def _xafsft(self, chi, group=None, rmax_out=10, **kws):
"returns "
for key, val in kws:
if key == 'kw':
key = 'kweight'
setattr(self, key, val)
self.make_karrays()
out = self.fftf(chi)
irmax = min(self.nfft / 2, int(1.01 + rmax_out / self.rstep))
group = set_xafsGroup(group, _larch=self._larch)
r = self.rstep * arange(irmax)
mag = sqrt(out.real**2 + out.imag**2)
group.kwin = self.kwin[:len(chi)]
group.r = r[:irmax]
group.chir = out[:irmax]
group.chir_mag = mag[:irmax]
group.chir_pha = complex_phase(out[:irmax])
group.chir_re = out.real[:irmax]
group.chir_im = out.imag[:irmax]
def _xafsft(self, chi, group=None, rmax_out=10, **kws):
"returns "
for key, val in kws:
if key == 'kw':
key = 'kweight'
setattr(self, key, val)
self.make_karrays()
out = self.fftf(chi)
irmax = min(self.nfft/2, int(1.01 + rmax_out/self.rstep))
group = set_xafsGroup(group, _larch=self._larch)
r = self.rstep * arange(irmax)
mag = sqrt(out.real**2 + out.imag**2)
group.kwin = self.kwin[:len(chi)]
group.r = r[:irmax]
group.chir = out[:irmax]
group.chir_mag = mag[:irmax]
group.chir_pha = complex_phase(out[:irmax])
group.chir_re = out.real[:irmax]
group.chir_im = out.imag[:irmax]
def xftf(k, chi=None, group=None, kmin=0, kmax=20, kweight=0,
dk=1, dk2=None, with_phase=False, window='kaiser', rmax_out=10,
nfft=2048, kstep=0.05, _larch=None, **kws):
"""
forward XAFS Fourier transform, from chi(k) to chi(R), using
common XAFS conventions.
Parameters:
-----------
k: 1-d array of photo-electron wavenumber in Ang^-1 or group
chi: 1-d array of chi
group: output Group
rmax_out: highest R for output data (10 Ang)
kweight: exponent for weighting spectra by k**kweight
kmin: starting k for FT Window
kmax: ending k for FT Window
dk: tapering parameter for FT Window
dk2: second tapering parameter for FT Window
window: name of window type
nfft: value to use for N_fft (2048).
kstep: value to use for delta_k (0.05 Ang^-1).
with_phase: output the phase as well as magnitude, real, imag [False]
Returns:
---------
None -- outputs are written to supplied group.
Notes:
-------
Arrays written to output group:
kwin window function Omega(k) (length of input chi(k)).
r uniform array of R, out to rmax_out.
chir complex array of chi(R).
chir_mag magnitude of chi(R).
chir_re real part of chi(R).
chir_im imaginary part of chi(R).
chir_pha phase of chi(R) if with_phase=True
(a noticable performance hit)
Supports First Argument Group convention (with group member names 'k' and 'chi')
"""
# allow kweight keyword == kw
if 'kw' in kws:
kweight = kws['kw']
k, chi, group = parse_group_args(k, members=('k', 'chi'),
defaults=(chi,), group=group,
fcn_name='xftf')
cchi, win = xftf_prep(k, chi, kmin=kmin, kmax=kmax, kweight=kweight,
dk=dk, dk2=dk2, nfft=nfft, kstep=kstep,
window=window, _larch=_larch)
out = xftf_fast(cchi*win, kstep=kstep, nfft=nfft)
rstep = pi/(kstep*nfft)
irmax = min(nfft/2, int(1.01 + rmax_out/rstep))
group = set_xafsGroup(group, _larch=_larch)
r = rstep * arange(irmax)
mag = sqrt(out.real**2 + out.imag**2)
group.kwin = win[:len(chi)]
group.r = r[:irmax]
group.chir = out[:irmax]
group.chir_mag = mag[:irmax]
group.chir_re = out.real[:irmax]
group.chir_im = out.imag[:irmax]
if with_phase:
group.chir_pha = complex_phase(out[:irmax])
def xftr(r, chir=None, group=None, rmin=0, rmax=20, with_phase=False,
dr=1, dr2=None, rw=0, window='kaiser', qmax_out=None,
nfft=2048, kstep=0.05, _larch=None, **kws):
"""
reverse XAFS Fourier transform, from chi(R) to chi(q).
calculate reverse XAFS Fourier transform
This assumes that chir_re and (optional chir_im are
on a uniform r-grid given by r.
Parameters:
------------
r: 1-d array of distance, or group.
chir: 1-d array of chi(R)
group: output Group
qmax_out: highest *k* for output data (30 Ang^-1)
rweight: exponent for weighting spectra by r^rweight (0)
rmin: starting *R* for FT Window
rmax: ending *R* for FT Window
dr: tapering parameter for FT Window
dr2: second tapering parameter for FT Window
window: name of window type
nfft: value to use for N_fft (2048).
kstep: value to use for delta_k (0.05).
with_phase: output the phase as well as magnitude, real, imag [False]
Returns:
---------
None -- outputs are written to supplied group.
Notes:
-------
Arrays written to output group:
rwin window Omega(R) (length of input chi(R)).
q uniform array of k, out to qmax_out.
chiq complex array of chi(k).
chiq_mag magnitude of chi(k).
chiq_re real part of chi(k).
chiq_im imaginary part of chi(k).
chiq_pha phase of chi(k) if with_phase=True
(a noticable performance hit)
Supports First Argument Group convention (with group member names 'r' and 'chir')
"""
if 'rweight' in kws:
rw = kws['rweight']
r, chir, group = parse_group_args(r, members=('r', 'chir'),
defaults=(chir,), group=group,
fcn_name='xftr')
rstep = r[1] - r[0]
kstep = pi/(rstep*nfft)
scale = 1.0
cchir = zeros(nfft, dtype='complex128')
r_ = rstep * arange(nfft, dtype='float64')
cchir[0:len(chir)] = chir
if chir.dtype == np.dtype('complex128'):
scale = 0.5
win = ftwindow(r_, xmin=rmin, xmax=rmax, dx=dr, dx2=dr2, window=window)
out = scale * xftr_fast( cchir*win * r_**rw, kstep=kstep, nfft=nfft)
if qmax_out is None: qmax_out = 30.0
q = linspace(0, qmax_out, int(1.05 + qmax_out/kstep))
nkpts = len(q)
group = set_xafsGroup(group, _larch=_larch)
group.q = q
mag = sqrt(out.real**2 + out.imag**2)
group.rwin = win[:len(chir)]
group.chiq = out[:nkpts]
group.chiq_mag = mag[:nkpts]
group.chiq_re = out.real[:nkpts]
group.chiq_im = out.imag[:nkpts]
if with_phase:
group.chiq_pha = complex_phase(out[:nkpts])
def xftf(k,
chi=None,
group=None,
kmin=0,
kmax=20,
kweight=0,
dk=1,
dk2=None,
with_phase=False,
window='kaiser',
rmax_out=10,
nfft=2048,
kstep=0.05,
_larch=None,
**kws):
"""
forward XAFS Fourier transform, from chi(k) to chi(R), using
common XAFS conventions.
Parameters:
-----------
k: 1-d array of photo-electron wavenumber in Ang^-1 or group
chi: 1-d array of chi
group: output Group
rmax_out: highest R for output data (10 Ang)
kweight: exponent for weighting spectra by k**kweight
kmin: starting k for FT Window
kmax: ending k for FT Window
dk: tapering parameter for FT Window
dk2: second tapering parameter for FT Window
window: name of window type
nfft: value to use for N_fft (2048).
kstep: value to use for delta_k (0.05 Ang^-1).
with_phase: output the phase as well as magnitude, real, imag [False]
Returns:
---------
None -- outputs are written to supplied group.
Notes:
-------
Arrays written to output group:
kwin window function Omega(k) (length of input chi(k)).
r uniform array of R, out to rmax_out.
chir complex array of chi(R).
chir_mag magnitude of chi(R).
chir_re real part of chi(R).
chir_im imaginary part of chi(R).
chir_pha phase of chi(R) if with_phase=True
(a noticable performance hit)
Supports First Argument Group convention (with group member names 'k' and 'chi')
"""
# allow kweight keyword == kw
if 'kw' in kws:
kweight = kws['kw']
k, chi, group = parse_group_args(k,
members=('k', 'chi'),
defaults=(chi, ),
group=group,
fcn_name='xftf')
cchi, win = xftf_prep(k,
chi,
kmin=kmin,
kmax=kmax,
kweight=kweight,
dk=dk,
dk2=dk2,
nfft=nfft,
kstep=kstep,
window=window,
_larch=_larch)
out = xftf_fast(cchi * win, kstep=kstep, nfft=nfft)
rstep = pi / (kstep * nfft)
irmax = min(nfft / 2, int(1.01 + rmax_out / rstep))
group = set_xafsGroup(group, _larch=_larch)
r = rstep * arange(irmax)
mag = sqrt(out.real**2 + out.imag**2)
group.kwin = win[:len(chi)]
group.r = r[:irmax]
group.chir = out[:irmax]
group.chir_mag = mag[:irmax]
group.chir_re = out.real[:irmax]
group.chir_im = out.imag[:irmax]
if with_phase:
group.chir_pha = complex_phase(out[:irmax])
def xftr(r,
chir=None,
group=None,
rmin=0,
rmax=20,
with_phase=False,
dr=1,
dr2=None,
rw=0,
window='kaiser',
qmax_out=None,
nfft=2048,
kstep=0.05,
_larch=None,
**kws):
"""
reverse XAFS Fourier transform, from chi(R) to chi(q).
calculate reverse XAFS Fourier transform
This assumes that chir_re and (optional chir_im are
on a uniform r-grid given by r.
Parameters:
------------
r: 1-d array of distance, or group.
chir: 1-d array of chi(R)
group: output Group
qmax_out: highest *k* for output data (30 Ang^-1)
rweight: exponent for weighting spectra by r^rweight (0)
rmin: starting *R* for FT Window
rmax: ending *R* for FT Window
dr: tapering parameter for FT Window
dr2: second tapering parameter for FT Window
window: name of window type
nfft: value to use for N_fft (2048).
kstep: value to use for delta_k (0.05).
with_phase: output the phase as well as magnitude, real, imag [False]
Returns:
---------
None -- outputs are written to supplied group.
Notes:
-------
Arrays written to output group:
rwin window Omega(R) (length of input chi(R)).
q uniform array of k, out to qmax_out.
chiq complex array of chi(k).
chiq_mag magnitude of chi(k).
chiq_re real part of chi(k).
chiq_im imaginary part of chi(k).
chiq_pha phase of chi(k) if with_phase=True
(a noticable performance hit)
Supports First Argument Group convention (with group member names 'r' and 'chir')
"""
if 'rweight' in kws:
rw = kws['rweight']
r, chir, group = parse_group_args(r,
members=('r', 'chir'),
defaults=(chir, ),
group=group,
fcn_name='xftr')
rstep = r[1] - r[0]
kstep = pi / (rstep * nfft)
scale = 1.0
cchir = zeros(nfft, dtype='complex128')
r_ = rstep * arange(nfft, dtype='float64')
cchir[0:len(chir)] = chir
if chir.dtype == np.dtype('complex128'):
scale = 0.5
win = ftwindow(r_, xmin=rmin, xmax=rmax, dx=dr, dx2=dr2, window=window)
out = scale * xftr_fast(cchir * win * r_**rw, kstep=kstep, nfft=nfft)
if qmax_out is None: qmax_out = 30.0
q = linspace(0, qmax_out, int(1.05 + qmax_out / kstep))
nkpts = len(q)
group = set_xafsGroup(group, _larch=_larch)
group.q = q
mag = sqrt(out.real**2 + out.imag**2)
group.rwin = win[:len(chir)]
group.chiq = out[:nkpts]
group.chiq_mag = mag[:nkpts]
group.chiq_re = out.real[:nkpts]
group.chiq_im = out.imag[:nkpts]
if with_phase:
group.chiq_pha = complex_phase(out[:nkpts])
