def healpix_interp_along_axis(indata, theta_phi=None, inloc_axis=None,
outloc_axis=None, axis=-1, kind='linear',
bounds_error=True, fill_value=NP.nan,
assume_sorted=False, nest=False):
"""
-----------------------------------------------------------------------------
Interpolate healpix data to specified angular locations (HEALPIX
interpolation) and along one other specified axis (usually frequency axis,
for instance) via SciPy interpolation. Wraps HEALPIX and SciPy interpolations
into one routine.
Inputs:
indata [numpy array] input data to be interpolated. Must be of shape
(nhpy x nax1 x nax2 x ...). Currently works only for
(nhpy x nax1). nhpy is a HEALPIX compatible npix
theta_phi [numpy array] spherical angle locations (in radians) at which
the healpix data is to be interpolated to at each of the other
given axes. It must be of size nang x 2 where nang is the number
of spherical angle locations, 2 denotes theta and phi. If set to
None (default), no healpix interpolation is performed
inloc_axis [numpy array] locations along the axis specified in axis (to be
interpolated with SciPy) in which indata is specified. It
should be of size nax1, nax2, ... or naxm. Currently it works
only if set to nax1
outloc_axis [numpy array] locations along the axis specified in axis to be
interpolated to with SciPy. The axis over which this
interpolation is to be done is specified in axis. It must be of
size nout. If this is set exactly equal to inloc_axis, no
interpolation along this axis is performed
axis [integer] axis along which SciPy interpolation is to be done.
If set to -1 (default), the interpolation happens over the last
axis. Since the first axis of indata is reserved for the healpix
pixels, axis must be set to 1 or above (upto indata.ndim-1).
kind [str or int] Specifies the kind of interpolation as a
string ('linear', 'nearest', 'zero', 'slinear', 'quadratic',
'cubic' where 'slinear', 'quadratic' and 'cubic' refer to a
spline interpolation of first, second or third order) or as an
integer specifying the order of the spline interpolator to use.
Default is 'linear'.
bounds_error
[bool, optional] If True, a ValueError is raised any time
interpolation is attempted on a value outside of the range of x
(where extrapolation is necessary). If False, out of bounds
values are assigned fill_value. By default, an error is raised.
fill_value [float] If provided, then this value will be used to fill in
for requested points outside of the data range. If not provided,
then the default is NaN.
assume_sorted
[bool] If False, values of inloc_axis can be in any order and
they are sorted first. If True, inloc_axis has to be an array
of monotonically increasing values.
nest [bool] if True, the is assumed to be in NESTED ordering.
Outputs:
HEALPIX interpolated and SciPy interpolated output. Will be of size
nang x ... x nout x ... x naxm. Currently returns an array of shape
nang x nout
-----------------------------------------------------------------------------
"""
try:
indata
except NameError:
raise NameError('input data not specified')
if not isinstance(indata, NP.ndarray):
raise TypeError('input data must be a numpy array')
if theta_phi is not None:
if not isinstance(theta_phi, NP.ndarray):
raise TypeError('output locations must be a numpy array')
if theta_phi.ndim != 2:
raise ValueError('Output locations must be a 2D array')
if axis == -1:
axis = indata.ndim - 1
if (axis < 1) or (axis >= indata.ndim):
raise ValueError('input axis out of range')
if theta_phi is not None:
intermediate_data_shape = list(indata.shape)
intermediate_data_shape[0] = theta_phi.shape[0]
intermediate_data_shape = tuple(intermediate_data_shape)
intermediate_data = NP.zeros(intermediate_data_shape, dtype=NP.float64)
for ax in range(1,indata.ndim):
for i in xrange(indata.shape[ax]):
intermediate_data[:,i] = HP.get_interp_val(indata[:,i], theta_phi[:,0], theta_phi[:,1], nest=nest)
else:
intermediate_data = NP.copy(indata)
if outloc_axis is not None:
if inloc_axis is not None:
outloc_axis = outloc_axis.flatten()
inloc_axis = inloc_axis.flatten()
eps = 1e-8
if (outloc_axis.size == inloc_axis.size) and (NP.abs(inloc_axis-outloc_axis).max() <= eps):
outdata = intermediate_data
else:
if kind == 'fft':
df_inp = NP.mean(NP.diff(inloc_axis))
df_out = NP.mean(NP.diff(outloc_axis))
ntau = df_inp / df_out * inloc_axis.size
ntau = NP.round(ntau).astype(int)
tau_inp = DSP.spectral_axis(inloc_axis.size, delx=df_inp, shift=True)
fftinp = NP.fft.fft(intermediate_data, axis=axis)
fftinp_shifted = NP.fft.fftshift(fftinp, axes=axis)
if fftinp.size % 2 == 0:
fftinp_shifted[:,0] = 0.0 # Blank out the N/2 element (0 element when FFT-shifted) for conjugate symmetry
npad = ntau - inloc_axis.size
if npad % 2 == 0:
npad_before = npad/2
npad_after = npad/2
else:
npad_before = npad/2 + 1
npad_after = npad/2
fftinp_shifted_padded = NP.pad(fftinp_shifted, [(0,0), (npad_before, npad_after)], mode='constant')
fftinp_padded = NP.fft.ifftshift(fftinp_shifted_padded, axes=axis)
ifftout = NP.fft.ifft(fftinp_padded, axis=axis) * (1.0 * ntau / inloc_axis.size)
eps_imag = 1e-10
if NP.any(NP.abs(ifftout.imag) > eps_imag):
raise ValueError('Significant imaginary component has been introduced unintentionally during the FFT based interpolation. Debug the code.')
else:
ifftout = ifftout.real
fout = DSP.spectral_axis(ntau, delx=tau_inp[1]-tau_inp[0], shift=True)
fout -= fout.min()
fout += inloc_axis.min()
ind_outloc, ind_fout, dfreq = LKP.find_1NN(fout.reshape(-1,1), outloc_axis.reshape(-1,1), distance_ULIM=0.5*(fout[1]-fout[0]), remove_oob=True)
outdata = ifftout[:,ind_fout]
# npad = 2 * (outloc_axis.size - inloc_axis.size)
# dt_inp = DSP.spectral_axis(2*inloc_axis.size, delx=inloc_axis[1]-inloc_axis[0], shift=True)
# dt_out = DSP.spectral_axis(2*outloc_axis.size, delx=outloc_axis[1]-outloc_axis[0], shift=True)
# fftinp = NP.fft.fft(NP.pad(intermediate_data, [(0,0), (0,inloc_axis.size)], mode='constant'), axis=axis) * (1.0 * outloc_axis.size / inloc_axis.size)
# fftinp = NP.fft.fftshift(fftinp, axes=axis)
# fftinp[0,0] = 0.0 # Blank out the N/2 element for conjugate symmetry
# fftout = NP.pad(fftinp, [(0,0), (npad/2, npad/2)], mode='constant')
# fftout = NP.fft.ifftshift(fftout, axes=axis)
# outdata = NP.fft.ifft(fftout, axis=axis)
# outdata = outdata[0,:outloc_axis.size]
else:
interp_func = interpolate.interp1d(inloc_axis, intermediate_data, axis=axis, kind=kind, bounds_error=bounds_error, fill_value=fill_value, assume_sorted=assume_sorted)
outdata = interp_func(outloc_axis)
else:
raise ValueError('input inloc_axis not specified')
else:
outdata = intermediate_data
return outdata
def healpix_interp_along_axis(indata, theta_phi=None, inloc_axis=None,
outloc_axis=None, axis=-1, kind='linear',
bounds_error=True, fill_value=NP.nan,
assume_sorted=False, nest=False):
"""
-----------------------------------------------------------------------------
Interpolate healpix data to specified angular locations (HEALPIX
interpolation) and along one other specified axis (usually frequency axis,
for instance) via SciPy interpolation. Wraps HEALPIX and SciPy interpolations
into one routine.
Inputs:
indata [numpy array] input data to be interpolated. Must be of shape
(nhpy x nax1 x nax2 x ...). Currently works only for
(nhpy x nax1). nhpy is a HEALPIX compatible npix
theta_phi [numpy array] spherical angle locations (in radians) at which
the healpix data is to be interpolated to at each of the other
given axes. It must be of size nang x 2 where nang is the number
of spherical angle locations, 2 denotes theta and phi. If set to
None (default), no healpix interpolation is performed
inloc_axis [numpy array] locations along the axis specified in axis (to be
interpolated with SciPy) in which indata is specified. It
should be of size nax1, nax2, ... or naxm. Currently it works
only if set to nax1
outloc_axis [numpy array] locations along the axis specified in axis to be
interpolated to with SciPy. The axis over which this
interpolation is to be done is specified in axis. It must be of
size nout. If this is set exactly equal to inloc_axis, no
interpolation along this axis is performed
axis [integer] axis along which SciPy interpolation is to be done.
If set to -1 (default), the interpolation happens over the last
axis. Since the first axis of indata is reserved for the healpix
pixels, axis must be set to 1 or above (upto indata.ndim-1).
kind [str or int] Specifies the kind of interpolation as a
string ('linear', 'nearest', 'zero', 'slinear', 'quadratic',
'cubic' where 'slinear', 'quadratic' and 'cubic' refer to a
spline interpolation of first, second or third order) or as an
integer specifying the order of the spline interpolator to use.
Default is 'linear'.
bounds_error
[bool, optional] If True, a ValueError is raised any time
interpolation is attempted on a value outside of the range of x
(where extrapolation is necessary). If False, out of bounds
values are assigned fill_value. By default, an error is raised.
fill_value [float] If provided, then this value will be used to fill in
for requested points outside of the data range. If not provided,
then the default is NaN.
assume_sorted
[bool] If False, values of x can be in any order and they are
sorted first. If True, x has to be an array of monotonically
increasing values.
nest [bool] if True, the is assumed to be in NESTED ordering.
Outputs:
HEALPIX interpolated and SciPy interpolated output. Will be of size
nang x ... x nout x ... x naxm. Currently returns an array of shape
nang x nout
-----------------------------------------------------------------------------
"""
try:
indata
except NameError:
raise NameError('input data not specified')
if not isinstance(indata, NP.ndarray):
raise TypeError('input data must be a numpy array')
if theta_phi is not None:
if not isinstance(theta_phi, NP.ndarray):
raise TypeError('output locations must be a numpy array')
if theta_phi.ndim != 2:
raise ValueError('Output locations must be a 2D array')
if axis == -1:
axis = indata.ndim - 1
if (axis < 1) or (axis >= indata.ndim):
raise ValueError('input axis out of range')
if theta_phi is not None:
intermediate_data_shape = list(indata.shape)
intermediate_data_shape[0] = theta_phi.shape[0]
intermediate_data_shape = tuple(intermediate_data_shape)
intermediate_data = NP.zeros(intermediate_data_shape, dtype=NP.float32)
for ax in range(1,indata.ndim):
for i in xrange(indata.shape[ax]):
intermediate_data[:,i] = HP.get_interp_val(indata[:,i], theta_phi[:,0], theta_phi[:,1], nest=nest)
else:
intermediate_data = NP.copy(indata)
if outloc_axis is not None:
if inloc_axis is not None:
outloc_axis = outloc_axis.flatten()
inloc_axis = inloc_axis.flatten()
eps = 1e-8
if (outloc_axis.size == inloc_axis.size) and (NP.abs(inloc_axis-outloc_axis).max() <= eps):
outdata = intermediate_data
else:
if kind == 'fft':
df_inp = NP.mean(NP.diff(inloc_axis))
df_out = NP.mean(NP.diff(outloc_axis))
ntau = df_inp / df_out * inloc_axis.size
ntau = NP.round(ntau).astype(int)
tau_inp = DSP.spectral_axis(inloc_axis.size, delx=df_inp, shift=True)
fftinp = NP.fft.fft(intermediate_data, axis=axis)
fftinp_shifted = NP.fft.fftshift(fftinp, axes=axis)
if fftinp.size % 2 == 0:
fftinp_shifted[:,0] = 0.0 # Blank out the N/2 element (0 element when FFT-shifted) for conjugate symmetry
npad = ntau - inloc_axis.size
if npad % 2 == 0:
npad_before = npad/2
npad_after = npad/2
else:
npad_before = npad/2 + 1
npad_after = npad/2
fftinp_shifted_padded = NP.pad(fftinp_shifted, [(0,0), (npad_before, npad_after)], mode='constant')
fftinp_padded = NP.fft.ifftshift(fftinp_shifted_padded, axes=axis)
ifftout = NP.fft.ifft(fftinp_padded, axis=axis) * (1.0 * ntau / inloc_axis.size)
eps_imag = 1e-10
if NP.any(NP.abs(ifftout.imag) > eps_imag):
raise ValueError('Significant imaginary component has been introduced unintentionally during the FFT based interpolation. Debug the code.')
else:
ifftout = ifftout.real
fout = DSP.spectral_axis(ntau, delx=tau_inp[1]-tau_inp[0], shift=True)
fout -= fout.min()
fout += inloc_axis.min()
ind_outloc, ind_fout, dfreq = LKP.find_1NN(fout.reshape(-1,1), outloc_axis.reshape(-1,1), distance_ULIM=0.5*(fout[1]-fout[0]), remove_oob=True)
outdata = ifftout[:,ind_fout]
# npad = 2 * (outloc_axis.size - inloc_axis.size)
# dt_inp = DSP.spectral_axis(2*inloc_axis.size, delx=inloc_axis[1]-inloc_axis[0], shift=True)
# dt_out = DSP.spectral_axis(2*outloc_axis.size, delx=outloc_axis[1]-outloc_axis[0], shift=True)
# fftinp = NP.fft.fft(NP.pad(intermediate_data, [(0,0), (0,inloc_axis.size)], mode='constant'), axis=axis) * (1.0 * outloc_axis.size / inloc_axis.size)
# fftinp = NP.fft.fftshift(fftinp, axes=axis)
# fftinp[0,0] = 0.0 # Blank out the N/2 element for conjugate symmetry
# fftout = NP.pad(fftinp, [(0,0), (npad/2, npad/2)], mode='constant')
# fftout = NP.fft.ifftshift(fftout, axes=axis)
# outdata = NP.fft.ifft(fftout, axis=axis)
# outdata = outdata[0,:outloc_axis.size]
else:
interp_func = interpolate.interp1d(inloc_axis, intermediate_data, axis=axis, kind=kind, bounds_error=bounds_error, fill_value=fill_value, assume_sorted=assume_sorted)
outdata = interp_func(outloc_axis)
else:
raise ValueError('input inloc_axis not specified')
else:
outdata = intermediate_data
return outdata
def generate_spectrum(self, frequency=None):
"""
-------------------------------------------------------------------------
Generate and return a spectrum from functional spectral parameters
Inputs:
frequency [scalar or numpy array] Frequencies at which the spectrum at
all object locations is to be created. Must be in same units
as the attribute frequency and values under key 'freq-ref'
of attribute spec_parms. If not provided (default=None), a
spectrum is generated for all the frequencies specified in
the attribute frequency and values under keys 'freq-ref' and
'z-width' of attribute spec_parms.
Outputs:
spectrum [numpy array] Spectrum of the sky model at the respective
sky locations. Has shape nobj x nfreq.
Power law calculation uses the convention,
spectrum = flux_offset + flux_scale * (freq/freq0)**spindex
Monotone places a delta function at the frequency channel closest to the
reference frequency if it lies inside the frequency range, otherwise
a zero spectrum is assigned.
Thus spectrum = flux_scale * delta(freq-freq0)
Random (currently only gaussian) places random fluxes in the spectrum
spectrum = flux_offset + flux_scale * random_normal(freq.size)
tanh spectrum is defined as (Bowman & Rogers 2010):
spectrum = flux_scale * sqrt((1+z)/10) * 0.5 * [tanh((z-zr)/dz) + 1]
where, flux_scale is typically 0.027 K, zr = reionization redshift
when x_i = 0.5, and dz = redshift width (dz ~ 1)
If the attribute spec_type is 'spectrum' the attribute spectrum is
returned without any modifications.
-------------------------------------------------------------------------
"""
if self.spec_type == 'func':
if frequency is not None:
if isinstance(frequency, (int,float,NP.ndarray)):
frequency = NP.asarray(frequency)
else:
raise ValueError('Input parameter frequency must be a scalar or a numpy array')
if NP.any(frequency <= 0.0):
raise ValueError('Input parameter frequency must contain positive values')
else:
frequency = NP.copy(self.frequency)
spectrum = NP.empty((self.location.shape[0], frequency.size))
spectrum.fill(NP.nan)
uniq_names, invind = NP.unique(self.spec_parms['name'], return_inverse=True)
if len(uniq_names) > 1:
counts, edges, bnum, ri = OPS.binned_statistic(invind, statistic='count', bins=range(len(uniq_names)))
else:
counts = len(invind)
ri = range(counts)
for i, name in enumerate(uniq_names):
if len(uniq_names) > 1:
indices = ri[ri[i]:ri[i+1]]
else:
indices = ri
if name == 'random':
spectrum[indices,:] = self.spec_parms['flux-offset'][indices].reshape(-1,1) + self.spec_parms['flux-scale'][indices].reshape(-1,1) * NP.random.randn(counts[i], frequency.size)
if name == 'monotone': # Needs serious testing
spectrum[indices,:] = 0.0
inpind, refind, dNN = LKP.find_1NN(frequency, self.spec_parms['freq-ref'][indices], distance=frequency[1]-frequency[0], remove_oob=True)
ind = indices[inpind]
ind2d = zip(ind, refind)
spectrum[zip(*ind2d)] = self.spec_parms['flux-scale'][ind]
if name == 'power-law':
spectrum[indices,:] = self.spec_parms['flux-offset'][indices].reshape(-1,1) + self.spec_parms['flux-scale'][indices].reshape(-1,1) * (frequency.reshape(1,-1)/self.spec_parms['freq-ref'][indices].reshape(-1,1))**self.spec_parms['power-law-index'][indices].reshape(-1,1)
if name == 'tanh':
z = CNST.rest_freq_HI/frequency.reshape(1,-1) - 1
zr = CNST.rest_freq_HI/self.spec_parms['freq-ref'][indices].reshape(-1,1) - 1
dz = self.spec_parms['z-width'][indices].reshape(-1,1)
amp = self.spec_parms['flux-scale'][indices].reshape(-1,1) * NP.sqrt((1+z)/10)
xh = 0.5 * (NP.tanh((z-zr)/dz) + 1)
spectrum[indices,:] = amp * xh
return spectrum
else:
return self.spectrum