARYOP.MAX))
display_func(af.scan_by_key(k, a, 0, af.BINARYOP.ADD))
display_func(af.scan_by_key(k, a, 1, af.BINARYOP.MAX))
display_func(af.sort(a, is_ascending=True))
display_func(af.sort(a, is_ascending=False))
b = (a > 0.1) * a
c = (a > 0.4) * a
d = b / c
print_func(af.sum(d))
print_func(af.sum(d, nan_val=0.0))
display_func(af.sum(d, dim=0, nan_val=0.0))
val, idx = af.sort_index(a, is_ascending=True)
display_func(val)
display_func(idx)
val, idx = af.sort_index(a, is_ascending=False)
display_func(val)
display_func(idx)
b = af.randu(3, 3)
keys, vals = af.sort_by_key(a, b, is_ascending=True)
display_func(keys)
display_func(vals)
keys, vals = af.sort_by_key(a, b, is_ascending=False)
display_func(keys)
display_func(vals)
c = af.randu(5, 1)
d = af.randu(5, 1)
cc = af.set_unique(c, is_sorted=False)
dd = af.set_unique(af.sort(d), is_sorted=True)
display_func(cc)
display_func(dd)
display_func(af.set_union(cc, dd, is_unique=True))
display_func(af.set_union(cc, dd, is_unique=False))
display_func(af.set_intersect(cc, cc, is_unique=True))
display_func(af.set_intersect(cc, cc, is_unique=False))