def draw(self,animating = False):
cols, rows = self.size
minx, maxx = self.xlimits
miny, maxy = self.ylimits
cwidth, cheight = self.cell_size
x = map(lambda i: minx + cwidth*i, range(cols+1))
y = map(lambda i: miny + cheight*i, range(rows+1))
if(not animating):
f = plt.figure(figsize=self.figsize)
else:
plt.clf()
hlines = np.column_stack(np.broadcast_arrays(x[0], y, x[-1], y))
vlines = np.column_stack(np.broadcast_arrays(x, y[0], x, y[-1]))
lines = np.concatenate([hlines, vlines]).reshape(-1, 2, 2)
line_collection = LineCollection(lines, color="black", linewidths=0.5)
ax = plt.gca()
ax.add_collection(line_collection)
ax.set_xlim(x[0]-1, x[-1]+1)
ax.set_ylim(y[0]-1, y[-1]+1)
plt.gca().set_aspect('equal', adjustable='box')
plt.axis('off')
self._draw_obstacles(plt.gca())
self._draw_start_goal(plt.gca())
return plt.gca()
def refractions(n1, n2, ray_dirs, normals): """Generates directions of rays refracted according to Snells's law (in its vector form, [2] Arguments: n1, n2 - respectively the refractive indices of the medium the unrefracted ray travels in and of the medium the ray is entering. ray_dirs, normals - each a row of 3-component vectors (as an array) with the direction of incoming rays and corresponding normals at the points of incidence with the refracting surface. Returns: refracted - a boolean array stating which of the incoming rays has not undergone total internal reflection. refr_dirs - new ray directions as the result of refraction, for the non-TIR rays in the input bundle. """ # Broadcast all necessary arrays to the larger size required: n = N.broadcast_arrays(n2/n1, ray_dirs[0])[0] normals = N.broadcast_arrays(normals, ray_dirs)[0] cos1 = (normals*ray_dirs).sum(axis=0) refracted = cos1**2 >= 1 - n**2 # Throw away totally-reflected rays. cos1 = cos1[refracted] ray_dirs = ray_dirs[:,refracted] normals = normals[:,refracted] n = n[refracted] refr_dirs = (ray_dirs - cos1*normals)/n cos2 = N.sqrt(1 - 1./n**2*(1 - cos1**2)) refr_dirs += normals*cos2*N.where(cos1 < 0, -1, 1) return refracted, refr_dirs
def draw(self):
cols, rows = self.size
minx, maxx = self.xlimits
miny, maxy = self.ylimits
width, height = self.cell_dimensions
x = map(lambda i: minx + width*i, range(cols+1))
y = map(lambda i: miny + height*i, range(rows+1))
f = plt.figure(figsize=self.figsize)
hlines = np.column_stack(np.broadcast_arrays(x[0], y, x[-1], y))
vlines = np.column_stack(np.broadcast_arrays(x, y[0], x, y[-1]))
lines = np.concatenate([hlines, vlines]).reshape(-1, 2, 2)
line_collection = LineCollection(lines, color="black", linewidths=0.5)
ax = plt.gca()
ax.add_collection(line_collection)
ax.set_xlim(x[0]-1, x[-1]+1)
ax.set_ylim(y[0]-1, y[-1]+1)
plt.gca().set_aspect('equal', adjustable='box')
plt.axis('off')
self.draw_obstacles(plt.gca())
return plt.gca()
def test_simple(self):
orig = np.ma.masked_array([[1], [2], [3]], mask=[[1], [0], [1]])
result = BroadcastArray(orig, {1: 2}, (2,)).masked_array()
expected, _ = np.broadcast_arrays(orig.data, result)
expected_mask, _ = np.broadcast_arrays(orig.mask, result)
expected = np.ma.masked_array(expected, mask=expected_mask)
assert_array_equal(result.mask, expected.mask)
assert_array_equal(result.data, expected.data)
def half_edge_align(p, pts, polys):
poly = align_polys(p, polys)
mid = pts[poly].mean(1)
left = pts[poly[:,[0,2]]].mean(1)
right = pts[poly[:,[0,1]]].mean(1)
s1 = np.array(np.broadcast_arrays(pts[p], mid, left)).swapaxes(0,1)
s2 = np.array(np.broadcast_arrays(pts[p], mid, right)).swapaxes(0,1)
return np.vstack([s1, s2])
def axes_to_table(axes):
"""Fill the observation group axes into a table.
Define one row for each possible combination of the
observation group axis bins. Each row will represent
an observation group.
Parameters
----------
axes : `~gammapy.data.ObservationGroupAxis`
List of observation group axes.
Returns
-------
table : `~astropy.table.Table`
Table containing the observation group definitions.
"""
# define table column data
column_data_min = []
column_data_max = []
# loop over observation axes
for i_axis in range(len(axes)):
if axes[i_axis].fmt == 'values':
column_data_min.append(axes[i_axis].bins)
column_data_max.append(axes[i_axis].bins)
elif axes[i_axis].fmt == 'edges':
column_data_min.append(axes[i_axis].bins[:-1])
column_data_max.append(axes[i_axis].bins[1:])
# define grids of column data
ndim = len(axes)
s0 = (1,) * ndim
expanding_arrays = [x.reshape(s0[:i] + (-1,) + s0[i + 1::])
for i, x in enumerate(column_data_min)]
column_data_expanded_min = np.broadcast_arrays(*expanding_arrays)
expanding_arrays = [x.reshape(s0[:i] + (-1,) + s0[i + 1::])
for i, x in enumerate(column_data_max)]
column_data_expanded_max = np.broadcast_arrays(*expanding_arrays)
# recover units
for i_dim in range(ndim):
column_data_expanded_min[i_dim] = _recover_units(column_data_expanded_min[i_dim],
column_data_min[i_dim])
column_data_expanded_max[i_dim] = _recover_units(column_data_expanded_max[i_dim],
column_data_max[i_dim])
# Make the table
table = Table()
for i_axis in range(len(axes)):
if axes[i_axis].fmt == 'values':
table[axes[i_axis].name] = column_data_expanded_min[i_axis].flatten()
elif axes[i_axis].fmt == 'edges':
table[axes[i_axis].name + "_MIN"] = column_data_expanded_min[i_axis].flatten()
table[axes[i_axis].name + "_MAX"] = column_data_expanded_max[i_axis].flatten()
ObservationGroups._add_group_id(table, axes)
return table
def _bandflux(model, band, time_or_phase, zp, zpsys):
"""Support function for bandflux in Source and Model.
This is necessary to have outside because ``phase`` is used in Source
and ``time`` is used in Model.
"""
if zp is not None and zpsys is None:
raise ValueError('zpsys must be given if zp is not None')
# broadcast arrays
if zp is None:
time_or_phase, band = np.broadcast_arrays(time_or_phase, band)
else:
time_or_phase, band, zp, zpsys = \
np.broadcast_arrays(time_or_phase, band, zp, zpsys)
# convert all to 1d arrays
ndim = time_or_phase.ndim # save input ndim for return val
time_or_phase = np.atleast_1d(time_or_phase)
band = np.atleast_1d(band)
if zp is not None:
zp = np.atleast_1d(zp)
zpsys = np.atleast_1d(zpsys)
# initialize output arrays
bandflux = np.zeros(time_or_phase.shape, dtype=np.float)
# Loop over unique bands.
for b in set(band):
mask = band == b
b = get_bandpass(b)
# Raise an exception if bandpass is out of model range.
if (b.wave[0] < model.minwave() or b.wave[-1] > model.maxwave()):
raise ValueError(
'bandpass {0!r:s} [{1:.6g}, .., {2:.6g}] '
'outside spectral range [{3:.6g}, .., {4:.6g}]'
.format(b.name, b.wave[0], b.wave[-1],
model.minwave(), model.maxwave()))
# Get the flux
f = model._flux(time_or_phase[mask], b.wave)
fsum = np.sum(f * b.trans * b.wave * b.dwave, axis=1) / HC_ERG_AA
if zp is not None:
zpnorm = 10.**(0.4 * zp[mask])
bandzpsys = zpsys[mask]
for ms in set(bandzpsys):
mask2 = bandzpsys == ms
ms = get_magsystem(ms)
zpnorm[mask2] = zpnorm[mask2] / ms.zpbandflux(b)
fsum *= zpnorm
bandflux[mask] = fsum
if ndim == 0:
return bandflux[0]
return bandflux
def _reduce_points_and_bounds(points, lower_and_upper_bounds=None):
"""
Reduce the dimensionality of arrays of coordinate points (and optionally
bounds).
Dimensions over which all values are the same are reduced to size 1, using
:func:`_collapse_degenerate_points_and_bounds`.
All size-1 dimensions are then removed.
If the bounds arrays are also passed in, then all three arrays must have
the same shape or be capable of being broadcast to match.
Args:
* points (array-like):
Coordinate point values.
Kwargs:
* lower_and_upper_bounds (pair of array-like, or None):
Corresponding bounds values (lower, upper), if any.
Returns:
dims (iterable of ints), points(array), bounds(array)
* 'dims' is the mapping from the result array dimensions to the
original dimensions. However, when 'array' is scalar, 'dims' will
be None (rather than an empty tuple).
* 'points' and 'bounds' are the reduced arrays.
If no bounds were passed, None is returned.
"""
orig_points_dtype = np.asarray(points).dtype
bounds = None
if lower_and_upper_bounds is not None:
lower_bounds, upper_bounds = np.broadcast_arrays(
*lower_and_upper_bounds)
orig_bounds_dtype = lower_bounds.dtype
bounds = np.vstack((lower_bounds, upper_bounds)).T
# Attempt to broadcast points to match bounds to handle scalars.
if bounds is not None and points.shape != bounds.shape[:-1]:
points, _ = np.broadcast_arrays(points, bounds[..., 0])
points, bounds = _collapse_degenerate_points_and_bounds(points, bounds)
used_dims = tuple(i_dim for i_dim in range(points.ndim)
if points.shape[i_dim] > 1)
reshape_inds = tuple([points.shape[dim] for dim in used_dims])
points = points.reshape(reshape_inds)
points = points.astype(orig_points_dtype)
if bounds is not None:
bounds = bounds.reshape(reshape_inds + (2,))
bounds = bounds.astype(orig_bounds_dtype)
if not used_dims:
used_dims = None
return used_dims, points, bounds
def uniform_distribution_overlap(m1, s1, m2, s2):
'''Find the overlap between two uniform distributions
Compute the integral of two uniform distributions
centered on m1 and m2
with widths 2 * s1 and 2 * s2
and heights 1 / (2 * s1) and 1 / (2 * s2)
'''
h1h2 = 1 / (4 * s1 * s2)
return np.clip((np.min(np.broadcast_arrays(m1 + s1, m2 + s2), axis=0) -
np.max(np.broadcast_arrays(m1 - s1, m2 - s2), axis=0)),
0, None) / h1h2
def test_broadcast_arrays():
# Currently arrayfire is missing support for int64
x2 = numpy.array([[1,2,3]], dtype=numpy.float32)
y2 = numpy.array([[1],[2],[3]], dtype=numpy.float32)
x1 = afnumpy.array(x2)
y1 = afnumpy.array(y2)
iassert(afnumpy.broadcast_arrays(x1, y1), numpy.broadcast_arrays(x2, y2))
x1 = afnumpy.array([2])
y1 = afnumpy.array(2)
x2 = numpy.array([2])
y2 = numpy.array(2)
iassert(afnumpy.broadcast_arrays(x1, y1), numpy.broadcast_arrays(x2, y2))
def bkgsubtract(space, bkg):
if space.dimension == bkg.dimension:
bkg.photons = bkg.photons * space.contributions / bkg.contributions
bkg.photons[bkg.contributions == 0] = 0
bkg.contributions = space.contributions
return space - bkg
else:
photons = numpy.broadcast_arrays(space.photons, bkg.photons)[1]
contributions = numpy.broadcast_arrays(space.contributions, bkg.contributions)[1]
bkg = Space(space.axes)
bkg.photons = photons
bkg.contributions = contributions
return bkgsubtract(space, bkg)
def score(self, outcomes, modelparams, expparams, return_L=False):
na = np.newaxis
n_m = modelparams.shape[0]
n_e = expparams.shape[0]
n_o = outcomes.shape[0]
n_p = self.n_modelparams
m = expparams['m'].reshape((1, 1, 1, n_e))
L = self.likelihood(outcomes, modelparams, expparams)[na, ...]
outcomes = outcomes.reshape((1, n_o, 1, 1))
if not self._il:
p, A, B = modelparams.T[:, :, np.newaxis]
p = p.reshape((1, 1, n_m, 1))
A = A.reshape((1, 1, n_m, 1))
B = B.reshape((1, 1, n_m, 1))
q = (-1)**(1-outcomes) * np.concatenate(np.broadcast_arrays(
A * m * (p ** (m-1)), p**m, np.ones_like(p),
), axis=0) / L
else:
p_tilde, p_ref, A, B = modelparams.T[:, :, np.newaxis]
p_C = p_tilde * p_ref
mode = expparams['reference'][np.newaxis, :]
p = np.where(mode, p_ref, p_C)
p = p.reshape((1, 1, n_m, n_e))
A = A.reshape((1, 1, n_m, 1))
B = B.reshape((1, 1, n_m, 1))
q = (-1)**(1-outcomes) * np.concatenate(np.broadcast_arrays(
np.where(mode, 0, A * m * (p_tilde ** (m - 1)) * (p_ref ** m)),
np.where(mode,
A * m * (p_ref ** (m - 1)),
A * m * (p_ref ** (m - 1)) * (p_tilde ** m)
),
p**m, np.ones_like(p)
), axis=0) / L
if return_L:
# Need to strip off the extra axis we added for broadcasting to q.
return q, L[0, ...]
else:
return q
def __setitem__(self, key, x):
row, col = self._validate_indices(key)
if isinstance(row, INT_TYPES) and isinstance(col, INT_TYPES):
x = np.asarray(x, dtype=self.dtype)
if x.size != 1:
raise ValueError('Trying to assign a sequence to an item')
self._set_intXint(row, col, x.flat[0])
return
if isinstance(row, slice):
row = np.arange(*row.indices(self.shape[0]))[:, None]
else:
row = np.atleast_1d(row)
if isinstance(col, slice):
col = np.arange(*col.indices(self.shape[1]))[None, :]
if row.ndim == 1:
row = row[:, None]
else:
col = np.atleast_1d(col)
i, j = np.broadcast_arrays(row, col)
if i.shape != j.shape:
raise IndexError('number of row and column indices differ')
from .base import isspmatrix
if isspmatrix(x):
if i.ndim == 1:
# Inner indexing, so treat them like row vectors.
i = i[None]
j = j[None]
broadcast_row = x.shape[0] == 1 and i.shape[0] != 1
broadcast_col = x.shape[1] == 1 and i.shape[1] != 1
if not ((broadcast_row or x.shape[0] == i.shape[0]) and
(broadcast_col or x.shape[1] == i.shape[1])):
raise ValueError('shape mismatch in assignment')
if x.size == 0:
return
x = x.tocoo(copy=True)
x.sum_duplicates()
self._set_arrayXarray_sparse(i, j, x)
else:
# Make x and i into the same shape
x = np.asarray(x, dtype=self.dtype)
x, _ = np.broadcast_arrays(x, i)
if x.shape != i.shape:
raise ValueError("shape mismatch in assignment")
if x.size == 0:
return
self._set_arrayXarray(i, j, x)
def _index_to_arrays(self, i, j):
if isinstance(i, np.ndarray) and i.dtype.kind == 'b':
i = self._boolean_index_to_array(i)
if len(i)==2:
if isinstance(j, slice):
j = i[1]
else:
raise ValueError('too many indices for array')
i = i[0]
if isinstance(j, np.ndarray) and j.dtype.kind == 'b':
j = self._boolean_index_to_array(j)[0]
i_slice = isinstance(i, slice)
if i_slice:
i = self._slicetoarange(i, self.shape[0])[:,None]
else:
i = np.atleast_1d(i)
if isinstance(j, slice):
j = self._slicetoarange(j, self.shape[1])[None,:]
if i.ndim == 1:
i = i[:,None]
elif not i_slice:
raise IndexError('index returns 3-dim structure')
elif isscalarlike(j):
# row vector special case
j = np.atleast_1d(j)
if i.ndim == 1:
i, j = np.broadcast_arrays(i, j)
i = i[:, None]
j = j[:, None]
return i, j
else:
j = np.atleast_1d(j)
if i_slice and j.ndim>1:
raise IndexError('index returns 3-dim structure')
i, j = np.broadcast_arrays(i, j)
if i.ndim == 1:
# return column vectors for 1-D indexing
i = i[None,:]
j = j[None,:]
elif i.ndim > 2:
raise IndexError("Index dimension must be <= 2")
return i, j
def noisepower(self, bl_indices, f_indices, ndays=None):
"""Calculate the instrumental noise power spectrum.
Assume we are still within the regime where the power spectrum is white
in `m` modes.
Parameters
----------
bl_indices : array_like
Indices of baselines to calculate.
f_indices : array_like
Indices of frequencies to calculate. Must be broadcastable against
`bl_indices`.
ndays : integer
The number of sidereal days observed.
Returns
-------
noise_ps : np.ndarray
The noise power spectrum.
"""
ndays = self.ndays if not ndays else ndays # Set to value if not set.
# Broadcast arrays against each other
bl_indices, f_indices = np.broadcast_arrays(bl_indices, f_indices)
bw = np.abs(self.frequencies[1] - self.frequencies[0]) * 1e6
# bw = 1.0e6 * (self.freq_upper - self.freq_lower) / self.num_freq
delnu = units.t_sidereal * bw / (2*np.pi)
noisepower = self.tsys(f_indices)**2 / (2 * np.pi * delnu * ndays)
noisebase = noisepower / self.redundancy[bl_indices]
return noisebase
def check_shape(interpolator_cls, x_shape, y_shape, deriv_shape=None, axis=0):
np.random.seed(1234)
x = [-1, 0, 1]
s = list(range(1, len(y_shape)+1))
s.insert(axis % (len(y_shape)+1), 0)
y = np.random.rand(*((3,) + y_shape)).transpose(s)
# Cython code chokes on y.shape = (0, 3) etc, skip them
if y.size == 0:
return
xi = np.zeros(x_shape)
yi = interpolator_cls(x, y, axis=axis)(xi)
target_shape = ((deriv_shape or ()) + y.shape[:axis]
+ x_shape + y.shape[axis:][1:])
assert_equal(yi.shape, target_shape)
# check it works also with lists
if x_shape and y.size > 0:
interpolator_cls(list(x), list(y), axis=axis)(list(xi))
# check also values
if xi.size > 0 and deriv_shape is None:
bs_shape = (y.shape[:axis] + ((1,)*len(x_shape)) + y.shape[axis:][1:])
yv = y[((slice(None,None,None),)*(axis % y.ndim))+(1,)].reshape(bs_shape)
yi, y = np.broadcast_arrays(yi, yv)
assert_allclose(yi, y)
def cart2sphere(x, y, z):
r''' Return angles for Cartesian 3D coordinates `x`, `y`, and `z`
See doc for ``sphere2cart`` for angle conventions and derivation
of the formulae.
$0\le\theta\mathrm{(theta)}\le\pi$ and $-\pi\le\phi\mathrm{(phi)}\le\pi$
Parameters
------------
x : array-like
x coordinate in Cartesian space
y : array-like
y coordinate in Cartesian space
z : array-like
z coordinate
Returns
---------
r : array
radius
theta : array
inclination (polar) angle
phi : array
azimuth angle
'''
r = np.sqrt(x*x + y*y + z*z)
theta = np.arccos(z/r)
phi = np.arctan2(y, x)
r, theta, phi = np.broadcast_arrays(r, theta, phi)
return r, theta, phi
def noise_variance(self, bl_indices, f_indices, nt_per_day, ndays=None):
"""Calculate the instrumental noise variance.
Parameters
----------
bl_indices : array_like
Indices of baselines to calculate.
f_indices : array_like
Indices of frequencies to calculate. Must be broadcastable against
`bl_indices`.
nt_per_day : integer
The number of time samples in one sidereal day.
ndays : integer
The number of sidereal days observed.
Returns
-------
noise_var : np.ndarray
The noise variance.
"""
ndays = self.ndays if not ndays else ndays # Set to value if not set.
t_int = ndays * units.t_sidereal / nt_per_day
# bw = 1.0e6 * (self.freq_upper - self.freq_lower) / self.num_freq
bw = np.abs(self.frequencies[1] - self.frequencies[0]) * 1e6
# Broadcast arrays against each other
bl_indices, f_indices = np.broadcast_arrays(bl_indices, f_indices)
return 2.0*self.tsys(f_indices)**2 / (t_int * bw * self.redundancy[bl_indices]) # 2.0 for two pol
def _lazywhere(cond, arrays, f, fillvalue=None, f2=None):
"""
np.where(cond, x, fillvalue) always evaluates x even where cond is False.
This one only evaluates f(arr1[cond], arr2[cond], ...).
For example,
>>> a, b = np.array([1, 2, 3, 4]), np.array([5, 6, 7, 8])
>>> def f(a, b):
return a*b
>>> _lazywhere(a > 2, (a, b), f, np.nan)
array([ nan, nan, 21., 32.])
Notice it assumes that all `arrays` are of the same shape, or can be
broadcasted together.
"""
if fillvalue is None:
if f2 is None:
raise ValueError("One of (fillvalue, f2) must be given.")
else:
fillvalue = np.nan
else:
if f2 is not None:
raise ValueError("Only one of (fillvalue, f2) can be given.")
arrays = np.broadcast_arrays(*arrays)
temp = tuple(np.extract(cond, arr) for arr in arrays)
tcode = np.mintypecode([a.dtype.char for a in arrays])
out = _valarray(np.shape(arrays[0]), value=fillvalue, typecode=tcode)
np.place(out, cond, f(*temp))
if f2 is not None:
temp = tuple(np.extract(~cond, arr) for arr in arrays)
np.place(out, ~cond, f2(*temp))
return out
def day_of_year_to_cal(year, N, gregorian=True):
"""Convert a day of year number to a month and day in the Julian or
Gregorian calendars.
Arguments:
- `year` : year
- `N` : day of year, 1..365 (or 366 for leap years)
Keywords:
- `gregorian` : If True, use Gregorian calendar, else use Julian calendar
(default: True)
Return:
- (month, day) : (tuple)
"""
year = np.atleast_1d(year)
N = np.atleast_1d(N)
year, N = np.broadcast_arrays(year, N)
K = np.ones_like(N)
K[:] = 2
K[np.atleast_1d(is_leap_year(year, gregorian))] = 1
mon = (9 * (K + N) / 275.0 + 0.98).astype(np.int64)
mon[N < 32] = 1
day = (N - (275 * mon / 9.0).astype(np.int64) +
K * ((mon + 9) / 12.0).astype(np.int64) + 30).astype(np.int64)
return _scalar_if_one(mon), _scalar_if_one(day)
def frac_yr_to_jd(year, gregorian=True):
"""Convert a date in the Julian or Gregorian fractional year to the
Julian Day Number (Meeus 7.1).
Arguments:
- `year` : (int, float) year
Keywords:
- `gregorian` : (bool, default=True) If True, use Gregorian calendar,
else use Julian calendar
Returns:
- (float)
"""
year = np.atleast_1d(year)
day = np.atleast_1d(0.0).astype(np.float64)
year, day = list(map(np.array, np.broadcast_arrays(year, day)))
# For float years abuse the day variable
fyear = year - year.astype('i')
mask = fyear > 0
if np.any(mask):
year = year.astype('i')
days_in_year = cal_to_jd(year[mask] + 1) - cal_to_jd(year[mask])
day[mask] = days_in_year*fyear[mask]
return _scalar_if_one(cal_to_jd(year) + day)
return _scalar_if_one(cal_to_jd(year))
def _ndim_coords_from_arrays(points, ndim=None):
"""
Convert a tuple of coordinate arrays to a (..., ndim)-shaped array.
"""
if isinstance(points, tuple) and len(points) == 1:
# handle argument tuple
points = points[0]
if isinstance(points, tuple):
p = np.broadcast_arrays(*points)
for j in xrange(1, len(p)):
if p[j].shape != p[0].shape:
raise ValueError(
"coordinate arrays do not have the same shape")
points = np.empty(p[0].shape + (len(points),), dtype=float)
for j, item in enumerate(p):
points[..., j] = item
else:
points = np.asanyarray(points)
# XXX Feed back to scipy.
if points.ndim <= 1:
if ndim is None:
points = points.reshape(-1, 1)
else:
points = points.reshape(-1, ndim)
return points
def cal_to_day_of_year(year, mon, day, gregorian=True):
"""Convert a date in the Julian or Gregorian calendars to day of the year
(Meeus 7.1).
Arguments:
- `year` : (int) year
- `mon` : (int) month
- `day` : (int) day
Keywords:
- `gregorian` : (bool, default=True) If True, use Gregorian calendar,
else use Julian calendar
Return:
- day number : 1 = Jan 1...365 (or 366 for leap years) = Dec 31.
"""
year = np.atleast_1d(year).astype(np.int64)
mon = np.atleast_1d(mon).astype(np.int64)
day = np.atleast_1d(day).astype(np.int64)
year, mon, day = np.broadcast_arrays(year, mon, day)
K = np.ones_like(year)
K[:] = 2
K[np.atleast_1d(is_leap_year(year, gregorian))] = 1
return _scalar_if_one(
(275 * mon / 9.0).astype(np.int64) -
(K * ((mon + 9) / 12.0).astype(np.int64)) + day - 30)
def test_broadcast_arrays():
# Test user defined dtypes
a = np.array([(1, 2, 3)], dtype='u4,u4,u4')
b = np.array([(1, 2, 3), (4, 5, 6), (7, 8, 9)], dtype='u4,u4,u4')
result = np.broadcast_arrays(a, b)
assert_equal(result[0], np.array([(1, 2, 3), (1, 2, 3), (1, 2, 3)], dtype='u4,u4,u4'))
assert_equal(result[1], np.array([(1, 2, 3), (4, 5, 6), (7, 8, 9)], dtype='u4,u4,u4'))
def test_beta():
np.random.seed(1234)
b = np.r_[np.logspace(-200, 200, 4),
np.logspace(-10, 10, 4),
np.logspace(-1, 1, 4),
-1, -2.3, -3, -100.3, -10003.4]
a = b
ab = np.array(np.broadcast_arrays(a[:,None], b[None,:])).reshape(2, -1).T
old_dps, old_prec = mpmath.mp.dps, mpmath.mp.prec
try:
mpmath.mp.dps = 400
assert_func_equal(sc.beta,
lambda a, b: float(mpmath.beta(a, b)),
ab,
vectorized=False,
rtol=1e-10)
assert_func_equal(
sc.betaln,
lambda a, b: float(mpmath.log(abs(mpmath.beta(a, b)))),
ab,
vectorized=False,
rtol=1e-10)
finally:
mpmath.mp.dps, mpmath.mp.prec = old_dps, old_prec
def hyp0f1(v, z):
r"""Confluent hypergeometric limit function 0F1.
Parameters
----------
v, z : array_like
Input values.
Returns
-------
hyp0f1 : ndarray
The confluent hypergeometric limit function.
Notes
-----
This function is defined as:
.. math:: _0F_1(v,z) = \sum_{k=0}^{\inf}\frac{z^k}{(v)_k k!}.
It's also the limit as q -> infinity of ``1F1(q;v;z/q)``, and satisfies
the differential equation :math:``f''(z) + vf'(z) = f(z)`.
"""
v = atleast_1d(v)
z = atleast_1d(z)
v, z = np.broadcast_arrays(v, z)
arg = 2 * sqrt(abs(z))
old_err = np.seterr(all='ignore') # for z=0, a<1 and num=inf, next lines
num = where(z.real >= 0, iv(v - 1, arg), jv(v - 1, arg))
den = abs(z)**((v - 1.0) / 2)
num *= gamma(v)
np.seterr(**old_err)
num[z == 0] = 1
den[z == 0] = 1
return num / den
def transform(self, pixel):
"""
Transform pixel to world coordinates. You should pass in a Nx2 array
of (x, y) pixel coordinates to transform to world coordinates. This
will then return an NxM array where M is the number of dimensions in
the WCS
"""
if self.slice is None:
pixel_full = pixel.copy()
else:
pixel_full = []
for index in self.slice:
if index == 'x':
pixel_full.append(pixel[:, 0])
elif index == 'y':
pixel_full.append(pixel[:, 1])
else:
pixel_full.append(index)
pixel_full = np.array(np.broadcast_arrays(*pixel_full)).transpose()
pixel_full += 1
world = self.wcs.wcs_pix2world(pixel_full, 1)
# At the moment, one has to manually check that the transformation
# round-trips, otherwise it should be considered invalid.
pixel_check = self.wcs.wcs_world2pix(world, 1)
with np.errstate(invalid='ignore'):
invalid = np.any(np.abs(pixel_check - pixel_full) > 1., axis=1)
world[invalid] = np.nan
return world
def validate_inputs(*arrays, **kwargs):
"""Validate input arrays
This checks that
- Arrays are mutually broadcastable
- Broadcasted arrays are one-dimensional
Optionally, arrays are sorted according to the ``sort_by`` argument.
Parameters
----------
*args : ndarrays
All non-keyword arguments are arrays which will be validated
sort_by : array
If specified, sort all inputs by the order given in this array.
"""
arrays = np.broadcast_arrays(*arrays)
sort_by = kwargs.pop('sort_by', None)
if kwargs:
raise ValueError("unrecognized arguments: {0}".format(kwargs.keys()))
if arrays[0].ndim != 1:
raise ValueError("Input arrays should be one-dimensional.")
if sort_by is not None:
isort = np.argsort(sort_by)
if isort.shape != arrays[0].shape:
raise ValueError("sort shape must equal array shape.")
arrays = tuple([a[isort] for a in arrays])
return arrays
def max_pool_backward_reshape(dout, cache): """ A fast implementation of the backward pass for the max pooling layer that uses some clever broadcasting and reshaping. This can only be used if the forward pass was computed using max_pool_forward_reshape. NOTE: If there are multiple argmaxes, this method will assign gradient to ALL argmax elements of the input rather than picking one. In this case the gradient will actually be incorrect. However this is unlikely to occur in practice, so it shouldn't matter much. One possible solution is to split the upstream gradient equally among all argmax elements; this should result in a valid subgradient. You can make this happen by uncommenting the line below; however this results in a significant performance penalty (about 40% slower) and is unlikely to matter in practice so we don't do it. """ x, x_reshaped, out = cache dx_reshaped = np.zeros_like(x_reshaped) out_newaxis = out[:, :, :, np.newaxis, :, np.newaxis] mask = (x_reshaped == out_newaxis) dout_newaxis = dout[:, :, :, np.newaxis, :, np.newaxis] dout_broadcast, _ = np.broadcast_arrays(dout_newaxis, dx_reshaped) dx_reshaped[mask] = dout_broadcast[mask] dx_reshaped /= np.sum(mask, axis=(3, 5), keepdims=True) dx = dx_reshaped.reshape(x.shape) return dx
def aim(self, yo, yp=None, z=None, a=None, surface=None, filter=True):
if z is None:
z = self.pupil_distance
yo = np.atleast_2d(yo)
if yp is not None:
if a is None:
a = self.pupil_radius
a = np.array(((-a, -a), (a, a)))
a = np.arctan2(a, z)
yp = np.atleast_2d(yp)
yp = self.map_pupil(yp, a, filter)
yp = z*np.tan(yp)
yo, yp = np.broadcast_arrays(yo, yp)
y = np.zeros((yo.shape[0], 3))
y[..., :2] = -yo*self.radius
if surface:
y[..., 2] = -surface.surface_sag(y)
uz = (0, 0, z)
if self.telecentric:
u = uz
else:
u = uz - y
if yp is not None:
s, m = sagittal_meridional(u, uz)
u += yp[..., 0, None]*s + yp[..., 1, None]*m
normalize(u)
if z < 0:
u *= -1
return y, u
def dib(self, d1=None, d2=None):
"""Days in base according to day count convention of the object
Inputs:
d1 - Initial date
d2 - Final date
Returns:
dib - Integer or integer array with days in base
Note: unlike other functions in this obj, function will only return
array if two conditions are simultaneously met:
(1) User is passing an array (standard); AND
(2) There is potential ambiguity in the answer, i.e. if DB
truly depends on the input dates.
If one of the conditions above fails, function will return scalar.
"""
# Handle fixed cases with dict
dibd = {
'NL/365': 365,
'BUS/30': 30,
'BUS/252': 252,
'BUS/1': 1,
'ACT/365': 365,
'ACT/365F': 365,
'ACT/364': 364,
'ACT/360': 360,
'30A/360': 360,
'30E/360': 360,
'30E+/360': 360,
'30E/360 ISDA': 360,
'30U/360': 360
}
# Simply cases end here
try:
return dibd[self.dc]
except KeyError:
pass
# Throw error for ACT/ACT ISMA
if self.dc == 'ACT/ACT ICMA':
raise AttributeError('The concept of days in base does not apply '
'to the ACT/ACT ICMA convention')
# We worry about vectorization, so we will use pandas to do this
if self.dc == 'BUS/BUS':
# Error checking delegated to BDY
return self.bdy(d2)
elif self.dc == 'ACT/ACT ISDA':
# Error checking delegated to DY
return self.dy(d1)
elif self.dc == 'ACT/365L':
# Error checking delegated to DY
return self.dy(d2)
elif self.dc == 'ACT/365A':
# Note that this is NOT the same as the FRENCH case below,
# as the interval is standard (closed above, and not below)
d1 = self.adjust(d1)
d2 = self.adjust(d2)
if isinstance(d1, Timestamp) and isinstance(d2, Timestamp):
if d2.day == 29 and d2.month == 2:
return 366
else:
if self.hasleap(d1, d2):
return 366
else:
return 365
# For the vectorized case, we assume the ACT/ACT AFB logic and
# then fix the boundary
leap = self.hasleap(d1, d2)
base = asarray(366 * leap + 365 * ~leap, dtype='int64')
# Guarantee dimension conformity
d2, base = broadcast_arrays(d2, base)
d2 = DatetimeIndex(d2)
mask = (d2.day == 29) & (d2.month == 2)
base[mask] = 366
return base
elif self.dc == 'ACT/ACT AFB':
# The bizarre french case. No surprise here.
d1 = self.adjust(d1)
d2 = self.adjust(d2)
leap = self.hasleap(d1, d2)
if isinstance(leap, bool):
return 366 * leap + 365 * (not leap)
else:
return asarray(366 * leap + 365 * ~leap, dtype='int64')
elif self.dc == '1/1':
# There are two (seemingly?) very different definitions for this
# guy. The "FBF Master Agreement for Financial Transactions,
# Supplement to the Derivatives Annex, Edition 2004, section
# 7a." document states that no matter what, this will return 1.
# Same applies for the OpenGamma documentation. On the other
# hand, there are places that say that this is equivalent to
# DIB(ACT/ACT) unless d1 == d2, in which case DIB == 365.25
d1 = self.adjust(d1)
d2 = self.adjust(d2)
if isinstance(d1, Timestamp) and isinstance(d2, Timestamp):
if (d1.day == d2.day and d1.month == d2.month) \
or (d1.month == 2 and d2.month == 2 and
d1.day in [28, 29] and d2.day in [28, 29]):
return 365.25
else:
return self.dy(d1)
else: # We have at least 1 array. Because we only accept the
# combinations of equally sized arrays or array + scalar,
# we don't care about the broadcast
mask = ((d1.day == d2.day) & (d1.month == d2.month)) | \
((d1.month == 2) & (d2.month == 2) %
((d1.day == 28) | (d1.day == 29)) %
((d2.day == 28) | (d2.day == 29)))
base = self.dy(d1)
if isinstance(base, int):
# We handle the mask as two separate cases as the
# negation ~True returns -2
if isinstance(mask, bool):
nmask = not mask
else:
nmask = ~mask
return asarray(base * nmask + 365.25 * mask,
dtype='float64')
else:
base = base.astype('float64')
base[mask] = 365.25
return asarray(base, dtype='float64')
else:
raise NotImplementedError('Day count %s not supported' % self.dc)
def rsh(l, m, theta, phi, normalization='quantum', condon_shortley=True):
"""
Compute the real spherical harmonic (RSH) S_l^m(theta, phi).
The RSH are obtained from Complex Spherical Harmonics (CSH) as follows:
if m < 0:
S_l^m = i / sqrt(2) * (Y_l^m - (-1)^m Y_l^{-m})
if m == 0:
S_l^m = Y_l^0
if m > 0:
S_l^m = 1 / sqrt(2) * (Y_l^{-m} + (-1)^m Y_l^m)
(see [1])
Various normalizations for the CSH exist, see the CSH() function. Since the CSH->RSH change of basis is unitary,
the orthogonality and normalization properties of the RSH are the same as those of the CSH from which they were
obtained. Furthermore, the operation of changing normalization and that of changeing field
(complex->real or vice-versa) commute, because the ratio c_m of normalization constants are always the same for
m and -m (to see this that this implies commutativity, substitute Y_l^m * c_m for Y_l^m in the above formula).
Pinchon & Hoggan [2] define a different change of basis for CSH -> RSH, but they also use an unusual definition
of CSH. To obtain RSH as defined by Pinchon-Hoggan, use this function with normalization='quantum'.
References:
[1] http://en.wikipedia.org/wiki/Spherical_harmonics#Real_form
[2] Rotation matrices for real spherical harmonics: general rotations of atomic orbitals in space-fixed axes.
:param l: non-negative integer; the degree of the CSH.
:param m: integer, -l <= m <= l; the order of the CSH.
:param theta: the colatitude / polar angle,
ranging from 0 (North Pole, (X,Y,Z)=(0,0,1)) to pi (South Pole, (X,Y,Z)=(0,0,-1)).
:param phi: the longitude / azimuthal angle, ranging from 0 to 2 pi.
:param normalization: how to normalize the RSH:
'seismology', 'quantum', 'geodesy'.
these are immediately passed to the CSH functions, and since the change of basis
from CSH to RSH is unitary, the orthogonality and normalization properties are unchanged.
:return: the value of the real spherical harmonic S^l_m(theta, phi)
"""
l, m, theta, phi = np.broadcast_arrays(l, m, theta, phi)
# Get the CSH for m and -m, using Condon-Shortley phase (regardless of whhether CS is requested or not)
# The reason is that the code that changes from CSH to RSH assumes CS phase.
a = csh(l=l, m=m, theta=theta, phi=phi, normalization=normalization, condon_shortley=True)
b = csh(l=l, m=-m, theta=theta, phi=phi, normalization=normalization, condon_shortley=True)
#if m > 0:
# y = np.array((b + ((-1.)**m) * a).real / np.sqrt(2.))
#elif m < 0:
# y = np.array((1j * a - 1j * ((-1.)**(-m)) * b).real / np.sqrt(2.))
#else:
# # For m == 0, the complex spherical harmonics are already real
# y = np.array(a.real)
y = ((m > 0) * np.array((b + ((-1.)**m) * a).real / np.sqrt(2.))
+ (m < 0) * np.array((1j * a - 1j * ((-1.)**(-m)) * b).real / np.sqrt(2.))
+ (m == 0) * np.array(a.real))
if condon_shortley:
return y
else:
# Cancel the CS phase of y (i.e. multiply by -1 when m is both odd and greater than 0)
return y * ((-1.) ** (m * (m > 0)))
def interp_grid(
old_model_obj,
new_model_obj,
shift_east=0,
shift_north=0,
pad=1,
dim="2d",
smooth_kernel=None,
):
"""
interpolate an old grid onto a new one
"""
if dim == "2d":
north, east = np.broadcast_arrays(
old_model_obj.grid_north[:, None] + shift_north,
old_model_obj.grid_east[None, :] + shift_east,
)
# 2) do a 2D interpolation for each layer, much faster
new_res = np.zeros((
new_model_obj.grid_north.shape[0],
new_model_obj.grid_east.shape[0],
new_model_obj.grid_z.shape[0],
))
for zz in range(new_model_obj.grid_z.shape[0]):
try:
old_zz = np.where(
old_model_obj.grid_z >= new_model_obj.grid_z[zz])[0][0]
except IndexError:
old_zz = -1
print "New depth={0:.2f}; old depth={1:.2f}".format(
new_model_obj.grid_z[zz], old_model_obj.grid_z[old_zz])
new_res[:, :, zz] = spi.griddata(
(north.ravel(), east.ravel()),
old_model_obj.res_model[:, :, old_zz].ravel(),
(new_model_obj.grid_north[:, None],
new_model_obj.grid_east[None, :]),
method="linear",
)
new_res[0:pad, pad:-pad, zz] = new_res[pad, pad:-pad, zz]
new_res[-pad:, pad:-pad, zz] = new_res[-pad - 1, pad:-pad, zz]
new_res[:, 0:pad,
zz] = (new_res[:, pad,
zz].repeat(pad).reshape(new_res[:, 0:pad,
zz].shape))
new_res[:, -pad:,
zz] = (new_res[:, -pad - 1,
zz].repeat(pad).reshape(new_res[:, -pad:,
zz].shape))
if smooth_kernel is not None:
new_res[:, :, zz] = smooth_2d(new_res[:, :, zz], smooth_kernel)
elif dim == "3d":
# 1) first need to make x, y, z have dimensions (nx, ny, nz), similar to res
north, east, vert = np.broadcast_arrays(
old_model_obj.grid_north[:, None, None],
old_model_obj.grid_east[None, :, None],
old_model_obj.grid_z[None, None, :],
)
# 2) next interpolate ont the new mesh (3D interpolation, slow)
new_res = spi.griddata(
(north.ravel(), east.ravel(), vert.ravel()),
old_model_obj.res_model.ravel(),
(
new_model_obj.grid_north[:, None, None],
new_model_obj.grid_east[None, :, None],
new_model_obj.grid_z[None, None, :],
),
method="linear",
)
print "Shape of new res = {0}".format(new_res.shape)
return new_res
def implied_vol(underlying_price, strike, expiry, option_price, put=False,
initial_guess=0.5, assert_no_arbitrage=True):
"""Implied volatility function
Inverts the Black-Scholes formula to find the volatility that matches the
given option price. The implied volatility is computed using Newton's
method.
Parameters
----------
underlying_price : float
Price of the underlying asset.
strike : float
Strike of the option.
expiry : float
Time remaining until the expiry of the option.
option_price : float
Option price according to Black-Scholes formula.
put : bool, optional
Whether the option is a put option. Defaults to `False`.
initial_guess : float, optional
Initial guess for the implied volatility for the Newton's method.
Returns
-------
float
Implied volatility.
Example
-------
>>> import numpy as np
>>> from fyne import blackscholes
>>> call_price = 11.77
>>> put_price = 1.77
>>> underlying_price = 100.
>>> strike = 90.
>>> expiry = 0.5
>>> implied_vol = blackscholes.implied_vol(underlying_price, strike,
... expiry, call_price)
>>> np.round(implied_vol, 2)
0.2
>>> implied_vol = blackscholes.implied_vol(underlying_price, strike,
... expiry, put_price, put=True)
>>> np.round(implied_vol, 2)
0.2
"""
call = common._put_call_parity_reverse(option_price, underlying_price,
strike, put)
if assert_no_arbitrage:
common._assert_no_arbitrage(underlying_price, call, strike)
k = np.array(np.log(strike/underlying_price))
c = np.array(call/underlying_price)
k, expiry, c, initial_guess = np.broadcast_arrays(k, expiry, c, initial_guess)
noarb_mask = ~np.any(
common._check_arbitrage(underlying_price, call, strike), axis=0)
noarb_mask &= ~np.any(
tuple(map(np.isnan, (k, expiry, c, initial_guess))), axis=0)
iv = np.full(c.shape, np.nan)
iv[noarb_mask] = _reduced_implied_vol(k[noarb_mask], expiry[noarb_mask],
c[noarb_mask],
initial_guess[noarb_mask])
return iv
def test_complete_losses(self):
# this is testing full broadcasting
n = np.newaxis
(freqs, h_tgs, h_rgs, time_percents, versions, G_ts,
G_rs) = np.broadcast_arrays(
np.array(self.cases_freqs)[:, n, n, n, n],
np.array(self.cases_h_tgs)[n, :, n, n, n],
np.array(self.cases_h_rgs)[n, :, n, n, n],
np.array(self.cases_time_percents)[n, n, :, n, n],
np.array(self.cases_versions, dtype=np.int32)[n, n, n, :, n],
np.array(self.cases_G_ts)[n, n, n, n, :],
np.array(self.cases_G_rs)[n, n, n, n, :],
)
results = pathprof.losses_complete(
freqs * apu.GHz,
self.temperature,
self.pressure,
self.lon_t,
self.lat_t,
self.lon_r,
self.lat_r,
h_tgs * apu.m,
h_rgs * apu.m,
self.hprof_step,
time_percents * apu.percent,
G_t=G_ts * cnv.dBi,
G_r=G_rs * cnv.dBi,
omega=self.omega,
version=versions,
)
for tup in np.nditer([
freqs,
h_tgs,
h_rgs,
time_percents,
G_ts,
G_rs,
versions,
results['L_b0p'],
results['L_bd'],
results['L_bs'],
results['L_ba'],
results['L_b'],
results['L_b_corr'],
]):
with ZipFile(self.cases_zip_name) as myzip:
loss_name = self.loss_template.format(
float(tup[0]),
float(tup[1]),
float(tup[2]),
float(tup[3]),
float(tup[4]),
float(tup[5]),
int(tup[6]),
)
with myzip.open(loss_name, 'r') as f:
loss_true = json.loads(f.read().decode('utf-8'))
for i, k in enumerate([
'L_b0p',
'L_bd',
'L_bs',
'L_ba',
'L_b',
'L_b_corr',
]):
assert_quantity_allclose(tup[i + 7], loss_true[k + '_t'])
def float_array_broadcast(*args):
return num.broadcast_arrays(
*[num.asarray(x, dtype=num.float) for x in args])
def T_s(self, s, p=None, d=None, debug=False):
"""Temperature as a function of entropy
T = T_s(s)
or
T = T_s(s,p)
or
T = T_s(s,d)
Accepts unit_energy / unit_matter / unit_temperature
unit_pressure
unit_matter / unit_volume
Returns unit_temperature
"""
if p is None and d is None:
p = pm.config['def_p']
s = pm.units.energy(np.asarray(s, dtype=float), to_units='kJ')
s = pm.units.matter(s, self.data['mw'], to_units='kmol', exponent=-1)
s = pm.units.temperature(s, to_units='K', exponent=-1)
if s.ndim == 0:
s = np.reshape(s, (1, ))
# If isobaric
if p is not None:
p = pm.units.pressure(np.asarray(p, dtype=float), to_units='Pa')
if p.ndim == 0:
p = np.reshape(p, (1, ))
s, p = np.broadcast_arrays(s, p)
# Adjust s by the pressure term
s += pm.units.const_Ru * np.log(p / self.data['pref'])
I = np.ones_like(s, dtype=bool)
T = np.full_like(
s, 0.5 * (self.data['Tlim'][0] + self.data['Tlim'][-1]))
self._iter1(self._s,
'T',
s,
T,
I,
self.data['Tlim'][0],
self.data['Tlim'][-1],
verbose=debug)
# If isochoric
else:
d = pm.units.matter(np.asarray(d, dtype=float),
self.data['mw'],
to_units='kmol')
d = pm.units.volume(d, to_units='m3', exponent=-1)
s, d = np.broadcast_arrays(s, d)
R = pm.units.const_Ru
# Define a custom iterator function
def fn(T, d, diff):
sd = 0.
s, sT = self._s(T, diff)
s -= R * np.log(d * R * T * 1e3 / (self.data['pref']))
if diff:
sT -= R / T
sd = -R / d
return s, sT, sd
I = np.ones_like(s, dtype=bool)
T = np.full_like(
s, 0.5 * (self.data['Tlim'][0] + self.data['Tlim'][-1]))
self._iter1(fn,
'T',
s,
T,
I,
self.data['Tlim'][0],
self.data['Tlim'][-1],
param={'d': d},
verbose=debug)
pm.units.temperature_scale(T, from_units='K')
return T
def get_idx(self):
idxs = (0, 0)
if self.axes is not None:
for ax in self.axes:
idxs += (np.arange(ax.nbin).reshape((-1, 1, 1)),)
return np.broadcast_arrays(*idxs)
def chol_solve_numpy(t, b, diageps=None):
"""
t (..., n)
b (..., n, m) or (n,)
t[0] += diageps
m = toeplitz(t)
l = chol(m)
return solve(l, b)
pure numpy, object arrays supported
"""
t = numpy.copy(t, subok=True)
n = t.shape[-1]
b = numpy.asanyarray(b)
vec = b.ndim < 2
if vec:
b = b[:, None]
assert b.shape[-2] == n
if n == 0:
shape = numpy.broadcast_shapes(t.shape[:-1], b.shape[:-2])
shape += (n, ) if vec else b.shape[-2:]
dtype = numpy.result_type(t.dtype, b.dtype)
return numpy.empty(shape, dtype)
if diageps is not None:
t[..., 0] += diageps
if numpy.any(t[..., 0] <= 0):
msg = '1-th leading minor is not positive definite'
raise numpy.linalg.LinAlgError(msg)
norm = numpy.copy(t[..., 0, None], subok=True)
t /= norm
invLb = numpy.copy(numpy.broadcast_arrays(b, t[..., None])[0], subok=True)
prevLi = t
g = numpy.stack([numpy.roll(t, 1, -1), t], -2)
for i in range(1, n):
assert numpy.all(g[..., 0, i] > 0)
rho = -g[..., 1, i, None, None] / g[..., 0, i, None, None]
if numpy.any(numpy.abs(rho) >= 1):
msg = '{}-th leading minor is not positive definite'.format(i + 1)
raise numpy.linalg.LinAlgError(msg)
gamma = numpy.sqrt((1 - rho) * (1 + rho))
g[..., :, i:] += g[..., ::-1, i:] * rho
g[..., :, i:] /= gamma
Li = g[..., 0, i:] # i-th column of L from row i
invLb[..., i:, :] -= invLb[..., i - 1, None, :] * prevLi[..., i:, None]
invLb[..., i, :] /= Li[..., 0, None]
prevLi[..., i:] = Li
g[..., 0, i:] = numpy.roll(g[..., 0, i:], 1, -1)
invLb /= numpy.sqrt(norm[..., None])
if vec:
invLb = numpy.squeeze(invLb, -1)
return invLb
# plt.show()
# %%
# plt.figure(figsize=(12, 12))
# for i in range(0, 9):
# plt.subplot(3, 3, i+1)
# plt.title('Distance {} SD'.format(i+1))
# plt.imshow(np.logical_and(Zm < -i, Zm > -i-1))
# plt.axis('off')
# plt.show()
# Boundaries between center and surround and limit of surround
inner_b = 2
outer_b = 4
center_mask = np.logical_not(Zm < inner_b)
center_mask_3d = np.broadcast_arrays(sta, center_mask[..., None])[1]
surround_mask = np.logical_not(np.logical_and(Zm > inner_b, Zm < outer_b))
surround_mask_3d = np.broadcast_arrays(sta, surround_mask[..., None])[1]
# %%
plt.subplot(2, 3, 4)
plt.imshow(center_mask)
plt.title('Center (<{}$\sigma$)'.format(inner_b))
plt.subplot(2, 3, 5)
plt.imshow(surround_mask)
plt.title('Surround (Between {}$\sigma$ and {}$\sigma$)'.format(
inner_b, outer_b))
# plt.show()
sta_center = np.ma.array(sta, mask=center_mask_3d)
def _set_arrayXarray_sparse(self, row, col, x):
# Fall back to densifying x
x = np.asarray(x.toarray(), dtype=self.dtype)
x, _ = np.broadcast_arrays(x, row)
self._set_arrayXarray(row, col, x)
def _argparse(self, T=None, p=None, d=None,\
temperature=False, pressure=False, density=False):
"""Parse the arguments supplied to an IG2 property method
T = _argparse(*varg, **kwarg)
OR
T,p,d = _argparse(*varg, **kwarg, temperature=True, pressure=True,
density=True)
_ARGPARSE automatically applies the default temperature and pressure,
def_T or def_p, from the pyromat.config system to deal with unspecified
parameters. All inputs are re-cast as numpy arrays of at least one
dimension and inputs are automatically converted from the configured
user units into kJ, kmol, m^3.
The returned variables are arrays of temperature, T, pressure, p, and
the density, d. The optional keywords TEMPERATURE, PRESSURE, and
DENSITY are used to indicate which state variables should be returned.
They are always returned in the order T, p, d.
"""
nparam = ((0 if T is None else 1) + (0 if p is None else 1) +
(0 if d is None else 1))
if nparam == 1:
if T is None:
T = pm.config['def_T']
else:
p = pm.config['def_p']
elif nparam == 0:
T = pm.config['def_T']
p = pm.config['def_p']
elif nparam > 2:
raise utility.PMParameterError(
'Specifying more than two simultaneous parameters is illegal.')
# Perform the unit conversions, and format the arrays
if T is not None:
T = pm.units.temperature_scale(np.asarray(T, dtype=float),
to_units='K')
if T.ndim == 0:
T = np.reshape(T, (1, ))
if p is not None:
p = pm.units.pressure(np.asarray(p, dtype=float), to_units='Pa')
if p.ndim == 0:
p = np.reshape(p, (1, ))
if d is not None:
d = pm.units.matter(np.asarray(d, dtype=float),
self.data['mw'],
to_units='kmol')
pm.units.volume(d, to_units='m3', exponent=-1, inplace=True)
if d.ndim == 0:
d = np.reshape(d, (1, ))
# Convert the IG constant to J/kmol/K
R = 1000 * pm.units.const_Ru
# Case out the specified state variables
# There are three possible combinations
if T is not None:
# T,p
if p is not None:
# Broadcast the arrays
T, p = np.broadcast_arrays(T, p)
# Do we need density?
if density:
d = p / (R * T)
# T,d
else:
# Broadcast the arrays
T, d = np.broadcast_arrays(T, d)
# Do we need pressure?
if pressure:
p = d * R * T
# p,d
else:
# Broadcast the arrays
p, d = np.broadcast_arrays(p, d)
# Do we need temperature?
if temperature:
T = p / (R * d)
out = []
if temperature:
out.append(T)
if pressure:
out.append(p)
if density:
out.append(d)
if len(out) > 1:
return tuple(out)
elif len(out) == 1:
return out[0]
return
def logsumexp(a: np.ndarray,
axis: int = None,
b: np.ndarray = None,
keepdims: bool = False,
return_sign: bool = False,
base: float = 10.) -> float:
"""
Compute the log of the sum of exponentials of input elements.
Parameters
----------
a : array_like
Input array.
axis : None or int or tuple of ints, optional
Axis or axes over which the sum is taken. By default `axis` is None,
and all elements are summed.
keepdims : bool, optional
If this is set to True, the axes which are reduced are left in the
result as dimensions with size one. With this option, the result
will broadcast correctly against the original array.
base : float, optional
This base is used in the exponentiation and the logarithm.
$\log_{base} \sum (base)^{array}$
b : array-like, optional
Scaling factor for exp(`a`) must be of the same shape as `a` or
broadcastable to `a`. These values may be negative in order to
implement subtraction.
return_sign : bool, optional
If this is set to True, the result will be a pair containing sign
information; if False, results that are negative will be returned
as NaN. Default is False (no sign information).
Returns
-------
res : ndarray
The result, ``np.log(np.sum(np.exp(a)))`` calculated in a numerically
more stable way. If `b` is given then ``np.log(np.sum(b*np.exp(a)))``
is returned.
sgn : ndarray
If return_sign is True, this will be an array of floating-point
numbers matching res and +1, 0, or -1 depending on the sign
of the result. If False, only one result is returned.
See Also
--------
numpy.logaddexp, numpy.logaddexp2
Notes
-----
NumPy has a logaddexp function which is very similar to `logsumexp`, but
only handles two arguments. `logaddexp.reduce` is similar to this
function, but may be less stable.
"""
if b is not None:
a, b = np.broadcast_arrays(a, b)
if np.any(b == 0):
a = a + 0. # promote to at least float
a[b == 0] = -np.inf
a_max = np.amax(a, axis=axis, keepdims=True)
if a_max.ndim > 0:
a_max[~np.isfinite(a_max)] = 0
elif not np.isfinite(a_max):
a_max = 0
if b is not None:
b = np.asarray(b)
if base is None or base == np.e:
tmp = b * np.exp(a - a_max)
else:
tmp = b * base**(a - a_max)
else:
if base is None or base == np.e:
tmp = np.exp(a - a_max)
else:
tmp = base**(a - a_max)
# suppress warnings about log of zero
with np.errstate(divide='ignore'):
s = np.sum(tmp, axis=axis, keepdims=keepdims)
if return_sign:
sgn = np.sign(s)
s *= sgn # /= makes more sense but we need zero -> zero
log_base_conversion = 1 / np.log(base)
out = np.log(s) * log_base_conversion
if not keepdims:
a_max = np.squeeze(a_max, axis=axis)
out += a_max
if return_sign:
return out, sgn
else:
return out
def simple_broadcast(self, *args):
return np.broadcast_arrays(*args)
def geometry_area_weights(cube, geometry, normalize=False):
"""
Returns the array of weights corresponding to the area of overlap between
the cells of cube's horizontal grid, and the given shapely geometry.
The returned array is suitable for use with :const:`iris.analysis.MEAN`.
The cube must have bounded horizontal coordinates.
.. note::
This routine works in Euclidean space. Area calculations do not
account for the curvature of the Earth. And care must be taken to
ensure any longitude values are expressed over a suitable interval.
.. note::
This routine currently does not handle all out-of-bounds cases
correctly. In cases where both the coordinate bounds and the
geometry's bounds lie outside the physically realistic range
(i.e., abs(latitude) > 90., as it is commonly the case when
bounds are constructed via guess_bounds()), the weights
calculation might be wrong. In this case, a UserWarning will
be issued.
Args:
* cube (:class:`iris.cube.Cube`):
A Cube containing a bounded, horizontal grid definition.
* geometry (a shapely geometry instance):
The geometry of interest. To produce meaningful results this geometry
must have a non-zero area. Typically a Polygon or MultiPolygon.
Kwargs:
* normalize:
Calculate each individual cell weight as the cell area overlap between
the cell and the given shapely geometry divided by the total cell area.
Default is False.
"""
# extract smallest subcube containing geometry
shape = cube.shape
extraction_results = _extract_relevant_cube_slice(cube, geometry)
# test if there is overlap between cube and geometry
if extraction_results is None:
return np.zeros(shape)
subcube, subx_coord, suby_coord, bnds_ix = extraction_results
x_min_ix, y_min_ix, x_max_ix, y_max_ix = bnds_ix
# prepare the weights array
subshape = list(cube.shape)
x_dim = cube.coord_dims(subx_coord)[0]
y_dim = cube.coord_dims(suby_coord)[0]
subshape[x_dim] = subx_coord.shape[0]
subshape[y_dim] = suby_coord.shape[0]
subx_bounds = subx_coord.bounds
suby_bounds = suby_coord.bounds
subweights = np.empty(subshape, np.float32)
# calculate the area weights
for nd_index in np.ndindex(subweights.shape):
xi = nd_index[x_dim]
yi = nd_index[y_dim]
x0, x1 = subx_bounds[xi]
y0, y1 = suby_bounds[yi]
polygon = Polygon([(x0, y0), (x0, y1), (x1, y1), (x1, y0)])
subweights[nd_index] = polygon.intersection(geometry).area
if normalize:
subweights[nd_index] /= polygon.area
# pad the calculated weights with zeros to match original cube shape
weights = np.zeros(shape, np.float32)
slices = []
for i in range(weights.ndim):
if i == x_dim:
slices.append(slice(x_min_ix, x_max_ix + 1))
elif i == y_dim:
slices.append(slice(y_min_ix, y_max_ix + 1))
else:
slices.append(slice(None))
weights[tuple(slices)] = subweights
# Fix for the limitation of iris.analysis.MEAN weights handling.
# Broadcast the array to the full shape of the cube
weights = np.broadcast_arrays(weights, cube.data)[0]
return weights
def extirpolate(x, y, N=None, M=4):
"""
Extirpolate the values (x, y) onto an integer grid range(N),
using lagrange polynomial weights on the M nearest points.
Parameters
----------
x : array_like
array of abscissas
y : array_like
array of ordinates
N : int
number of integer bins to use. For best performance, N should be larger
than the maximum of x
M : int
number of adjoining points on which to extirpolate.
Returns
-------
yN : ndarray
N extirpolated values associated with range(N)
Example
-------
>>> rng = np.random.RandomState(0)
>>> x = 100 * rng.rand(20)
>>> y = np.sin(x)
>>> y_hat = extirpolate(x, y)
>>> x_hat = np.arange(len(y_hat))
>>> f = lambda x: np.sin(x / 10)
>>> np.allclose(np.sum(y * f(x)), np.sum(y_hat * f(x_hat)))
True
Notes
-----
This code is based on the C implementation of spread() presented in
Numerical Recipes in C, Second Edition (Press et al. 1989; p.583).
"""
x, y = map(np.ravel, np.broadcast_arrays(x, y))
if N is None:
N = int(np.max(x) + 0.5 * M + 1)
# Now use legendre polynomial weights to populate the results array;
# This is an efficient recursive implementation (See Press et al. 1989)
result = np.zeros(N, dtype=y.dtype)
# first take care of the easy cases where x is an integer
integers = (x % 1 == 0)
add_at(result, x[integers].astype(int), y[integers])
x, y = x[~integers], y[~integers]
# For each remaining x, find the index describing the extirpolation range.
# i.e. ilo[i] < x[i] < ilo[i] + M with x[i] in the center,
# adjusted so that the limits are within the range 0...N
ilo = np.clip((x - M // 2).astype(int), 0, N - M)
numerator = y * np.prod(x - ilo - np.arange(M)[:, np.newaxis], 0)
denominator = factorial(M - 1)
for j in range(M):
if j > 0:
denominator *= j / (j - M)
ind = ilo + (M - 1 - j)
add_at(result, ind, numerator / (denominator * (x - ind)))
return result
def lombscargle_fastchi2(t,
y,
dy,
f0,
df,
Nf,
normalization='standard',
fit_mean=True,
center_data=True,
nterms=1,
use_fft=True,
trig_sum_kwds=None):
"""Lomb-Scargle Periodogram
This implements a fast chi-squared periodogram using the algorithm
outlined in [4]_. The result is identical to the standard Lomb-Scargle
periodogram. The advantage of this algorithm is the
ability to compute multiterm periodograms relatively quickly.
Parameters
----------
t, y, dy : array_like (NOT astropy.Quantities)
times, values, and errors of the data points. These should be
broadcastable to the same shape.
f0, df, Nf : (float, float, int)
parameters describing the frequency grid, f = f0 + df * arange(Nf).
normalization : string (optional, default='standard')
Normalization to use for the periodogram.
Options are 'standard', 'model', 'log', or 'psd'.
fit_mean : bool (optional, default=True)
if True, include a constant offset as part of the model at each
frequency. This can lead to more accurate results, especially in the
case of incomplete phase coverage.
center_data : bool (optional, default=True)
if True, pre-center the data by subtracting the weighted mean
of the input data. This is especially important if ``fit_mean = False``
nterms : int (optional, default=1)
Number of Fourier terms in the fit
Returns
-------
power : array_like
Lomb-Scargle power associated with each frequency.
Units of the result depend on the normalization.
References
----------
.. [1] M. Zechmeister and M. Kurster, A&A 496, 577-584 (2009)
.. [2] W. Press et al, Numerical Recipies in C (2002)
.. [3] Scargle, J.D. ApJ 263:835-853 (1982)
.. [4] Palmer, J. ApJ 695:496-502 (2009)
"""
if nterms == 0 and not fit_mean:
raise ValueError("Cannot have nterms = 0 without fitting bias")
if dy is None:
dy = 1
# Validate and setup input data
t, y, dy = np.broadcast_arrays(t, y, dy)
if t.ndim != 1:
raise ValueError("t, y, dy should be one dimensional")
# Validate and setup frequency grid
if f0 < 0:
raise ValueError("Frequencies must be positive")
if df <= 0:
raise ValueError("Frequency steps must be positive")
if Nf <= 0:
raise ValueError("Number of frequencies must be positive")
w = dy**-2.0
ws = np.sum(w)
# if fit_mean is true, centering the data now simplifies the math below.
if center_data or fit_mean:
y = y - np.dot(w, y) / ws
yw = y / dy
chi2_ref = np.dot(yw, yw)
kwargs = dict.copy(trig_sum_kwds or {})
kwargs.update(f0=f0, df=df, use_fft=use_fft, N=Nf)
# Here we build-up the matrices XTX and XTy using pre-computed
# sums. The relevant identities are
# 2 sin(mx) sin(nx) = cos(m-n)x - cos(m+n)x
# 2 cos(mx) cos(nx) = cos(m-n)x + cos(m+n)x
# 2 sin(mx) cos(nx) = sin(m-n)x + sin(m+n)x
yws = np.sum(y * w)
SCw = [(np.zeros(Nf), ws * np.ones(Nf))]
SCw.extend([
trig_sum(t, w, freq_factor=i, **kwargs)
for i in range(1, 2 * nterms + 1)
])
Sw, Cw = zip(*SCw)
SCyw = [(np.zeros(Nf), yws * np.ones(Nf))]
SCyw.extend([
trig_sum(t, w * y, freq_factor=i, **kwargs)
for i in range(1, nterms + 1)
])
Syw, Cyw = zip(*SCyw)
# Now create an indexing scheme so we can quickly
# build-up matrices at each frequency
order = [('C', 0)] if fit_mean else []
order.extend(sum([[('S', i), ('C', i)] for i in range(1, nterms + 1)], []))
funcs = dict(S=lambda m, i: Syw[m][i],
C=lambda m, i: Cyw[m][i],
SS=lambda m, n, i: 0.5 * (Cw[abs(m - n)][i] - Cw[m + n][i]),
CC=lambda m, n, i: 0.5 * (Cw[abs(m - n)][i] + Cw[m + n][i]),
SC=lambda m, n, i: 0.5 *
(np.sign(m - n) * Sw[abs(m - n)][i] + Sw[m + n][i]),
CS=lambda m, n, i: 0.5 *
(np.sign(n - m) * Sw[abs(n - m)][i] + Sw[n + m][i]))
def compute_power(i):
XTX = np.array([[funcs[A[0] + B[0]](A[1], B[1], i) for A in order]
for B in order])
XTy = np.array([funcs[A[0]](A[1], i) for A in order])
return np.dot(XTy.T, np.linalg.solve(XTX, XTy))
p = np.array([compute_power(i) for i in range(Nf)])
if normalization == 'psd':
p *= 0.5 * t.size / ws
elif normalization == 'standard':
p /= chi2_ref
elif normalization == 'log':
p = -np.log(1 - p / chi2_ref)
elif normalization == 'model':
p /= chi2_ref - p
else:
raise ValueError("normalization='{0}' "
"not recognized".format(normalization))
return p
def sphere2cart(r, theta, phi):
""" Spherical to Cartesian coordinates
This is the standard physics convention where `theta` is the
inclination (polar) angle, and `phi` is the azimuth angle.
Imagine a sphere with center (0,0,0). Orient it with the z axis
running south-north, the y axis running west-east and the x axis
from posterior to anterior. `theta` (the inclination angle) is the
angle to rotate from the z-axis (the zenith) around the y-axis,
towards the x axis. Thus the rotation is counter-clockwise from the
point of view of positive y. `phi` (azimuth) gives the angle of
rotation around the z-axis towards the y axis. The rotation is
counter-clockwise from the point of view of positive z.
Equivalently, given a point P on the sphere, with coordinates x, y,
z, `theta` is the angle between P and the z-axis, and `phi` is
the angle between the projection of P onto the XY plane, and the X
axis.
Geographical nomenclature designates theta as 'co-latitude', and phi
as 'longitude'
Parameters
------------
r : array_like
radius
theta : array_like
inclination or polar angle
phi : array_like
azimuth angle
Returns
---------
x : array
x coordinate(s) in Cartesion space
y : array
y coordinate(s) in Cartesian space
z : array
z coordinate
Notes
--------
See these pages:
* http://en.wikipedia.org/wiki/Spherical_coordinate_system
* http://mathworld.wolfram.com/SphericalCoordinates.html
for excellent discussion of the many different conventions
possible. Here we use the physics conventions, used in the
wikipedia page.
Derivations of the formulae are simple. Consider a vector x, y, z of
length r (norm of x, y, z). The inclination angle (theta) can be
found from: cos(theta) == z / r -> z == r * cos(theta). This gives
the hypotenuse of the projection onto the XY plane, which we will
call Q. Q == r*sin(theta). Now x / Q == cos(phi) -> x == r *
sin(theta) * cos(phi) and so on.
We have deliberately named this function ``sphere2cart`` rather than
``sph2cart`` to distinguish it from the Matlab function of that
name, because the Matlab function uses an unusual convention for the
angles that we did not want to replicate. The Matlab function is
trivial to implement with the formulae given in the Matlab help.
"""
sin_theta = np.sin(theta)
x = r * np.cos(phi) * sin_theta
y = r * np.sin(phi) * sin_theta
z = r * np.cos(theta)
x, y, z = np.broadcast_arrays(x, y, z)
return x, y, z
def __init__(self, selection, array):
# some initial normalization
selection = ensure_tuple(selection)
selection = tuple([i] if is_integer(i) else i for i in selection)
selection = replace_lists(selection)
# validation
if not is_coordinate_selection(selection, array):
raise IndexError(
'invalid coordinate selection; expected one integer '
'(coordinate) array per dimension of the target array, '
'got {!r}'.format(selection))
# handle wraparound, boundscheck
for dim_sel, dim_len in zip(selection, array.shape):
# handle wraparound
wraparound_indices(dim_sel, dim_len)
# handle out of bounds
boundscheck_indices(dim_sel, dim_len)
# compute chunk index for each point in the selection
chunks_multi_index = tuple(
dim_sel // dim_chunk_len
for (dim_sel, dim_chunk_len) in zip(selection, array._chunks))
# broadcast selection - this will raise error if array dimensions don't match
selection = np.broadcast_arrays(*selection)
chunks_multi_index = np.broadcast_arrays(*chunks_multi_index)
# remember shape of selection, because we will flatten indices for processing
self.sel_shape = selection[0].shape if selection[0].shape else (1, )
# flatten selection
selection = [dim_sel.reshape(-1) for dim_sel in selection]
chunks_multi_index = [
dim_chunks.reshape(-1) for dim_chunks in chunks_multi_index
]
# ravel chunk indices
chunks_raveled_indices = np.ravel_multi_index(chunks_multi_index,
dims=array._cdata_shape)
# group points by chunk
if np.any(np.diff(chunks_raveled_indices) < 0):
# optimisation, only sort if needed
sel_sort = np.argsort(chunks_raveled_indices)
selection = tuple(dim_sel[sel_sort] for dim_sel in selection)
else:
sel_sort = None
# store attributes
self.selection = selection
self.sel_sort = sel_sort
self.shape = selection[0].shape if selection[0].shape else (1, )
self.drop_axes = None
self.array = array
# precompute number of selected items for each chunk
self.chunk_nitems = np.bincount(chunks_raveled_indices,
minlength=array.nchunks)
self.chunk_nitems_cumsum = np.cumsum(self.chunk_nitems)
# locate the chunks we need to process
self.chunk_rixs = np.nonzero(self.chunk_nitems)[0]
# unravel chunk indices
self.chunk_mixs = np.unravel_index(self.chunk_rixs,
dims=array._cdata_shape)
def trig_sum(t,
h,
df,
N,
f0=0,
freq_factor=1,
oversampling=5,
use_fft=True,
Mfft=4):
"""Compute (approximate) trigonometric sums for a number of frequencies
This routine computes weighted sine and cosine sums:
S_j = sum_i { h_i * sin(2 pi * f_j * t_i) }
C_j = sum_i { h_i * cos(2 pi * f_j * t_i) }
Where f_j = freq_factor * (f0 + j * df) for the values j in 1 ... N.
The sums can be computed either by a brute force O[N^2] method, or
by an FFT-based O[Nlog(N)] method.
Parameters
----------
t : array_like
array of input times
h : array_like
array weights for the sum
df : float
frequency spacing
N : int
number of frequency bins to return
f0 : float (optional, default=0)
The low frequency to use
freq_factor : float (optional, default=1)
Factor which multiplies the frequency
use_fft : bool
if True, use the approximate FFT algorithm to compute the result.
This uses the FFT with Press & Rybicki's Lagrangian extirpolation.
oversampling : int (default = 5)
oversampling freq_factor for the approximation; roughly the number of
time samples across the highest-frequency sinusoid. This parameter
contains the tradeoff between accuracy and speed. Not referenced
if use_fft is False.
Mfft : int
The number of adjacent points to use in the FFT approximation.
Not referenced if use_fft is False.
Returns
-------
S, C : ndarrays
summation arrays for frequencies f = df * np.arange(1, N + 1)
"""
df *= freq_factor
f0 *= freq_factor
if df <= 0:
raise ValueError("df must be positive")
t, h = map(np.ravel, np.broadcast_arrays(t, h))
if use_fft:
Mfft = int(Mfft)
if Mfft <= 0:
raise ValueError("Mfft must be positive")
# required size of fft is the power of 2 above the oversampling rate
Nfft = bitceil(N * oversampling)
t0 = t.min()
if f0 > 0:
h = h * np.exp(2j * np.pi * f0 * (t - t0))
tnorm = ((t - t0) * Nfft * df) % Nfft
grid = extirpolate(tnorm, h, Nfft, Mfft)
fftgrid = np.fft.ifft(grid)[:N]
if t0 != 0:
f = f0 + df * np.arange(N)
fftgrid *= np.exp(2j * np.pi * t0 * f)
C = Nfft * fftgrid.real
S = Nfft * fftgrid.imag
else:
f = f0 + df * np.arange(N)
C = np.dot(h, np.cos(2 * np.pi * f * t[:, np.newaxis]))
S = np.dot(h, np.sin(2 * np.pi * f * t[:, np.newaxis]))
return S, C
def allclose(a,
b,
rtol=4 * np.finfo(float).eps,
atol=0.0,
equal_nan=False,
verbose=False):
"""Returns True if two arrays are element-wise equal within a tolerance.
This function is essentially a wrapper for the `quaternion.isclose`
function, but returns a single boolean value of True if all elements
of the output from `quaternion.isclose` are True, and False otherwise.
This function also adds the option.
Note that this function has stricter tolerances than the
`numpy.allclose` function, as well as the additional `verbose` option.
Parameters
----------
a, b : array_like
Input arrays to compare.
rtol : float
The relative tolerance parameter (see Notes).
atol : float
The absolute tolerance parameter (see Notes).
equal_nan : bool
Whether to compare NaN's as equal. If True, NaN's in `a` will be
considered equal to NaN's in `b` in the output array.
verbose : bool
If the return value is False, all the non-close values are printed,
iterating through the non-close indices in order, displaying the
array values along with the index, with a separate line for each
pair of values.
See Also
--------
isclose, numpy.all, numpy.any, numpy.allclose
Returns
-------
allclose : bool
Returns True if the two arrays are equal within the given
tolerance; False otherwise.
Notes
-----
If the following equation is element-wise True, then allclose returns
True.
absolute(`a` - `b`) <= (`atol` + `rtol` * absolute(`b`))
The above equation is not symmetric in `a` and `b`, so that
`allclose(a, b)` might be different from `allclose(b, a)` in
some rare cases.
"""
close = isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan)
result = np.all(close)
if verbose and not result:
a, b = np.atleast_1d(a), np.atleast_1d(b)
a, b = np.broadcast_arrays(a, b)
print('Non-close values:')
for i in np.nonzero(close == False):
print(' a[{0}]={1}\n b[{0}]={2}'.format(i, a[i], b[i]))
return result
def logsumexp(a, axis=None, b=None, keepdims=False, return_sign=False):
"""Compute the log of the sum of exponentials of input elements.
Parameters
----------
a : array_like
Input array.
axis : None or int or tuple of ints, optional
Axis or axes over which the sum is taken. By default `axis` is None,
and all elements are summed.
.. versionadded:: 0.11.0
keepdims : bool, optional
If this is set to True, the axes which are reduced are left in the
result as dimensions with size one. With this option, the result
will broadcast correctly against the original array.
.. versionadded:: 0.15.0
b : array-like, optional
Scaling factor for exp(`a`) must be of the same shape as `a` or
broadcastable to `a`. These values may be negative in order to
implement subtraction.
.. versionadded:: 0.12.0
return_sign : bool, optional
If this is set to True, the result will be a pair containing sign
information; if False, results that are negative will be returned
as NaN. Default is False (no sign information).
.. versionadded:: 0.16.0
Returns
-------
res : ndarray
The result, ``np.log(np.sum(np.exp(a)))`` calculated in a numerically
more stable way. If `b` is given then ``np.log(np.sum(b*np.exp(a)))``
is returned.
sgn : ndarray
If return_sign is True, this will be an array of floating-point
numbers matching res and +1, 0, or -1 depending on the sign
of the result. If False, only one result is returned.
See Also
--------
numpy.logaddexp, numpy.logaddexp2
Notes
-----
NumPy has a logaddexp function which is very similar to `logsumexp`, but
only handles two arguments. `logaddexp.reduce` is similar to this
function, but may be less stable.
Examples
--------
>>> from scipy.special import logsumexp
>>> a = np.arange(10)
>>> np.log(np.sum(np.exp(a)))
9.4586297444267107
>>> logsumexp(a)
9.4586297444267107
With weights
>>> a = np.arange(10)
>>> b = np.arange(10, 0, -1)
>>> logsumexp(a, b=b)
9.9170178533034665
>>> np.log(np.sum(b*np.exp(a)))
9.9170178533034647
Returning a sign flag
>>> logsumexp([1,2],b=[1,-1],return_sign=True)
(1.5413248546129181, -1.0)
Notice that `logsumexp` does not directly support masked arrays. To use it
on a masked array, convert the mask into zero weights:
>>> a = np.ma.array([np.log(2), 2, np.log(3)],
... mask=[False, True, False])
>>> b = (~a.mask).astype(int)
>>> logsumexp(a.data, b=b), np.log(5)
1.6094379124341005, 1.6094379124341005
"""
a = _asarray_validated(a, check_finite=False)
if b is not None:
a, b = np.broadcast_arrays(a, b)
if np.any(b == 0):
a = a + 0. # promote to at least float
a[b == 0] = -np.inf
a_max = np.amax(a, axis=axis, keepdims=True)
if a_max.ndim > 0:
a_max[~np.isfinite(a_max)] = 0
elif not np.isfinite(a_max):
a_max = 0
if b is not None:
b = np.asarray(b)
tmp = b * np.exp(a - a_max)
else:
tmp = np.exp(a - a_max)
# suppress warnings about log of zero
with np.errstate(divide='ignore'):
s = np.sum(tmp, axis=axis, keepdims=keepdims)
if return_sign:
sgn = np.sign(s)
s *= sgn # /= makes more sense but we need zero -> zero
out = np.log(s)
if not keepdims:
a_max = np.squeeze(a_max, axis=axis)
out += a_max
if return_sign:
return out, sgn
else:
return out
def ipmt(rate, per, nper, pv, fv=0.0, when='end'):
"""
Compute the interest portion of a payment.
Parameters
----------
rate : scalar or array_like of shape(M, )
Rate of interest as decimal (not per cent) per period
per : scalar or array_like of shape(M, )
Interest paid against the loan changes during the life or the loan.
The `per` is the payment period to calculate the interest amount.
nper : scalar or array_like of shape(M, )
Number of compounding periods
pv : scalar or array_like of shape(M, )
Present value
fv : scalar or array_like of shape(M, ), optional
Future value
when : {{'begin', 1}, {'end', 0}}, {string, int}, optional
When payments are due ('begin' (1) or 'end' (0)).
Defaults to {'end', 0}.
Returns
-------
out : ndarray
Interest portion of payment. If all input is scalar, returns a scalar
float. If any input is array_like, returns interest payment for each
input element. If multiple inputs are array_like, they all must have
the same shape.
See Also
--------
ppmt, pmt, pv
Notes
-----
The total payment is made up of payment against principal plus interest.
``pmt = ppmt + ipmt``
Examples
--------
What is the amortization schedule for a 1 year loan of $2500 at
8.24% interest per year compounded monthly?
>>> principal = 2500.00
The 'per' variable represents the periods of the loan. Remember that
financial equations start the period count at 1!
>>> per = np.arange(1*12) + 1
>>> ipmt = np.ipmt(0.0824/12, per, 1*12, principal)
>>> ppmt = np.ppmt(0.0824/12, per, 1*12, principal)
Each element of the sum of the 'ipmt' and 'ppmt' arrays should equal
'pmt'.
>>> pmt = np.pmt(0.0824/12, 1*12, principal)
>>> np.allclose(ipmt + ppmt, pmt)
True
>>> fmt = '{0:2d} {1:8.2f} {2:8.2f} {3:8.2f}'
>>> for payment in per:
... index = payment - 1
... principal = principal + ppmt[index]
... print fmt.format(payment, ppmt[index], ipmt[index], principal)
1 -200.58 -17.17 2299.42
2 -201.96 -15.79 2097.46
3 -203.35 -14.40 1894.11
4 -204.74 -13.01 1689.37
5 -206.15 -11.60 1483.22
6 -207.56 -10.18 1275.66
7 -208.99 -8.76 1066.67
8 -210.42 -7.32 856.25
9 -211.87 -5.88 644.38
10 -213.32 -4.42 431.05
11 -214.79 -2.96 216.26
12 -216.26 -1.49 -0.00
>>> interestpd = np.sum(ipmt)
>>> np.round(interestpd, 2)
-112.98
"""
when = _convert_when(when)
rate, per, nper, pv, fv, when = np.broadcast_arrays(
rate, per, nper, pv, fv, when)
total_pmt = pmt(rate, nper, pv, fv, when)
ipmt = _rbl(rate, per, total_pmt, pv, when) * rate
try:
ipmt = np.where(when == 1, ipmt / (1 + rate), ipmt)
ipmt = np.where(np.logical_and(when == 1, per == 1), 0.0, ipmt)
except IndexError:
pass
return ipmt
def addEquations(self, op):
"""
Function to generate equations corresponding to all types of add/subtraction operations
Arguments:
op: (tf.op) representing addition or subtraction operations
"""
# We may have included the add equation with a prior matmul equation
if op in self.varMap:
return
# Get inputs and outputs
assert len(op.inputs) == 2
input1, input1_isVar = self.getValues(op.inputs[0].op)
input2, input2_isVar = self.getValues(op.inputs[1].op)
outputVars = self.makeNewVariables(op).flatten()
# Special case for BiasAdd with NCHW format. We need to add the bias along the channels dimension
if op.node_def.op == 'BiasAdd':
data_format = 'NHWC'
if 'data_format' in op.node_def.attr:
data_format = op.node_def.attr['data_format'].s.decode().upper(
)
if data_format == 'NCHW':
input2 = input2.reshape((1, len(input2), 1, 1))
# Broadcast and flatten. Assert that lengths are all the same
input1, input2 = np.broadcast_arrays(input1, input2)
input1 = input1.flatten()
input2 = input2.flatten()
assert len(input1) == len(input2)
assert len(outputVars) == len(input1)
# Signs for addition/subtraction
sgn1 = 1
sgn2 = 1
if op.node_def.op in ["Sub"]:
sgn2 = -1
# Create new equations depending on if the inputs are variables or constants
# At least one input must be a variable, otherwise this operation is a constant,
# which gets caught in makeGraphEquations.
assert input1_isVar or input2_isVar
# Always negate the scalar term because it changes sides in equation, from
# w1*x1+...wk*xk + b = x_out
# to
# w1*x1+...wk+xk - x_out = -b
if input1_isVar and input2_isVar:
for i in range(len(outputVars)):
e = MarabouUtils.Equation()
e.addAddend(sgn1, input1[i])
e.addAddend(sgn2, input2[i])
e.addAddend(-1, outputVars[i])
e.setScalar(0.0)
self.addEquation(e)
elif input1_isVar:
for i in range(len(outputVars)):
e = MarabouUtils.Equation()
e.addAddend(sgn1, input1[i])
e.addAddend(-1, outputVars[i])
e.setScalar(-sgn2 * input2[i])
self.addEquation(e)
else:
for i in range(len(outputVars)):
e = MarabouUtils.Equation()
e.addAddend(sgn2, input2[i])
e.addAddend(-1, outputVars[i])
e.setScalar(-sgn1 * input1[i])
self.addEquation(e)
def plot_diagram(self, pers_dgm, skew=True, ax=None, out_file=None):
""" Plot a persistence diagram.
Parameters
----------
pers_dgm : (-,2) numpy.ndarray
A persistence diagram.
skew : boolean
Flag indicating if diagram needs to first be converted to birth-persistence coordinates (default: True).
ax : matplotlib.Axes
Instance of a matplotlib.Axes object in which to plot (default: None, generates a new figure)
out_file : str
Path and file name including extension to save the figure (default: None, figure not saved).
Returns
-------
matplotlib.Axes
The matplotlib.Axes which contains the persistence diagram
"""
pers_dgm = np.copy(pers_dgm)
if skew:
pers_dgm[:, 1] = pers_dgm[:, 1] - pers_dgm[:, 0]
ylabel = 'persistence'
else:
ylabel = 'death'
# setup plot range
plot_buff_frac = 0.05
bmin = np.min((np.min(pers_dgm[:, 0]), np.min(self._bpnts)))
bmax = np.max((np.max(pers_dgm[:, 0]), np.max(self._bpnts)))
b_plot_buff = (bmax - bmin) * plot_buff_frac
bmin -= b_plot_buff
bmax += b_plot_buff
pmin = np.min((np.min(pers_dgm[:, 1]), np.min(self._ppnts)))
pmax = np.max((np.max(pers_dgm[:, 1]), np.max(self._ppnts)))
p_plot_buff = (pmax - pmin) * plot_buff_frac
pmin -= p_plot_buff
pmax += p_plot_buff
ax = ax or plt.gca()
ax.set_xlim(bmin, bmax)
ax.set_ylim(pmin, pmax)
# compute reasonable line width for pixel overlay (initially 1/50th of the width of a pixel)
linewidth = (1/50 * self.pixel_size) * 72 * plt.gcf().bbox_inches.width * ax.get_position().width / \
np.min((bmax - bmin, pmax - pmin))
# plot the persistence image grid
if skew:
hlines = np.column_stack(np.broadcast_arrays(self._bpnts[0], self._ppnts, self._bpnts[-1], self._ppnts))
vlines = np.column_stack(np.broadcast_arrays(self._bpnts, self._ppnts[0], self._bpnts, self._ppnts[-1]))
lines = np.concatenate([hlines, vlines]).reshape(-1, 2, 2)
line_collection = LineCollection(lines, color='black', linewidths=linewidth)
ax.add_collection(line_collection)
# plot persistence diagram
ax.scatter(pers_dgm[:, 0], pers_dgm[:, 1])
# plot diagonal if necessary
if not skew:
min_diag = np.min((np.min(ax.get_xlim()), np.min(ax.get_ylim())))
max_diag = np.min((np.max(ax.get_xlim()), np.max(ax.get_ylim())))
ax.plot([min_diag, max_diag], [min_diag, max_diag])
# fix and label axes
ax.set_aspect('equal')
ax.set_xlabel('birth')
ax.set_ylabel(ylabel)
# optionally save figure
if out_file:
plt.savefig(out_file, bbox_inches='tight')
return ax
def broadcast_to(arr, shape):
"Broadcast an array to a desired shape. Returns a view."
return np.broadcast_arrays(arr, np.empty(shape, dtype=np.bool))[0]
avg_elev_index = 66
elev_mod = modem.Model()
elev_mod.read_model_file(elev_model_fn)
avg_mod = modem.Model()
avg_mod.read_model_file(avg_model_fn)
data_obj = modem.Data()
data_obj.read_data_file(data_fn)
avg_elev = elev_mod.grid_z[avg_elev_index]
elev_res = np.zeros_like(elev_mod.res_model)
avg_north, avg_east = np.broadcast_arrays(avg_mod.grid_north[:, None],
avg_mod.grid_east[None, :])
elev_north, elev_east = np.broadcast_arrays(elev_mod.grid_north[:, None],
elev_mod.grid_east[None, :])
# interpolate the avg grid onto elevation model
# assuming mono lake is 0 elevation
for zz in range(elev_mod.grid_z.shape[0]):
try:
avg_zz = np.where(
avg_mod.grid_z >= elev_mod.grid_z[zz] - avg_elev)[0][0]
except IndexError:
avg_zz = -1
print "New depth={0:.2f}; elev depth={1:.2f}".format(
avg_mod.grid_z[avg_zz], elev_mod.grid_z[zz])
elev_res[:, :, zz] = avg_mod.res_model[:, :, avg_zz]
def subset(self, raster_data, **kwargs):
# It is possible our user has drawn a polygon where part of the
# shape is outside the dataset, intersect with the rasterdata
# shape to make sure we don't try to select/mask data that is
# outside the bounds of our dataset.
clipped = self.intersection(raster_data.shape)
# Polygon is completely outside the dataset, return whatever
# would have been returned by get_data()
if not bool(clipped):
ul = raster_data.index(self.bounds[0], self.bounds[1])
lr = raster_data.index(self.bounds[2], self.bounds[3])
window = self.get_data_window(ul[0], ul[1], lr[0], lr[1])
return raster_data.get_data(window=window, **kwargs)
ul = raster_data.index(clipped.bounds[0], clipped.bounds[1])
lr = raster_data.index(clipped.bounds[2], clipped.bounds[3])
window = self.get_data_window(ul[0], ul[1], lr[0], lr[1])
data = raster_data.get_data(window=window, **kwargs)
# out_shape must be determined from data's shape, get_data
# may have returned a bounding box of data that is smaller than
# the implicit shape of the window we passed. e.g. if the window
# is partially outside the extent of the raster data. Note that
# we index with negative numbers here because we may or may not
# have a time dimension.
num_bands = len(raster_data.band_indexes)
if num_bands > 1:
out_shape = data.shape[-3], data.shape[-2]
else:
out_shape = data.shape[-2], data.shape[-1]
coordinates = []
for lat, lon in clipped.exterior.coords:
x, y = raster_data.index(lat, lon)
coordinates.append((y - window[0][1], x - window[0][0]))
# Mask the final polygon
mask = rasterize([({
'type': 'Polygon',
'coordinates': [coordinates]
}, 0)],
out_shape=out_shape,
fill=1,
all_touched=True,
dtype=np.uint8)
# If we have more than one band, expand the mask so it includes
# A "channel" dimension (e.g. shape is now (lat, lon, channel))
if num_bands > 1:
mask = mask[..., np.newaxis] * np.ones(num_bands)
# Finally broadcast mask to data because data may be from a
# Raster data collection and include a time component
# (e.g. shape could be (time, lat, lon), or even
# (time, lat, lon, channels))
_, mask = np.broadcast_arrays(data, mask)
data[mask.astype(bool)] = raster_data.nodata
return np.ma.masked_equal(data, raster_data.nodata)
def _broadcast_to(array, shape):
if hasattr(numpy, 'broadcast_to'):
return numpy.broadcast_to(array, shape)
dummy = numpy.empty(shape, array.dtype)
return numpy.broadcast_arrays(array, dummy)[0]
def ndgrid(*args, **kwargs):
"""
Form tensorial grid for 1, 2, or 3 dimensions.
Returns as column vectors by default.
To return as matrix input:
ndgrid(..., vector=False)
The inputs can be a list or separate arguments.
e.g.::
a = np.array([1, 2, 3])
b = np.array([1, 2])
XY = ndgrid(a, b)
> [[1 1]
[2 1]
[3 1]
[1 2]
[2 2]
[3 2]]
X, Y = ndgrid(a, b, vector=False)
> X = [[1 1]
[2 2]
[3 3]]
> Y = [[1 2]
[1 2]
[1 2]]
"""
# Read the keyword arguments, and only accept a vector=True/False
vector = kwargs.pop('vector', True)
assert type(vector) == bool, "'vector' keyword must be a bool"
assert len(kwargs) == 0, "Only 'vector' keyword accepted"
# you can either pass a list [x1, x2, x3] or each seperately
if type(args[0]) == list:
xin = args[0]
else:
xin = args
# Each vector needs to be a numpy array
assert np.all([isinstance(x, np.ndarray)
for x in xin]), "All vectors must be numpy arrays."
if len(xin) == 1:
return xin[0]
elif len(xin) == 2:
XY = np.broadcast_arrays(mkvc(xin[1], 1), mkvc(xin[0], 2))
if vector:
X2, X1 = [mkvc(x) for x in XY]
return np.c_[X1, X2]
else:
return XY[1], XY[0]
elif len(xin) == 3:
XYZ = np.broadcast_arrays(mkvc(xin[2], 1), mkvc(xin[1], 2),
mkvc(xin[0], 3))
if vector:
X3, X2, X1 = [mkvc(x) for x in XYZ]
return np.c_[X1, X2, X3]
else:
return XYZ[2], XYZ[1], XYZ[0]
