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awacha/sastool | sastool/io/credo_saxsctrl/header.py | Header.date | def date(self) -> datetime.datetime:
"""Date of the experiment (start of exposure)"""
return self._data['Date'] - datetime.timedelta(0, float(self.exposuretime), 0) | python | def date(self) -> datetime.datetime:
"""Date of the experiment (start of exposure)"""
return self._data['Date'] - datetime.timedelta(0, float(self.exposuretime), 0) | [
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awacha/sastool | sastool/io/credo_saxsctrl/header.py | Header.flux | def flux(self) -> ErrorValue:
"""X-ray flux in photons/sec."""
try:
return ErrorValue(self._data['Flux'], self._data.setdefault('FluxError',0.0))
except KeyError:
return 1 / self.pixelsizex / self.pixelsizey / ErrorValue(self._data['NormFactor'],
self._data.setdefault('NormFactorError',0.0)) | python | def flux(self) -> ErrorValue:
"""X-ray flux in photons/sec."""
try:
return ErrorValue(self._data['Flux'], self._data.setdefault('FluxError',0.0))
except KeyError:
return 1 / self.pixelsizex / self.pixelsizey / ErrorValue(self._data['NormFactor'],
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awacha/sastool | sastool/misc/easylsq.py | nonlinear_leastsquares | def nonlinear_leastsquares(x: np.ndarray, y: np.ndarray, dy: np.ndarray, func: Callable, params_init: np.ndarray,
verbose: bool = False, **kwargs):
"""Perform a non-linear least squares fit, return the results as
ErrorValue() instances.
Inputs:
x: one-dimensional numpy array of the independent variable
y: one-dimensional numpy array of the dependent variable
dy: absolute error (square root of the variance) of the dependent
variable. Either a one-dimensional numpy array or None. In the array
case, if any of its elements is NaN, the whole array is treated as
NaN (= no weighting)
func: a callable with the signature
func(x,par1,par2,par3,...)
params_init: list or tuple of the first estimates of the
parameters par1, par2, par3 etc. to be fitted
`verbose`: if various messages useful for debugging should be printed on
stdout.
other optional keyword arguments will be passed to leastsq().
Outputs: par1, par2, par3, ... , statdict
par1, par2, par3, ...: fitted values of par1, par2, par3 etc
as instances of ErrorValue.
statdict: dictionary of various statistical parameters:
'DoF': Degrees of freedom
'Chi2': Chi-squared
'Chi2_reduced': Reduced Chi-squared
'R2': Coefficient of determination
'num_func_eval': number of function evaluations during fit.
'func_value': the function evaluated in the best fitting parameters
'message': status message from leastsq()
'error_flag': integer status flag from leastsq() ('ier')
'Covariance': covariance matrix (variances in the diagonal)
'Correlation_coeffs': Pearson's correlation coefficients (usually
denoted by 'r') in a matrix. The diagonal is unity.
Notes:
for the actual fitting, nlsq_fit() is used, which in turn delegates the
job to scipy.optimize.leastsq().
"""
newfunc, newparinit = hide_fixedparams(func, params_init)
p, dp, statdict = nlsq_fit(x, y, dy, newfunc, newparinit, verbose, **kwargs)
p, statdict['Covariance'] = resubstitute_fixedparams(p, params_init, statdict['Covariance'])
dp, statdict['Correlation_coeffs'] = resubstitute_fixedparams(dp, [type(p_)(0) for p_ in params_init], statdict['Correlation_coeffs'])
def convert(p_, dp_):
if isinstance(p_, FixedParameter) or isinstance(dp_, FixedParameter):
return p_
else:
return ErrorValue(p_, dp_)
return tuple([convert(p_, dp_) for (p_, dp_) in zip(p, dp)] + [statdict]) | python | def nonlinear_leastsquares(x: np.ndarray, y: np.ndarray, dy: np.ndarray, func: Callable, params_init: np.ndarray,
verbose: bool = False, **kwargs):
"""Perform a non-linear least squares fit, return the results as
ErrorValue() instances.
Inputs:
x: one-dimensional numpy array of the independent variable
y: one-dimensional numpy array of the dependent variable
dy: absolute error (square root of the variance) of the dependent
variable. Either a one-dimensional numpy array or None. In the array
case, if any of its elements is NaN, the whole array is treated as
NaN (= no weighting)
func: a callable with the signature
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params_init: list or tuple of the first estimates of the
parameters par1, par2, par3 etc. to be fitted
`verbose`: if various messages useful for debugging should be printed on
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other optional keyword arguments will be passed to leastsq().
Outputs: par1, par2, par3, ... , statdict
par1, par2, par3, ...: fitted values of par1, par2, par3 etc
as instances of ErrorValue.
statdict: dictionary of various statistical parameters:
'DoF': Degrees of freedom
'Chi2': Chi-squared
'Chi2_reduced': Reduced Chi-squared
'R2': Coefficient of determination
'num_func_eval': number of function evaluations during fit.
'func_value': the function evaluated in the best fitting parameters
'message': status message from leastsq()
'error_flag': integer status flag from leastsq() ('ier')
'Covariance': covariance matrix (variances in the diagonal)
'Correlation_coeffs': Pearson's correlation coefficients (usually
denoted by 'r') in a matrix. The diagonal is unity.
Notes:
for the actual fitting, nlsq_fit() is used, which in turn delegates the
job to scipy.optimize.leastsq().
"""
newfunc, newparinit = hide_fixedparams(func, params_init)
p, dp, statdict = nlsq_fit(x, y, dy, newfunc, newparinit, verbose, **kwargs)
p, statdict['Covariance'] = resubstitute_fixedparams(p, params_init, statdict['Covariance'])
dp, statdict['Correlation_coeffs'] = resubstitute_fixedparams(dp, [type(p_)(0) for p_ in params_init], statdict['Correlation_coeffs'])
def convert(p_, dp_):
if isinstance(p_, FixedParameter) or isinstance(dp_, FixedParameter):
return p_
else:
return ErrorValue(p_, dp_)
return tuple([convert(p_, dp_) for (p_, dp_) in zip(p, dp)] + [statdict]) | [
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params_init: list or tuple of the first estimates of the
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`verbose`: if various messages useful for debugging should be printed on
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other optional keyword arguments will be passed to leastsq().
Outputs: par1, par2, par3, ... , statdict
par1, par2, par3, ...: fitted values of par1, par2, par3 etc
as instances of ErrorValue.
statdict: dictionary of various statistical parameters:
'DoF': Degrees of freedom
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'Chi2_reduced': Reduced Chi-squared
'R2': Coefficient of determination
'num_func_eval': number of function evaluations during fit.
'func_value': the function evaluated in the best fitting parameters
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'error_flag': integer status flag from leastsq() ('ier')
'Covariance': covariance matrix (variances in the diagonal)
'Correlation_coeffs': Pearson's correlation coefficients (usually
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awacha/sastool | sastool/misc/easylsq.py | nonlinear_odr | def nonlinear_odr(x, y, dx, dy, func, params_init, **kwargs):
"""Perform a non-linear orthogonal distance regression, return the results as
ErrorValue() instances.
Inputs:
x: one-dimensional numpy array of the independent variable
y: one-dimensional numpy array of the dependent variable
dx: absolute error (square root of the variance) of the independent
variable. Either a one-dimensional numpy array or None. If None,
weighting is disabled. Non-finite (NaN or inf) elements signify
that the corresponding element in x is to be treated as fixed by
ODRPACK.
dy: absolute error (square root of the variance) of the dependent
variable. Either a one-dimensional numpy array or None. If None,
weighting is disabled.
func: a callable with the signature
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params_init: list or tuple of the first estimates of the
parameters par1, par2, par3 etc. to be fitted
other optional keyword arguments will be passed to leastsq().
Outputs: par1, par2, par3, ... , statdict
par1, par2, par3, ...: fitted values of par1, par2, par3 etc
as instances of ErrorValue.
statdict: dictionary of various statistical parameters:
'DoF': Degrees of freedom
'Chi2': Chi-squared
'Chi2_reduced': Reduced Chi-squared
'num_func_eval': number of function evaluations during fit.
'func_value': the function evaluated in the best fitting parameters
'message': status message from leastsq()
'error_flag': integer status flag from leastsq() ('ier')
'Covariance': covariance matrix (variances in the diagonal)
'Correlation_coeffs': Pearson's correlation coefficients (usually
denoted by 'r') in a matrix. The diagonal is unity.
Notes:
for the actual fitting, the module scipy.odr is used.
"""
odrmodel=odr.Model(lambda pars, x: func(x,*pars))
if dx is not None:
# treat non-finite values as fixed
xfixed=np.isfinite(dx)
else:
xfixed=None
odrdata=odr.RealData(x, y, sx=dx,sy=dy, fix=xfixed)
odrodr=odr.ODR(odrdata,odrmodel,params_init,ifixb=[not(isinstance(p,FixedParameter)) for p in params_init],
**kwargs)
odroutput=odrodr.run()
statdict=odroutput.__dict__.copy()
statdict['Covariance']=odroutput.cov_beta
statdict['Correlation_coeffs']=odroutput.cov_beta/np.outer(odroutput.sd_beta,odroutput.sd_beta)
statdict['DoF']=len(x)-len(odroutput.beta)
statdict['Chi2_reduced']=statdict['res_var']
statdict['func_value']=statdict['y']
statdict['Chi2']=statdict['sum_square']
def convert(p_, dp_, pi):
if isinstance(pi, FixedParameter):
return FixedParameter(p_)
else:
return ErrorValue(p_, dp_)
return tuple([convert(p_, dp_, pi) for (p_, dp_, pi) in zip(odroutput.beta, odroutput.sd_beta, params_init)] + [statdict]) | python | def nonlinear_odr(x, y, dx, dy, func, params_init, **kwargs):
"""Perform a non-linear orthogonal distance regression, return the results as
ErrorValue() instances.
Inputs:
x: one-dimensional numpy array of the independent variable
y: one-dimensional numpy array of the dependent variable
dx: absolute error (square root of the variance) of the independent
variable. Either a one-dimensional numpy array or None. If None,
weighting is disabled. Non-finite (NaN or inf) elements signify
that the corresponding element in x is to be treated as fixed by
ODRPACK.
dy: absolute error (square root of the variance) of the dependent
variable. Either a one-dimensional numpy array or None. If None,
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func: a callable with the signature
func(x,par1,par2,par3,...)
params_init: list or tuple of the first estimates of the
parameters par1, par2, par3 etc. to be fitted
other optional keyword arguments will be passed to leastsq().
Outputs: par1, par2, par3, ... , statdict
par1, par2, par3, ...: fitted values of par1, par2, par3 etc
as instances of ErrorValue.
statdict: dictionary of various statistical parameters:
'DoF': Degrees of freedom
'Chi2': Chi-squared
'Chi2_reduced': Reduced Chi-squared
'num_func_eval': number of function evaluations during fit.
'func_value': the function evaluated in the best fitting parameters
'message': status message from leastsq()
'error_flag': integer status flag from leastsq() ('ier')
'Covariance': covariance matrix (variances in the diagonal)
'Correlation_coeffs': Pearson's correlation coefficients (usually
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Notes:
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"""
odrmodel=odr.Model(lambda pars, x: func(x,*pars))
if dx is not None:
# treat non-finite values as fixed
xfixed=np.isfinite(dx)
else:
xfixed=None
odrdata=odr.RealData(x, y, sx=dx,sy=dy, fix=xfixed)
odrodr=odr.ODR(odrdata,odrmodel,params_init,ifixb=[not(isinstance(p,FixedParameter)) for p in params_init],
**kwargs)
odroutput=odrodr.run()
statdict=odroutput.__dict__.copy()
statdict['Covariance']=odroutput.cov_beta
statdict['Correlation_coeffs']=odroutput.cov_beta/np.outer(odroutput.sd_beta,odroutput.sd_beta)
statdict['DoF']=len(x)-len(odroutput.beta)
statdict['Chi2_reduced']=statdict['res_var']
statdict['func_value']=statdict['y']
statdict['Chi2']=statdict['sum_square']
def convert(p_, dp_, pi):
if isinstance(pi, FixedParameter):
return FixedParameter(p_)
else:
return ErrorValue(p_, dp_)
return tuple([convert(p_, dp_, pi) for (p_, dp_, pi) in zip(odroutput.beta, odroutput.sd_beta, params_init)] + [statdict]) | [
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statdict: dictionary of various statistical parameters:
'DoF': Degrees of freedom
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awacha/sastool | sastool/misc/easylsq.py | simultaneous_nonlinear_leastsquares | def simultaneous_nonlinear_leastsquares(xs, ys, dys, func, params_inits, verbose=False, **kwargs):
"""Do a simultaneous nonlinear least-squares fit and return the fitted
parameters as instances of ErrorValue.
Input:
------
`xs`: tuple of abscissa vectors (1d numpy ndarrays)
`ys`: tuple of ordinate vectors (1d numpy ndarrays)
`dys`: tuple of the errors of ordinate vectors (1d numpy ndarrays or Nones)
`func`: fitting function (the same for all the datasets)
`params_init`: tuples of *lists* or *tuples* (not numpy ndarrays!) of the
initial values of the parameters to be fitted. The special value `None`
signifies that the corresponding parameter is the same as in the
previous dataset. Of course, none of the parameters of the first dataset
can be None.
`verbose`: if various messages useful for debugging should be printed on
stdout.
additional keyword arguments get forwarded to nlsq_fit()
Output:
-------
`parset1, parset2 ...`: tuples of fitted parameters corresponding to curve1,
curve2, etc. Each tuple contains the values of the fitted parameters
as instances of ErrorValue, in the same order as they are in
`params_init`.
`statdict`: statistics dictionary. This is of the same form as in
`nlsq_fit`, except that func_value is a sequence of one-dimensional
np.ndarrays containing the best-fitting function values for each curve.
"""
p, dp, statdict = simultaneous_nlsq_fit(xs, ys, dys, func, params_inits,
verbose, **kwargs)
params = [[ErrorValue(p_, dp_) for (p_, dp_) in zip(pcurrent, dpcurrent)]
for (pcurrent, dpcurrent) in zip(p, dp)]
return tuple(params + [statdict]) | python | def simultaneous_nonlinear_leastsquares(xs, ys, dys, func, params_inits, verbose=False, **kwargs):
"""Do a simultaneous nonlinear least-squares fit and return the fitted
parameters as instances of ErrorValue.
Input:
------
`xs`: tuple of abscissa vectors (1d numpy ndarrays)
`ys`: tuple of ordinate vectors (1d numpy ndarrays)
`dys`: tuple of the errors of ordinate vectors (1d numpy ndarrays or Nones)
`func`: fitting function (the same for all the datasets)
`params_init`: tuples of *lists* or *tuples* (not numpy ndarrays!) of the
initial values of the parameters to be fitted. The special value `None`
signifies that the corresponding parameter is the same as in the
previous dataset. Of course, none of the parameters of the first dataset
can be None.
`verbose`: if various messages useful for debugging should be printed on
stdout.
additional keyword arguments get forwarded to nlsq_fit()
Output:
-------
`parset1, parset2 ...`: tuples of fitted parameters corresponding to curve1,
curve2, etc. Each tuple contains the values of the fitted parameters
as instances of ErrorValue, in the same order as they are in
`params_init`.
`statdict`: statistics dictionary. This is of the same form as in
`nlsq_fit`, except that func_value is a sequence of one-dimensional
np.ndarrays containing the best-fitting function values for each curve.
"""
p, dp, statdict = simultaneous_nlsq_fit(xs, ys, dys, func, params_inits,
verbose, **kwargs)
params = [[ErrorValue(p_, dp_) for (p_, dp_) in zip(pcurrent, dpcurrent)]
for (pcurrent, dpcurrent) in zip(p, dp)]
return tuple(params + [statdict]) | [
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Input:
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`xs`: tuple of abscissa vectors (1d numpy ndarrays)
`ys`: tuple of ordinate vectors (1d numpy ndarrays)
`dys`: tuple of the errors of ordinate vectors (1d numpy ndarrays or Nones)
`func`: fitting function (the same for all the datasets)
`params_init`: tuples of *lists* or *tuples* (not numpy ndarrays!) of the
initial values of the parameters to be fitted. The special value `None`
signifies that the corresponding parameter is the same as in the
previous dataset. Of course, none of the parameters of the first dataset
can be None.
`verbose`: if various messages useful for debugging should be printed on
stdout.
additional keyword arguments get forwarded to nlsq_fit()
Output:
-------
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curve2, etc. Each tuple contains the values of the fitted parameters
as instances of ErrorValue, in the same order as they are in
`params_init`.
`statdict`: statistics dictionary. This is of the same form as in
`nlsq_fit`, except that func_value is a sequence of one-dimensional
np.ndarrays containing the best-fitting function values for each curve. | [
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awacha/sastool | sastool/misc/easylsq.py | nlsq_fit | def nlsq_fit(x, y, dy, func, params_init, verbose=False, **kwargs):
"""Perform a non-linear least squares fit
Inputs:
x: one-dimensional numpy array of the independent variable
y: one-dimensional numpy array of the dependent variable
dy: absolute error (square root of the variance) of the dependent
variable. Either a one-dimensional numpy array or None. In the array
case, if any of its elements is NaN, the whole array is treated as
NaN (= no weighting)
func: a callable with the signature
func(x,par1,par2,par3,...)
params_init: list or tuple of the first estimates of the
parameters par1, par2, par3 etc. to be fitted
`verbose`: if various messages useful for debugging should be printed on
stdout.
other optional keyword arguments will be passed to leastsq().
Outputs: p, dp, statdict where
p: list of fitted values of par1, par2 etc.
dp: list of estimated errors
statdict: dictionary of various statistical parameters:
'DoF': Degrees of freedom
'Chi2': Chi-squared
'Chi2_reduced': Reduced Chi-squared
'R2': Coefficient of determination
'num_func_eval': number of function evaluations during fit.
'func_value': the function evaluated in the best fitting parameters
'message': status message from leastsq()
'error_flag': integer status flag from leastsq() ('ier')
'Covariance': covariance matrix (variances in the diagonal)
'Correlation_coeffs': Pearson's correlation coefficients (usually
denoted by 'r') in a matrix. The diagonal is unity.
Notes:
for the actual fitting, scipy.optimize.leastsq() is used.
"""
if verbose:
t0 = time.monotonic()
print("nlsq_fit starting.")
else:
t0 = 0
func_orig = func
params_init_orig = params_init
func, params_init = hide_fixedparams(func_orig, params_init_orig)
if (dy is None) or (dy == np.nan).sum() > 0 or (dy <= 0).sum() > 0:
if verbose:
print("nlsq_fit: no weighting")
dy = None
def objectivefunc(params, x, y, dy):
"""The target function for leastsq()."""
if dy is None:
return (func(x, *(params.tolist())) - y)
else:
return (func(x, *(params.tolist())) - y) / dy
# do the fitting
if verbose:
print("nlsq_fit: now doing the fitting...")
t1 = time.monotonic()
else:
t1 = 0
par, cov, infodict, mesg, ier = leastsq(objectivefunc,
np.array(params_init),
(x, y, dy), full_output=True,
**kwargs)
if verbose:
print("nlsq_fit: fitting done in %.2f seconds." % (time.monotonic() - t1))
print("nlsq_fit: status from scipy.optimize.leastsq(): %d (%s)" % (ier, mesg))
print("nlsq_fit: extracting statistics.")
# test if the covariance was singular (cov is None)
if cov is None:
cov = np.ones((len(par), len(par))) * np.nan # set it to a NaN matrix
# calculate the Pearson's R^2 parameter (coefficient of determination)
if dy is None:
sserr = np.sum(((func(x, *(par.tolist())) - y)) ** 2)
sstot = np.sum((y - np.mean(y)) ** 2)
else:
sserr = np.sum(((func(x, *(par.tolist())) - y) / dy) ** 2)
sstot = np.sum((y - np.mean(y)) ** 2 / dy ** 2)
r2 = 1 - sserr / sstot
# assemble the statistics dictionary
statdict = {'DoF' : len(x) - len(par), # degrees of freedom
'Chi2' : (infodict['fvec'] ** 2).sum(),
'R2' : r2,
'num_func_eval' : infodict['nfev'],
'func_value' : func(x, *(par.tolist())),
'message' : mesg,
'error_flag' : ier,
}
statdict['Chi2_reduced'] = statdict['Chi2'] / statdict['DoF']
statdict['Covariance'] = cov * statdict['Chi2_reduced']
par, statdict['Covariance'] = resubstitute_fixedparams(par, params_init_orig, statdict['Covariance'])
# calculate the estimated errors of the fit parameters
dpar = np.sqrt(statdict['Covariance'].diagonal())
# Pearson's correlation coefficients (usually 'r') in a matrix.
statdict['Correlation_coeffs'] = statdict['Covariance'] / np.outer(dpar,
dpar)
if verbose:
print("nlsq_fit: returning with results.")
print("nlsq_fit: total time: %.2f sec." % (time.monotonic() - t0))
return par, dpar, statdict | python | def nlsq_fit(x, y, dy, func, params_init, verbose=False, **kwargs):
"""Perform a non-linear least squares fit
Inputs:
x: one-dimensional numpy array of the independent variable
y: one-dimensional numpy array of the dependent variable
dy: absolute error (square root of the variance) of the dependent
variable. Either a one-dimensional numpy array or None. In the array
case, if any of its elements is NaN, the whole array is treated as
NaN (= no weighting)
func: a callable with the signature
func(x,par1,par2,par3,...)
params_init: list or tuple of the first estimates of the
parameters par1, par2, par3 etc. to be fitted
`verbose`: if various messages useful for debugging should be printed on
stdout.
other optional keyword arguments will be passed to leastsq().
Outputs: p, dp, statdict where
p: list of fitted values of par1, par2 etc.
dp: list of estimated errors
statdict: dictionary of various statistical parameters:
'DoF': Degrees of freedom
'Chi2': Chi-squared
'Chi2_reduced': Reduced Chi-squared
'R2': Coefficient of determination
'num_func_eval': number of function evaluations during fit.
'func_value': the function evaluated in the best fitting parameters
'message': status message from leastsq()
'error_flag': integer status flag from leastsq() ('ier')
'Covariance': covariance matrix (variances in the diagonal)
'Correlation_coeffs': Pearson's correlation coefficients (usually
denoted by 'r') in a matrix. The diagonal is unity.
Notes:
for the actual fitting, scipy.optimize.leastsq() is used.
"""
if verbose:
t0 = time.monotonic()
print("nlsq_fit starting.")
else:
t0 = 0
func_orig = func
params_init_orig = params_init
func, params_init = hide_fixedparams(func_orig, params_init_orig)
if (dy is None) or (dy == np.nan).sum() > 0 or (dy <= 0).sum() > 0:
if verbose:
print("nlsq_fit: no weighting")
dy = None
def objectivefunc(params, x, y, dy):
"""The target function for leastsq()."""
if dy is None:
return (func(x, *(params.tolist())) - y)
else:
return (func(x, *(params.tolist())) - y) / dy
# do the fitting
if verbose:
print("nlsq_fit: now doing the fitting...")
t1 = time.monotonic()
else:
t1 = 0
par, cov, infodict, mesg, ier = leastsq(objectivefunc,
np.array(params_init),
(x, y, dy), full_output=True,
**kwargs)
if verbose:
print("nlsq_fit: fitting done in %.2f seconds." % (time.monotonic() - t1))
print("nlsq_fit: status from scipy.optimize.leastsq(): %d (%s)" % (ier, mesg))
print("nlsq_fit: extracting statistics.")
# test if the covariance was singular (cov is None)
if cov is None:
cov = np.ones((len(par), len(par))) * np.nan # set it to a NaN matrix
# calculate the Pearson's R^2 parameter (coefficient of determination)
if dy is None:
sserr = np.sum(((func(x, *(par.tolist())) - y)) ** 2)
sstot = np.sum((y - np.mean(y)) ** 2)
else:
sserr = np.sum(((func(x, *(par.tolist())) - y) / dy) ** 2)
sstot = np.sum((y - np.mean(y)) ** 2 / dy ** 2)
r2 = 1 - sserr / sstot
# assemble the statistics dictionary
statdict = {'DoF' : len(x) - len(par), # degrees of freedom
'Chi2' : (infodict['fvec'] ** 2).sum(),
'R2' : r2,
'num_func_eval' : infodict['nfev'],
'func_value' : func(x, *(par.tolist())),
'message' : mesg,
'error_flag' : ier,
}
statdict['Chi2_reduced'] = statdict['Chi2'] / statdict['DoF']
statdict['Covariance'] = cov * statdict['Chi2_reduced']
par, statdict['Covariance'] = resubstitute_fixedparams(par, params_init_orig, statdict['Covariance'])
# calculate the estimated errors of the fit parameters
dpar = np.sqrt(statdict['Covariance'].diagonal())
# Pearson's correlation coefficients (usually 'r') in a matrix.
statdict['Correlation_coeffs'] = statdict['Covariance'] / np.outer(dpar,
dpar)
if verbose:
print("nlsq_fit: returning with results.")
print("nlsq_fit: total time: %.2f sec." % (time.monotonic() - t0))
return par, dpar, statdict | [
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Inputs:
x: one-dimensional numpy array of the independent variable
y: one-dimensional numpy array of the dependent variable
dy: absolute error (square root of the variance) of the dependent
variable. Either a one-dimensional numpy array or None. In the array
case, if any of its elements is NaN, the whole array is treated as
NaN (= no weighting)
func: a callable with the signature
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params_init: list or tuple of the first estimates of the
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`verbose`: if various messages useful for debugging should be printed on
stdout.
other optional keyword arguments will be passed to leastsq().
Outputs: p, dp, statdict where
p: list of fitted values of par1, par2 etc.
dp: list of estimated errors
statdict: dictionary of various statistical parameters:
'DoF': Degrees of freedom
'Chi2': Chi-squared
'Chi2_reduced': Reduced Chi-squared
'R2': Coefficient of determination
'num_func_eval': number of function evaluations during fit.
'func_value': the function evaluated in the best fitting parameters
'message': status message from leastsq()
'error_flag': integer status flag from leastsq() ('ier')
'Covariance': covariance matrix (variances in the diagonal)
'Correlation_coeffs': Pearson's correlation coefficients (usually
denoted by 'r') in a matrix. The diagonal is unity.
Notes:
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awacha/sastool | sastool/misc/easylsq.py | simultaneous_nlsq_fit | def simultaneous_nlsq_fit(xs, ys, dys, func, params_inits, verbose=False,
**kwargs):
"""Do a simultaneous nonlinear least-squares fit
Input:
------
`xs`: tuple of abscissa vectors (1d numpy ndarrays)
`ys`: tuple of ordinate vectors (1d numpy ndarrays)
`dys`: tuple of the errors of ordinate vectors (1d numpy ndarrays or Nones)
`func`: fitting function (the same for all the datasets)
`params_init`: tuples of *lists* or *tuples* (not numpy ndarrays!) of the
initial values of the parameters to be fitted. The special value `None`
signifies that the corresponding parameter is the same as in the
previous dataset. Of course, none of the parameters of the first dataset
can be None.
`verbose`: if various messages useful for debugging should be printed on
stdout.
additional keyword arguments get forwarded to nlsq_fit()
Output:
-------
`p`: tuple of a list of fitted parameters
`dp`: tuple of a list of errors of the fitted parameters
`statdict`: statistics dictionary. This is of the same form as in
`nlsq_fit` except that func_value is a sequence of one-dimensional
np.ndarrays containing the best-fitting function values for each curve.
"""
if not isinstance(xs, collections.Sequence) or \
not isinstance(ys, collections.Sequence) or \
not isinstance(dys, collections.Sequence) or \
not isinstance(params_inits, collections.Sequence):
raise ValueError('Parameters `xs`, `ys`, `dys` and `params_inits` should be tuples or lists.')
Ndata = len(xs)
if len(ys) != Ndata or len(dys) != Ndata or len(params_inits) != Ndata:
raise ValueError('Parameters `xs`, `ys`, `dys` and `params_inits` should have the same length.')
if not all([isinstance(x, collections.Sequence) for x in params_inits]):
raise ValueError('Elements of `params_inits` should be tuples or Python lists.')
Ns = set([len(x) for x in params_inits])
if len(Ns) != 1:
raise ValueError('Elements of `params_inits` should have the same length.')
Npar = Ns.pop()
for i in range(Ndata):
if dys[i] is None:
dys[i] = np.ones(len(xs[i]), np.double) * np.nan
# concatenate the x, y and dy vectors
xcat = np.concatenate(xs)
ycat = np.concatenate(ys)
dycat = np.concatenate(dys)
# find the start and end indices for each dataset in the concatenated datasets.
lens = [len(x) for x in xs]
starts = [int(sum(lens[:i])) for i in range(len(lens))]
ends = [int(sum(lens[:i + 1])) for i in range(len(lens))]
# flatten the initial parameter list. A single list is needed, where the
# constrained parameters occur only once. Of course, we have to do some
# bookkeeping to be able to find the needed parameters for each sub-range
# later during the fit.
paramcat = [] # this will be the concatenated list of parameters
param_indices = [] # this will have the same structure as params_inits (i.e.
# a tuple of tuples of ints). Each tuple corresponds to a dataset.
# Each integer number in each tuple holds
# the index of the corresponding fit parameter in the
# concatenated parameter list.
for j in range(Ndata): # for each dataset
param_indices.append([])
jorig = j
for i in range(Npar):
j = jorig
while params_inits[j][i] is None and (j >= 0):
j = j - 1
if j < 0:
raise ValueError('None of the parameters in the very first dataset should be `None`.')
if jorig == j: # not constrained parameter
paramcat.append(params_inits[j][i])
param_indices[jorig].append(len(paramcat) - 1)
else:
param_indices[jorig].append(param_indices[j][i])
if verbose:
print("Number of datasets for simultaneous fitting:", Ndata)
print("Total number of data points:", len(xcat))
print("Number of parameters in each dataset:", Npar)
print("Total number of parameters:", Ndata * Npar)
print("Number of independent parameters:", len(paramcat))
# the flattened function
def func_flat(x, *params):
y = []
for j in range(Ndata):
if verbose > 1:
print("Simultaneous fitting: evaluating function for dataset #", j, "/", Ndata)
pars = [params[i] for i in param_indices[j]]
y.append(func(x[starts[j]:ends[j]], *pars))
return np.concatenate(tuple(y))
# Now we reduced the problem to a single least-squares fit. Carry it out and
# interpret the results.
pflat, dpflat, statdictflat = nlsq_fit(xcat, ycat, dycat, func_flat, paramcat, verbose, **kwargs)
for n in ['func_value', 'R2', 'Chi2', 'Chi2_reduced', 'DoF', 'Covariance', 'Correlation_coeffs']:
statdictflat[n + '_global'] = statdictflat[n]
statdictflat[n] = []
p = []
dp = []
for j in range(Ndata): # unpack the results
p.append([pflat[i] for i in param_indices[j]])
dp.append([dpflat[i] for i in param_indices[j]])
statdictflat['func_value'].append(statdictflat['func_value_global'][starts[j]:ends[j]])
if np.isfinite(dys[j]).all():
statdictflat['Chi2'].append((((statdictflat['func_value'][-1] - ys[j]) / dys[j]) ** 2).sum())
sstot = np.sum((ys[j] - np.mean(ys[j])) ** 2 / dys[j] ** 2)
else:
statdictflat['Chi2'].append(((statdictflat['func_value'][-1] - ys[j]) ** 2).sum())
sstot = np.sum((ys[j] - np.mean(ys[j])) ** 2)
sserr = statdictflat['Chi2'][-1]
statdictflat['R2'].append(1 - sserr / sstot)
statdictflat['DoF'].append(len(xs[j] - len(p[-1])))
statdictflat['Covariance'].append(slice_covarmatrix(statdictflat['Covariance_global'], param_indices[j]))
statdictflat['Correlation_coeffs'].append(slice_covarmatrix(statdictflat['Correlation_coeffs_global'], param_indices[j]))
statdictflat['Chi2_reduced'].append(statdictflat['Chi2'][-1] / statdictflat['DoF'][-1])
return p, dp, statdictflat | python | def simultaneous_nlsq_fit(xs, ys, dys, func, params_inits, verbose=False,
**kwargs):
"""Do a simultaneous nonlinear least-squares fit
Input:
------
`xs`: tuple of abscissa vectors (1d numpy ndarrays)
`ys`: tuple of ordinate vectors (1d numpy ndarrays)
`dys`: tuple of the errors of ordinate vectors (1d numpy ndarrays or Nones)
`func`: fitting function (the same for all the datasets)
`params_init`: tuples of *lists* or *tuples* (not numpy ndarrays!) of the
initial values of the parameters to be fitted. The special value `None`
signifies that the corresponding parameter is the same as in the
previous dataset. Of course, none of the parameters of the first dataset
can be None.
`verbose`: if various messages useful for debugging should be printed on
stdout.
additional keyword arguments get forwarded to nlsq_fit()
Output:
-------
`p`: tuple of a list of fitted parameters
`dp`: tuple of a list of errors of the fitted parameters
`statdict`: statistics dictionary. This is of the same form as in
`nlsq_fit` except that func_value is a sequence of one-dimensional
np.ndarrays containing the best-fitting function values for each curve.
"""
if not isinstance(xs, collections.Sequence) or \
not isinstance(ys, collections.Sequence) or \
not isinstance(dys, collections.Sequence) or \
not isinstance(params_inits, collections.Sequence):
raise ValueError('Parameters `xs`, `ys`, `dys` and `params_inits` should be tuples or lists.')
Ndata = len(xs)
if len(ys) != Ndata or len(dys) != Ndata or len(params_inits) != Ndata:
raise ValueError('Parameters `xs`, `ys`, `dys` and `params_inits` should have the same length.')
if not all([isinstance(x, collections.Sequence) for x in params_inits]):
raise ValueError('Elements of `params_inits` should be tuples or Python lists.')
Ns = set([len(x) for x in params_inits])
if len(Ns) != 1:
raise ValueError('Elements of `params_inits` should have the same length.')
Npar = Ns.pop()
for i in range(Ndata):
if dys[i] is None:
dys[i] = np.ones(len(xs[i]), np.double) * np.nan
# concatenate the x, y and dy vectors
xcat = np.concatenate(xs)
ycat = np.concatenate(ys)
dycat = np.concatenate(dys)
# find the start and end indices for each dataset in the concatenated datasets.
lens = [len(x) for x in xs]
starts = [int(sum(lens[:i])) for i in range(len(lens))]
ends = [int(sum(lens[:i + 1])) for i in range(len(lens))]
# flatten the initial parameter list. A single list is needed, where the
# constrained parameters occur only once. Of course, we have to do some
# bookkeeping to be able to find the needed parameters for each sub-range
# later during the fit.
paramcat = [] # this will be the concatenated list of parameters
param_indices = [] # this will have the same structure as params_inits (i.e.
# a tuple of tuples of ints). Each tuple corresponds to a dataset.
# Each integer number in each tuple holds
# the index of the corresponding fit parameter in the
# concatenated parameter list.
for j in range(Ndata): # for each dataset
param_indices.append([])
jorig = j
for i in range(Npar):
j = jorig
while params_inits[j][i] is None and (j >= 0):
j = j - 1
if j < 0:
raise ValueError('None of the parameters in the very first dataset should be `None`.')
if jorig == j: # not constrained parameter
paramcat.append(params_inits[j][i])
param_indices[jorig].append(len(paramcat) - 1)
else:
param_indices[jorig].append(param_indices[j][i])
if verbose:
print("Number of datasets for simultaneous fitting:", Ndata)
print("Total number of data points:", len(xcat))
print("Number of parameters in each dataset:", Npar)
print("Total number of parameters:", Ndata * Npar)
print("Number of independent parameters:", len(paramcat))
# the flattened function
def func_flat(x, *params):
y = []
for j in range(Ndata):
if verbose > 1:
print("Simultaneous fitting: evaluating function for dataset #", j, "/", Ndata)
pars = [params[i] for i in param_indices[j]]
y.append(func(x[starts[j]:ends[j]], *pars))
return np.concatenate(tuple(y))
# Now we reduced the problem to a single least-squares fit. Carry it out and
# interpret the results.
pflat, dpflat, statdictflat = nlsq_fit(xcat, ycat, dycat, func_flat, paramcat, verbose, **kwargs)
for n in ['func_value', 'R2', 'Chi2', 'Chi2_reduced', 'DoF', 'Covariance', 'Correlation_coeffs']:
statdictflat[n + '_global'] = statdictflat[n]
statdictflat[n] = []
p = []
dp = []
for j in range(Ndata): # unpack the results
p.append([pflat[i] for i in param_indices[j]])
dp.append([dpflat[i] for i in param_indices[j]])
statdictflat['func_value'].append(statdictflat['func_value_global'][starts[j]:ends[j]])
if np.isfinite(dys[j]).all():
statdictflat['Chi2'].append((((statdictflat['func_value'][-1] - ys[j]) / dys[j]) ** 2).sum())
sstot = np.sum((ys[j] - np.mean(ys[j])) ** 2 / dys[j] ** 2)
else:
statdictflat['Chi2'].append(((statdictflat['func_value'][-1] - ys[j]) ** 2).sum())
sstot = np.sum((ys[j] - np.mean(ys[j])) ** 2)
sserr = statdictflat['Chi2'][-1]
statdictflat['R2'].append(1 - sserr / sstot)
statdictflat['DoF'].append(len(xs[j] - len(p[-1])))
statdictflat['Covariance'].append(slice_covarmatrix(statdictflat['Covariance_global'], param_indices[j]))
statdictflat['Correlation_coeffs'].append(slice_covarmatrix(statdictflat['Correlation_coeffs_global'], param_indices[j]))
statdictflat['Chi2_reduced'].append(statdictflat['Chi2'][-1] / statdictflat['DoF'][-1])
return p, dp, statdictflat | [
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] | Do a simultaneous nonlinear least-squares fit
Input:
------
`xs`: tuple of abscissa vectors (1d numpy ndarrays)
`ys`: tuple of ordinate vectors (1d numpy ndarrays)
`dys`: tuple of the errors of ordinate vectors (1d numpy ndarrays or Nones)
`func`: fitting function (the same for all the datasets)
`params_init`: tuples of *lists* or *tuples* (not numpy ndarrays!) of the
initial values of the parameters to be fitted. The special value `None`
signifies that the corresponding parameter is the same as in the
previous dataset. Of course, none of the parameters of the first dataset
can be None.
`verbose`: if various messages useful for debugging should be printed on
stdout.
additional keyword arguments get forwarded to nlsq_fit()
Output:
-------
`p`: tuple of a list of fitted parameters
`dp`: tuple of a list of errors of the fitted parameters
`statdict`: statistics dictionary. This is of the same form as in
`nlsq_fit` except that func_value is a sequence of one-dimensional
np.ndarrays containing the best-fitting function values for each curve. | [
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awacha/sastool | sastool/misc/errorvalue.py | ErrorValue.tostring | def tostring(self: 'ErrorValue', extra_digits: int = 0, plusminus: str = ' +/- ', fmt: str = None) -> str:
"""Make a string representation of the value and its uncertainty.
Inputs:
-------
``extra_digits``: integer
how many extra digits should be shown (plus or minus, zero means
that the number of digits should be defined by the magnitude of
the uncertainty).
``plusminus``: string
the character sequence to be inserted in place of '+/-'
including delimiting whitespace.
``fmt``: string or None
how to format the output. Currently only strings ending in 'tex'
are supported, which render ascii-exponentials (i.e. 3.1415e-2)
into a format which is more appropriate to TeX.
Outputs:
--------
the string representation.
"""
if isinstance(fmt, str) and fmt.lower().endswith('tex'):
return re.subn('(\d*)(\.(\d)*)?[eE]([+-]?\d+)',
lambda m: (r'$%s%s\cdot 10^{%s}$' % (m.group(1), m.group(2), m.group(4))).replace('None',
''),
self.tostring(extra_digits=extra_digits, plusminus=plusminus, fmt=None))[0]
if isinstance(self.val, numbers.Real):
try:
Ndigits = -int(math.floor(math.log10(self.err))) + extra_digits
except (OverflowError, ValueError):
return str(self.val) + plusminus + str(self.err)
else:
return str(round(self.val, Ndigits)) + plusminus + str(round(self.err, Ndigits))
return str(self.val) + ' +/- ' + str(self.err) | python | def tostring(self: 'ErrorValue', extra_digits: int = 0, plusminus: str = ' +/- ', fmt: str = None) -> str:
"""Make a string representation of the value and its uncertainty.
Inputs:
-------
``extra_digits``: integer
how many extra digits should be shown (plus or minus, zero means
that the number of digits should be defined by the magnitude of
the uncertainty).
``plusminus``: string
the character sequence to be inserted in place of '+/-'
including delimiting whitespace.
``fmt``: string or None
how to format the output. Currently only strings ending in 'tex'
are supported, which render ascii-exponentials (i.e. 3.1415e-2)
into a format which is more appropriate to TeX.
Outputs:
--------
the string representation.
"""
if isinstance(fmt, str) and fmt.lower().endswith('tex'):
return re.subn('(\d*)(\.(\d)*)?[eE]([+-]?\d+)',
lambda m: (r'$%s%s\cdot 10^{%s}$' % (m.group(1), m.group(2), m.group(4))).replace('None',
''),
self.tostring(extra_digits=extra_digits, plusminus=plusminus, fmt=None))[0]
if isinstance(self.val, numbers.Real):
try:
Ndigits = -int(math.floor(math.log10(self.err))) + extra_digits
except (OverflowError, ValueError):
return str(self.val) + plusminus + str(self.err)
else:
return str(round(self.val, Ndigits)) + plusminus + str(round(self.err, Ndigits))
return str(self.val) + ' +/- ' + str(self.err) | [
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``extra_digits``: integer
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``plusminus``: string
the character sequence to be inserted in place of '+/-'
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``fmt``: string or None
how to format the output. Currently only strings ending in 'tex'
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--------
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awacha/sastool | sastool/misc/errorvalue.py | ErrorValue.random | def random(self: 'ErrorValue') -> np.ndarray:
"""Sample a random number (array) of the distribution defined by
mean=`self.val` and variance=`self.err`^2.
"""
if isinstance(self.val, np.ndarray):
# IGNORE:E1103
return np.random.randn(self.val.shape) * self.err + self.val
else:
return np.random.randn() * self.err + self.val | python | def random(self: 'ErrorValue') -> np.ndarray:
"""Sample a random number (array) of the distribution defined by
mean=`self.val` and variance=`self.err`^2.
"""
if isinstance(self.val, np.ndarray):
# IGNORE:E1103
return np.random.randn(self.val.shape) * self.err + self.val
else:
return np.random.randn() * self.err + self.val | [
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awacha/sastool | sastool/misc/errorvalue.py | ErrorValue.evalfunc | def evalfunc(cls, func, *args, **kwargs):
"""Evaluate a function with error propagation.
Inputs:
-------
``func``: callable
this is the function to be evaluated. Should return either a
number or a np.ndarray.
``*args``: other positional arguments of func. Arguments which are
not instances of `ErrorValue` are taken as constants.
keyword arguments supported:
``NMC``: number of Monte-Carlo steps. If not defined, defaults
to 1000
``exceptions_to_retry``: list of exception types to ignore:
if one of these is raised the given MC step is repeated once
again. Notice that this might induce an infinite loop!
The exception types in this list should be subclasses of
``Exception``.
``exceptions_to_skip``: list of exception types to skip: if
one of these is raised the given MC step is skipped, never
to be repeated. The exception types in this list should be
subclasses of ``Exception``.
Output:
-------
``result``: an `ErrorValue` with the result. The error is estimated
via a Monte-Carlo approach to Gaussian error propagation.
"""
def do_random(x):
if isinstance(x, cls):
return x.random()
else:
return x
if 'NMC' not in kwargs:
kwargs['NMC'] = 1000
if 'exceptions_to_skip' not in kwargs:
kwargs['exceptions_to_skip'] = []
if 'exceptions_to_repeat' not in kwargs:
kwargs['exceptions_to_repeat'] = []
meanvalue = func(*args)
# this way we get either a number or a np.array
stdcollector = meanvalue * 0
mciters = 0
while mciters < kwargs['NMC']:
try:
# IGNORE:W0142
stdcollector += (func(*[do_random(a)
for a in args]) - meanvalue) ** 2
mciters += 1
except Exception as e: # IGNORE:W0703
if any(isinstance(e, etype) for etype in kwargs['exceptions_to_skip']):
kwargs['NMC'] -= 1
elif any(isinstance(e, etype) for etype in kwargs['exceptions_to_repeat']):
pass
else:
raise
return cls(meanvalue, stdcollector ** 0.5 / (kwargs['NMC'] - 1)) | python | def evalfunc(cls, func, *args, **kwargs):
"""Evaluate a function with error propagation.
Inputs:
-------
``func``: callable
this is the function to be evaluated. Should return either a
number or a np.ndarray.
``*args``: other positional arguments of func. Arguments which are
not instances of `ErrorValue` are taken as constants.
keyword arguments supported:
``NMC``: number of Monte-Carlo steps. If not defined, defaults
to 1000
``exceptions_to_retry``: list of exception types to ignore:
if one of these is raised the given MC step is repeated once
again. Notice that this might induce an infinite loop!
The exception types in this list should be subclasses of
``Exception``.
``exceptions_to_skip``: list of exception types to skip: if
one of these is raised the given MC step is skipped, never
to be repeated. The exception types in this list should be
subclasses of ``Exception``.
Output:
-------
``result``: an `ErrorValue` with the result. The error is estimated
via a Monte-Carlo approach to Gaussian error propagation.
"""
def do_random(x):
if isinstance(x, cls):
return x.random()
else:
return x
if 'NMC' not in kwargs:
kwargs['NMC'] = 1000
if 'exceptions_to_skip' not in kwargs:
kwargs['exceptions_to_skip'] = []
if 'exceptions_to_repeat' not in kwargs:
kwargs['exceptions_to_repeat'] = []
meanvalue = func(*args)
# this way we get either a number or a np.array
stdcollector = meanvalue * 0
mciters = 0
while mciters < kwargs['NMC']:
try:
# IGNORE:W0142
stdcollector += (func(*[do_random(a)
for a in args]) - meanvalue) ** 2
mciters += 1
except Exception as e: # IGNORE:W0703
if any(isinstance(e, etype) for etype in kwargs['exceptions_to_skip']):
kwargs['NMC'] -= 1
elif any(isinstance(e, etype) for etype in kwargs['exceptions_to_repeat']):
pass
else:
raise
return cls(meanvalue, stdcollector ** 0.5 / (kwargs['NMC'] - 1)) | [
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``*args``: other positional arguments of func. Arguments which are
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keyword arguments supported:
``NMC``: number of Monte-Carlo steps. If not defined, defaults
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``exceptions_to_retry``: list of exception types to ignore:
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``exceptions_to_skip``: list of exception types to skip: if
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awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | Fsphere | def Fsphere(q, R):
"""Scattering form-factor amplitude of a sphere normalized to F(q=0)=V
Inputs:
-------
``q``: independent variable
``R``: sphere radius
Formula:
--------
``4*pi/q^3 * (sin(qR) - qR*cos(qR))``
"""
return 4 * np.pi / q ** 3 * (np.sin(q * R) - q * R * np.cos(q * R)) | python | def Fsphere(q, R):
"""Scattering form-factor amplitude of a sphere normalized to F(q=0)=V
Inputs:
-------
``q``: independent variable
``R``: sphere radius
Formula:
--------
``4*pi/q^3 * (sin(qR) - qR*cos(qR))``
"""
return 4 * np.pi / q ** 3 * (np.sin(q * R) - q * R * np.cos(q * R)) | [
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awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | GeneralGuinier | def GeneralGuinier(q, G, Rg, s):
"""Generalized Guinier scattering
Inputs:
-------
``q``: independent variable
``G``: factor
``Rg``: radius of gyration
``s``: dimensionality parameter (can be 1, 2, 3)
Formula:
--------
``G/q**(3-s)*exp(-(q^2*Rg^2)/s)``
"""
return G / q ** (3 - s) * np.exp(-(q * Rg) ** 2 / s) | python | def GeneralGuinier(q, G, Rg, s):
"""Generalized Guinier scattering
Inputs:
-------
``q``: independent variable
``G``: factor
``Rg``: radius of gyration
``s``: dimensionality parameter (can be 1, 2, 3)
Formula:
--------
``G/q**(3-s)*exp(-(q^2*Rg^2)/s)``
"""
return G / q ** (3 - s) * np.exp(-(q * Rg) ** 2 / s) | [
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Inputs:
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``q``: independent variable
``G``: factor
``Rg``: radius of gyration
``s``: dimensionality parameter (can be 1, 2, 3)
Formula:
--------
``G/q**(3-s)*exp(-(q^2*Rg^2)/s)`` | [
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awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | GuinierPorod | def GuinierPorod(q, G, Rg, alpha):
"""Empirical Guinier-Porod scattering
Inputs:
-------
``q``: independent variable
``G``: factor of the Guinier-branch
``Rg``: radius of gyration
``alpha``: power-law exponent
Formula:
--------
``G * exp(-q^2*Rg^2/3)`` if ``q<q_sep`` and ``a*q^alpha`` otherwise.
``q_sep`` and ``a`` are determined from conditions of smoothness at
the cross-over.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
return GuinierPorodMulti(q, G, Rg, alpha) | python | def GuinierPorod(q, G, Rg, alpha):
"""Empirical Guinier-Porod scattering
Inputs:
-------
``q``: independent variable
``G``: factor of the Guinier-branch
``Rg``: radius of gyration
``alpha``: power-law exponent
Formula:
--------
``G * exp(-q^2*Rg^2/3)`` if ``q<q_sep`` and ``a*q^alpha`` otherwise.
``q_sep`` and ``a`` are determined from conditions of smoothness at
the cross-over.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
return GuinierPorodMulti(q, G, Rg, alpha) | [
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``Rg``: radius of gyration
``alpha``: power-law exponent
Formula:
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``G * exp(-q^2*Rg^2/3)`` if ``q<q_sep`` and ``a*q^alpha`` otherwise.
``q_sep`` and ``a`` are determined from conditions of smoothness at
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Literature:
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B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
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awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | PorodGuinier | def PorodGuinier(q, a, alpha, Rg):
"""Empirical Porod-Guinier scattering
Inputs:
-------
``q``: independent variable
``a``: factor of the power-law branch
``alpha``: power-law exponent
``Rg``: radius of gyration
Formula:
--------
``G * exp(-q^2*Rg^2/3)`` if ``q>q_sep`` and ``a*q^alpha`` otherwise.
``q_sep`` and ``G`` are determined from conditions of smoothness at
the cross-over.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
return PorodGuinierMulti(q, a, alpha, Rg) | python | def PorodGuinier(q, a, alpha, Rg):
"""Empirical Porod-Guinier scattering
Inputs:
-------
``q``: independent variable
``a``: factor of the power-law branch
``alpha``: power-law exponent
``Rg``: radius of gyration
Formula:
--------
``G * exp(-q^2*Rg^2/3)`` if ``q>q_sep`` and ``a*q^alpha`` otherwise.
``q_sep`` and ``G`` are determined from conditions of smoothness at
the cross-over.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
return PorodGuinierMulti(q, a, alpha, Rg) | [
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``a``: factor of the power-law branch
``alpha``: power-law exponent
``Rg``: radius of gyration
Formula:
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``G * exp(-q^2*Rg^2/3)`` if ``q>q_sep`` and ``a*q^alpha`` otherwise.
``q_sep`` and ``G`` are determined from conditions of smoothness at
the cross-over.
Literature:
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B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719. | [
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awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | PorodGuinierPorod | def PorodGuinierPorod(q, a, alpha, Rg, beta):
"""Empirical Porod-Guinier-Porod scattering
Inputs:
-------
``q``: independent variable
``a``: factor of the first power-law branch
``alpha``: exponent of the first power-law branch
``Rg``: radius of gyration
``beta``: exponent of the second power-law branch
Formula:
--------
``a*q^alpha`` if ``q<q_sep1``. ``G * exp(-q^2*Rg^2/3)`` if
``q_sep1<q<q_sep2`` and ``b*q^beta`` if ``q_sep2<q``.
``q_sep1``, ``q_sep2``, ``G`` and ``b`` are determined from conditions
of smoothness at the cross-overs.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
return PorodGuinierMulti(q, a, alpha, Rg, beta) | python | def PorodGuinierPorod(q, a, alpha, Rg, beta):
"""Empirical Porod-Guinier-Porod scattering
Inputs:
-------
``q``: independent variable
``a``: factor of the first power-law branch
``alpha``: exponent of the first power-law branch
``Rg``: radius of gyration
``beta``: exponent of the second power-law branch
Formula:
--------
``a*q^alpha`` if ``q<q_sep1``. ``G * exp(-q^2*Rg^2/3)`` if
``q_sep1<q<q_sep2`` and ``b*q^beta`` if ``q_sep2<q``.
``q_sep1``, ``q_sep2``, ``G`` and ``b`` are determined from conditions
of smoothness at the cross-overs.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
return PorodGuinierMulti(q, a, alpha, Rg, beta) | [
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``q``: independent variable
``a``: factor of the first power-law branch
``alpha``: exponent of the first power-law branch
``Rg``: radius of gyration
``beta``: exponent of the second power-law branch
Formula:
--------
``a*q^alpha`` if ``q<q_sep1``. ``G * exp(-q^2*Rg^2/3)`` if
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``q_sep1``, ``q_sep2``, ``G`` and ``b`` are determined from conditions
of smoothness at the cross-overs.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719. | [
"Empirical",
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"-",
"Guinier",
"-",
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] | train | https://github.com/awacha/sastool/blob/deaddfa3002f3f6818697e36139633b7e30427a3/sastool/fitting/fitfunctions/sasbasic.py#L132-L155 |
awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | GuinierPorodGuinier | def GuinierPorodGuinier(q, G, Rg1, alpha, Rg2):
"""Empirical Guinier-Porod-Guinier scattering
Inputs:
-------
``q``: independent variable
``G``: factor for the first Guinier-branch
``Rg1``: the first radius of gyration
``alpha``: the power-law exponent
``Rg2``: the second radius of gyration
Formula:
--------
``G*exp(-q^2*Rg1^2/3)`` if ``q<q_sep1``.
``A*q^alpha`` if ``q_sep1 <= q <=q_sep2``.
``G2*exp(-q^2*Rg2^2/3)`` if ``q_sep2<q``.
The parameters ``A``,``G2``, ``q_sep1``, ``q_sep2`` are determined
from conditions of smoothness at the cross-overs.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
return GuinierPorodMulti(q, G, Rg1, alpha, Rg2) | python | def GuinierPorodGuinier(q, G, Rg1, alpha, Rg2):
"""Empirical Guinier-Porod-Guinier scattering
Inputs:
-------
``q``: independent variable
``G``: factor for the first Guinier-branch
``Rg1``: the first radius of gyration
``alpha``: the power-law exponent
``Rg2``: the second radius of gyration
Formula:
--------
``G*exp(-q^2*Rg1^2/3)`` if ``q<q_sep1``.
``A*q^alpha`` if ``q_sep1 <= q <=q_sep2``.
``G2*exp(-q^2*Rg2^2/3)`` if ``q_sep2<q``.
The parameters ``A``,``G2``, ``q_sep1``, ``q_sep2`` are determined
from conditions of smoothness at the cross-overs.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
return GuinierPorodMulti(q, G, Rg1, alpha, Rg2) | [
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``G``: factor for the first Guinier-branch
``Rg1``: the first radius of gyration
``alpha``: the power-law exponent
``Rg2``: the second radius of gyration
Formula:
--------
``G*exp(-q^2*Rg1^2/3)`` if ``q<q_sep1``.
``A*q^alpha`` if ``q_sep1 <= q <=q_sep2``.
``G2*exp(-q^2*Rg2^2/3)`` if ``q_sep2<q``.
The parameters ``A``,``G2``, ``q_sep1``, ``q_sep2`` are determined
from conditions of smoothness at the cross-overs.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719. | [
"Empirical",
"Guinier",
"-",
"Porod",
"-",
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] | train | https://github.com/awacha/sastool/blob/deaddfa3002f3f6818697e36139633b7e30427a3/sastool/fitting/fitfunctions/sasbasic.py#L157-L182 |
awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | DampedPowerlaw | def DampedPowerlaw(q, a, alpha, sigma):
"""Damped power-law
Inputs:
-------
``q``: independent variable
``a``: factor
``alpha``: exponent
``sigma``: hwhm of the damping Gaussian
Formula:
--------
``a*q^alpha*exp(-q^2/(2*sigma^2))``
"""
return a * q ** alpha * np.exp(-q ** 2 / (2 * sigma ** 2)) | python | def DampedPowerlaw(q, a, alpha, sigma):
"""Damped power-law
Inputs:
-------
``q``: independent variable
``a``: factor
``alpha``: exponent
``sigma``: hwhm of the damping Gaussian
Formula:
--------
``a*q^alpha*exp(-q^2/(2*sigma^2))``
"""
return a * q ** alpha * np.exp(-q ** 2 / (2 * sigma ** 2)) | [
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Inputs:
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``q``: independent variable
``a``: factor
``alpha``: exponent
``sigma``: hwhm of the damping Gaussian
Formula:
--------
``a*q^alpha*exp(-q^2/(2*sigma^2))`` | [
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awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | LogNormSpheres | def LogNormSpheres(q, A, mu, sigma, N=1000):
"""Scattering of a population of non-correlated spheres (radii from a log-normal distribution)
Inputs:
-------
``q``: independent variable
``A``: scaling factor
``mu``: expectation of ``ln(R)``
``sigma``: hwhm of ``ln(R)``
Non-fittable inputs:
--------------------
``N``: the (integer) number of spheres
Formula:
--------
The integral of ``F_sphere^2(q,R) * P(R)`` where ``P(R)`` is a
log-normal distribution of the radii.
"""
Rmin = 0
Rmax = np.exp(mu + 3 * sigma)
R = np.linspace(Rmin, Rmax, N + 1)[1:]
P = 1 / np.sqrt(2 * np.pi * sigma ** 2 * R ** 2) * np.exp(-(np.log(R) - mu) ** 2 / (2 * sigma ** 2))
def Fsphere_outer(q, R):
qR = np.outer(q, R)
q1 = np.outer(q, np.ones_like(R))
return 4 * np.pi / q1 ** 3 * (np.sin(qR) - qR * np.cos(qR))
I = (Fsphere_outer(q, R) ** 2 * np.outer(np.ones_like(q), P))
return A * I.sum(1) / P.sum() | python | def LogNormSpheres(q, A, mu, sigma, N=1000):
"""Scattering of a population of non-correlated spheres (radii from a log-normal distribution)
Inputs:
-------
``q``: independent variable
``A``: scaling factor
``mu``: expectation of ``ln(R)``
``sigma``: hwhm of ``ln(R)``
Non-fittable inputs:
--------------------
``N``: the (integer) number of spheres
Formula:
--------
The integral of ``F_sphere^2(q,R) * P(R)`` where ``P(R)`` is a
log-normal distribution of the radii.
"""
Rmin = 0
Rmax = np.exp(mu + 3 * sigma)
R = np.linspace(Rmin, Rmax, N + 1)[1:]
P = 1 / np.sqrt(2 * np.pi * sigma ** 2 * R ** 2) * np.exp(-(np.log(R) - mu) ** 2 / (2 * sigma ** 2))
def Fsphere_outer(q, R):
qR = np.outer(q, R)
q1 = np.outer(q, np.ones_like(R))
return 4 * np.pi / q1 ** 3 * (np.sin(qR) - qR * np.cos(qR))
I = (Fsphere_outer(q, R) ** 2 * np.outer(np.ones_like(q), P))
return A * I.sum(1) / P.sum() | [
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-------
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``A``: scaling factor
``mu``: expectation of ``ln(R)``
``sigma``: hwhm of ``ln(R)``
Non-fittable inputs:
--------------------
``N``: the (integer) number of spheres
Formula:
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awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | GaussSpheres | def GaussSpheres(q, A, R0, sigma, N=1000, weighting='intensity'):
"""Scattering of a population of non-correlated spheres (radii from a gaussian distribution)
Inputs:
-------
``q``: independent variable
``A``: scaling factor
``R0``: expectation of ``R``
``sigma``: hwhm of ``R``
``weighting``: 'intensity' (default), 'volume' or 'number'
Non-fittable inputs:
--------------------
``N``: the (integer) number of spheres
Formula:
--------
The integral of ``F_sphere^2(q,R) * P(R)`` where ``P(R)`` is a
gaussian (normal) distribution of the radii.
"""
Rmin = max(0, R0 - 3 * sigma)
Rmax = R0 + 3 * sigma
R = np.linspace(Rmin, Rmax, N + 1)[1:]
P = 1 / np.sqrt(2 * np.pi * sigma ** 2) * np.exp(-(R - R0) ** 2 / (2 * sigma ** 2))
def Fsphere_outer(q, R):
qR = np.outer(q, R)
return 3 / qR ** 3 * (np.sin(qR) - qR * np.cos(qR))
V=R**3*4*np.pi/3.
if weighting=='intensity':
P=P*V*V
elif weighting=='volume':
P=P*V
elif weighting=='number':
pass
else:
raise ValueError('Invalid weighting: '+str(weighting))
I = (Fsphere_outer(q, R) ** 2 * np.outer(np.ones_like(q), P))
return A * I.sum(1) / P.sum() | python | def GaussSpheres(q, A, R0, sigma, N=1000, weighting='intensity'):
"""Scattering of a population of non-correlated spheres (radii from a gaussian distribution)
Inputs:
-------
``q``: independent variable
``A``: scaling factor
``R0``: expectation of ``R``
``sigma``: hwhm of ``R``
``weighting``: 'intensity' (default), 'volume' or 'number'
Non-fittable inputs:
--------------------
``N``: the (integer) number of spheres
Formula:
--------
The integral of ``F_sphere^2(q,R) * P(R)`` where ``P(R)`` is a
gaussian (normal) distribution of the radii.
"""
Rmin = max(0, R0 - 3 * sigma)
Rmax = R0 + 3 * sigma
R = np.linspace(Rmin, Rmax, N + 1)[1:]
P = 1 / np.sqrt(2 * np.pi * sigma ** 2) * np.exp(-(R - R0) ** 2 / (2 * sigma ** 2))
def Fsphere_outer(q, R):
qR = np.outer(q, R)
return 3 / qR ** 3 * (np.sin(qR) - qR * np.cos(qR))
V=R**3*4*np.pi/3.
if weighting=='intensity':
P=P*V*V
elif weighting=='volume':
P=P*V
elif weighting=='number':
pass
else:
raise ValueError('Invalid weighting: '+str(weighting))
I = (Fsphere_outer(q, R) ** 2 * np.outer(np.ones_like(q), P))
return A * I.sum(1) / P.sum() | [
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Inputs:
-------
``q``: independent variable
``A``: scaling factor
``R0``: expectation of ``R``
``sigma``: hwhm of ``R``
``weighting``: 'intensity' (default), 'volume' or 'number'
Non-fittable inputs:
--------------------
``N``: the (integer) number of spheres
Formula:
--------
The integral of ``F_sphere^2(q,R) * P(R)`` where ``P(R)`` is a
gaussian (normal) distribution of the radii. | [
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awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | PowerlawGuinierPorodConst | def PowerlawGuinierPorodConst(q, A, alpha, G, Rg, beta, C):
"""Sum of a Power-law, a Guinier-Porod curve and a constant.
Inputs:
-------
``q``: independent variable (momentum transfer)
``A``: scaling factor of the power-law
``alpha``: power-law exponent
``G``: scaling factor of the Guinier-Porod curve
``Rg``: Radius of gyration
``beta``: power-law exponent of the Guinier-Porod curve
``C``: additive constant
Formula:
--------
``A*q^alpha + GuinierPorod(q,G,Rg,beta) + C``
"""
return PowerlawPlusConstant(q, A, alpha, C) + GuinierPorod(q, G, Rg, beta) | python | def PowerlawGuinierPorodConst(q, A, alpha, G, Rg, beta, C):
"""Sum of a Power-law, a Guinier-Porod curve and a constant.
Inputs:
-------
``q``: independent variable (momentum transfer)
``A``: scaling factor of the power-law
``alpha``: power-law exponent
``G``: scaling factor of the Guinier-Porod curve
``Rg``: Radius of gyration
``beta``: power-law exponent of the Guinier-Porod curve
``C``: additive constant
Formula:
--------
``A*q^alpha + GuinierPorod(q,G,Rg,beta) + C``
"""
return PowerlawPlusConstant(q, A, alpha, C) + GuinierPorod(q, G, Rg, beta) | [
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Inputs:
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``q``: independent variable (momentum transfer)
``A``: scaling factor of the power-law
``alpha``: power-law exponent
``G``: scaling factor of the Guinier-Porod curve
``Rg``: Radius of gyration
``beta``: power-law exponent of the Guinier-Porod curve
``C``: additive constant
Formula:
--------
``A*q^alpha + GuinierPorod(q,G,Rg,beta) + C`` | [
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awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | GuinierPorodMulti | def GuinierPorodMulti(q, G, *Rgsalphas):
"""Empirical multi-part Guinier-Porod scattering
Inputs:
-------
``q``: independent variable
``G``: factor for the first Guinier-branch
other arguments: [Rg1, alpha1, Rg2, alpha2, Rg3 ...] the radii of
gyration and power-law exponents of the consecutive parts
Formula:
--------
The intensity is a piecewise function with continuous first derivatives.
The separating points in ``q`` between the consecutive parts and the
intensity factors of them (except the first) are determined from
conditions of smoothness (continuity of the function and its first
derivative) at the border points of the intervals. Guinier-type
(``G*exp(-q^2*Rg1^2/3)``) and Power-law type (``A*q^alpha``) parts
follow each other in alternating sequence.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
scalefactor = G
funcs = [lambda q: Guinier(q, G, Rgsalphas[0])]
indices = np.ones_like(q, dtype=np.bool)
constraints = []
for i in range(1, len(Rgsalphas)):
if i % 2:
# Rgsalphas[i] is an exponent, Rgsalphas[i-1] is a radius of gyration
qsep = _PGgen_qsep(Rgsalphas[i], Rgsalphas[i - 1], 3)
scalefactor = _PGgen_A(Rgsalphas[i], Rgsalphas[i - 1], 3, scalefactor)
funcs.append(lambda q, a=scalefactor, alpha=Rgsalphas[i]: Powerlaw(q, a, alpha))
else:
# Rgsalphas[i] is a radius of gyration, Rgsalphas[i-1] is a power-law exponent
qsep = _PGgen_qsep(Rgsalphas[i - 1], Rgsalphas[i], 3)
scalefactor = _PGgen_G(Rgsalphas[i - 1], Rgsalphas[i], 3, scalefactor)
funcs.append(lambda q, G=scalefactor, Rg=Rgsalphas[i]: Guinier(q, G, Rg))
# this belongs to the previous
constraints.append(indices & (q < qsep))
indices[q < qsep] = False
constraints.append(indices)
return np.piecewise(q, constraints, funcs) | python | def GuinierPorodMulti(q, G, *Rgsalphas):
"""Empirical multi-part Guinier-Porod scattering
Inputs:
-------
``q``: independent variable
``G``: factor for the first Guinier-branch
other arguments: [Rg1, alpha1, Rg2, alpha2, Rg3 ...] the radii of
gyration and power-law exponents of the consecutive parts
Formula:
--------
The intensity is a piecewise function with continuous first derivatives.
The separating points in ``q`` between the consecutive parts and the
intensity factors of them (except the first) are determined from
conditions of smoothness (continuity of the function and its first
derivative) at the border points of the intervals. Guinier-type
(``G*exp(-q^2*Rg1^2/3)``) and Power-law type (``A*q^alpha``) parts
follow each other in alternating sequence.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
scalefactor = G
funcs = [lambda q: Guinier(q, G, Rgsalphas[0])]
indices = np.ones_like(q, dtype=np.bool)
constraints = []
for i in range(1, len(Rgsalphas)):
if i % 2:
# Rgsalphas[i] is an exponent, Rgsalphas[i-1] is a radius of gyration
qsep = _PGgen_qsep(Rgsalphas[i], Rgsalphas[i - 1], 3)
scalefactor = _PGgen_A(Rgsalphas[i], Rgsalphas[i - 1], 3, scalefactor)
funcs.append(lambda q, a=scalefactor, alpha=Rgsalphas[i]: Powerlaw(q, a, alpha))
else:
# Rgsalphas[i] is a radius of gyration, Rgsalphas[i-1] is a power-law exponent
qsep = _PGgen_qsep(Rgsalphas[i - 1], Rgsalphas[i], 3)
scalefactor = _PGgen_G(Rgsalphas[i - 1], Rgsalphas[i], 3, scalefactor)
funcs.append(lambda q, G=scalefactor, Rg=Rgsalphas[i]: Guinier(q, G, Rg))
# this belongs to the previous
constraints.append(indices & (q < qsep))
indices[q < qsep] = False
constraints.append(indices)
return np.piecewise(q, constraints, funcs) | [
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Inputs:
-------
``q``: independent variable
``G``: factor for the first Guinier-branch
other arguments: [Rg1, alpha1, Rg2, alpha2, Rg3 ...] the radii of
gyration and power-law exponents of the consecutive parts
Formula:
--------
The intensity is a piecewise function with continuous first derivatives.
The separating points in ``q`` between the consecutive parts and the
intensity factors of them (except the first) are determined from
conditions of smoothness (continuity of the function and its first
derivative) at the border points of the intervals. Guinier-type
(``G*exp(-q^2*Rg1^2/3)``) and Power-law type (``A*q^alpha``) parts
follow each other in alternating sequence.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719. | [
"Empirical",
"multi",
"-",
"part",
"Guinier",
"-",
"Porod",
"scattering"
] | train | https://github.com/awacha/sastool/blob/deaddfa3002f3f6818697e36139633b7e30427a3/sastool/fitting/fitfunctions/sasbasic.py#L320-L364 |
awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | PorodGuinierMulti | def PorodGuinierMulti(q, A, *alphasRgs):
"""Empirical multi-part Porod-Guinier scattering
Inputs:
-------
``q``: independent variable
``A``: factor for the first Power-law-branch
other arguments: [alpha1, Rg1, alpha2, Rg2, alpha3 ...] the radii of
gyration and power-law exponents of the consecutive parts
Formula:
--------
The intensity is a piecewise function with continuous first derivatives.
The separating points in ``q`` between the consecutive parts and the
intensity factors of them (except the first) are determined from
conditions of smoothness (continuity of the function and its first
derivative) at the border points of the intervals. Guinier-type
(``G*exp(-q^2*Rg1^2/3)``) and Power-law type (``A*q^alpha``) parts
follow each other in alternating sequence.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
scalefactor = A
funcs = [lambda q: Powerlaw(q, A, alphasRgs[0])]
indices = np.ones_like(q, dtype=np.bool)
constraints = []
for i in range(1, len(alphasRgs)):
if i % 2:
# alphasRgs[i] is a radius of gyration, alphasRgs[i-1] is a power-law exponent
qsep = _PGgen_qsep(alphasRgs[i - 1], alphasRgs[i], 3)
scalefactor = _PGgen_G(alphasRgs[i - 1], alphasRgs[i], 3, scalefactor)
funcs.append(lambda q, G=scalefactor, Rg=alphasRgs[i]: Guinier(q, G, Rg))
else:
# alphasRgs[i] is an exponent, alphasRgs[i-1] is a radius of gyration
qsep = _PGgen_qsep(alphasRgs[i], alphasRgs[i - 1], 3)
scalefactor = _PGgen_A(alphasRgs[i], alphasRgs[i - 1], 3, scalefactor)
funcs.append(lambda q, a=scalefactor, alpha=alphasRgs[i]: a * q ** alpha)
# this belongs to the previous
constraints.append(indices & (q < qsep))
indices[q < qsep] = False
constraints.append(indices)
return np.piecewise(q, constraints, funcs) | python | def PorodGuinierMulti(q, A, *alphasRgs):
"""Empirical multi-part Porod-Guinier scattering
Inputs:
-------
``q``: independent variable
``A``: factor for the first Power-law-branch
other arguments: [alpha1, Rg1, alpha2, Rg2, alpha3 ...] the radii of
gyration and power-law exponents of the consecutive parts
Formula:
--------
The intensity is a piecewise function with continuous first derivatives.
The separating points in ``q`` between the consecutive parts and the
intensity factors of them (except the first) are determined from
conditions of smoothness (continuity of the function and its first
derivative) at the border points of the intervals. Guinier-type
(``G*exp(-q^2*Rg1^2/3)``) and Power-law type (``A*q^alpha``) parts
follow each other in alternating sequence.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
scalefactor = A
funcs = [lambda q: Powerlaw(q, A, alphasRgs[0])]
indices = np.ones_like(q, dtype=np.bool)
constraints = []
for i in range(1, len(alphasRgs)):
if i % 2:
# alphasRgs[i] is a radius of gyration, alphasRgs[i-1] is a power-law exponent
qsep = _PGgen_qsep(alphasRgs[i - 1], alphasRgs[i], 3)
scalefactor = _PGgen_G(alphasRgs[i - 1], alphasRgs[i], 3, scalefactor)
funcs.append(lambda q, G=scalefactor, Rg=alphasRgs[i]: Guinier(q, G, Rg))
else:
# alphasRgs[i] is an exponent, alphasRgs[i-1] is a radius of gyration
qsep = _PGgen_qsep(alphasRgs[i], alphasRgs[i - 1], 3)
scalefactor = _PGgen_A(alphasRgs[i], alphasRgs[i - 1], 3, scalefactor)
funcs.append(lambda q, a=scalefactor, alpha=alphasRgs[i]: a * q ** alpha)
# this belongs to the previous
constraints.append(indices & (q < qsep))
indices[q < qsep] = False
constraints.append(indices)
return np.piecewise(q, constraints, funcs) | [
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Inputs:
-------
``q``: independent variable
``A``: factor for the first Power-law-branch
other arguments: [alpha1, Rg1, alpha2, Rg2, alpha3 ...] the radii of
gyration and power-law exponents of the consecutive parts
Formula:
--------
The intensity is a piecewise function with continuous first derivatives.
The separating points in ``q`` between the consecutive parts and the
intensity factors of them (except the first) are determined from
conditions of smoothness (continuity of the function and its first
derivative) at the border points of the intervals. Guinier-type
(``G*exp(-q^2*Rg1^2/3)``) and Power-law type (``A*q^alpha``) parts
follow each other in alternating sequence.
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719. | [
"Empirical",
"multi",
"-",
"part",
"Porod",
"-",
"Guinier",
"scattering"
] | train | https://github.com/awacha/sastool/blob/deaddfa3002f3f6818697e36139633b7e30427a3/sastool/fitting/fitfunctions/sasbasic.py#L366-L410 |
awacha/sastool | sastool/fitting/fitfunctions/sasbasic.py | GeneralGuinierPorod | def GeneralGuinierPorod(q, factor, *args, **kwargs):
"""Empirical generalized multi-part Guinier-Porod scattering
Inputs:
-------
``q``: independent variable
``factor``: factor for the first branch
other arguments (*args): the defining arguments of the consecutive
parts: radius of gyration (``Rg``) and dimensionality
parameter (``s``) for Guinier and exponent (``alpha``) for
power-law parts.
supported keyword arguments:
``startswithguinier``: True if the first segment is a Guinier-type
scattering (this is the default) or False if it is a power-law
Formula:
--------
The intensity is a piecewise function with continuous first derivatives.
The separating points in ``q`` between the consecutive parts and the
intensity factors of them (except the first) are determined from
conditions of smoothness (continuity of the function and its first
derivative) at the border points of the intervals. Guinier-type
(``G*q**(3-s)*exp(-q^2*Rg1^2/s)``) and Power-law type (``A*q^alpha``)
parts follow each other in alternating sequence. The exact number of
parts is determined from the number of positional arguments (*args).
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
if kwargs.get('startswithguinier', True):
funcs = [lambda q, A = factor:GeneralGuinier(q, A, args[0], args[1])]
i = 2
guiniernext = False
else:
funcs = [lambda q, A = factor: Powerlaw(q, A, args[0])]
i = 1
guiniernext = True
indices = np.ones_like(q, dtype=np.bool)
constraints = []
while i < len(args):
if guiniernext:
# args[i] is a radius of gyration, args[i+1] is a dimensionality parameter, args[i-1] is a power-law exponent
qsep = _PGgen_qsep(args[i - 1], args[i], args[i + 1])
factor = _PGgen_G(args[i - 1], args[i], args[i + 1], factor)
funcs.append(lambda q, G=factor, Rg=args[i], s=args[i + 1]: GeneralGuinier(q, G, Rg, s))
guiniernext = False
i += 2
else:
# args[i] is an exponent, args[i-2] is a radius of gyration, args[i-1] is a dimensionality parameter
qsep = _PGgen_qsep(args[i], args[i - 2], args[i - 1])
factor = _PGgen_A(args[i], args[i - 2], args[i - 1], factor)
funcs.append(lambda q, a=factor, alpha=args[i]: a * q ** alpha)
guiniernext = True
i += 1
# this belongs to the previous
constraints.append(indices & (q < qsep))
indices[q < qsep] = False
constraints.append(indices)
return np.piecewise(q, constraints, funcs) | python | def GeneralGuinierPorod(q, factor, *args, **kwargs):
"""Empirical generalized multi-part Guinier-Porod scattering
Inputs:
-------
``q``: independent variable
``factor``: factor for the first branch
other arguments (*args): the defining arguments of the consecutive
parts: radius of gyration (``Rg``) and dimensionality
parameter (``s``) for Guinier and exponent (``alpha``) for
power-law parts.
supported keyword arguments:
``startswithguinier``: True if the first segment is a Guinier-type
scattering (this is the default) or False if it is a power-law
Formula:
--------
The intensity is a piecewise function with continuous first derivatives.
The separating points in ``q`` between the consecutive parts and the
intensity factors of them (except the first) are determined from
conditions of smoothness (continuity of the function and its first
derivative) at the border points of the intervals. Guinier-type
(``G*q**(3-s)*exp(-q^2*Rg1^2/s)``) and Power-law type (``A*q^alpha``)
parts follow each other in alternating sequence. The exact number of
parts is determined from the number of positional arguments (*args).
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719.
"""
if kwargs.get('startswithguinier', True):
funcs = [lambda q, A = factor:GeneralGuinier(q, A, args[0], args[1])]
i = 2
guiniernext = False
else:
funcs = [lambda q, A = factor: Powerlaw(q, A, args[0])]
i = 1
guiniernext = True
indices = np.ones_like(q, dtype=np.bool)
constraints = []
while i < len(args):
if guiniernext:
# args[i] is a radius of gyration, args[i+1] is a dimensionality parameter, args[i-1] is a power-law exponent
qsep = _PGgen_qsep(args[i - 1], args[i], args[i + 1])
factor = _PGgen_G(args[i - 1], args[i], args[i + 1], factor)
funcs.append(lambda q, G=factor, Rg=args[i], s=args[i + 1]: GeneralGuinier(q, G, Rg, s))
guiniernext = False
i += 2
else:
# args[i] is an exponent, args[i-2] is a radius of gyration, args[i-1] is a dimensionality parameter
qsep = _PGgen_qsep(args[i], args[i - 2], args[i - 1])
factor = _PGgen_A(args[i], args[i - 2], args[i - 1], factor)
funcs.append(lambda q, a=factor, alpha=args[i]: a * q ** alpha)
guiniernext = True
i += 1
# this belongs to the previous
constraints.append(indices & (q < qsep))
indices[q < qsep] = False
constraints.append(indices)
return np.piecewise(q, constraints, funcs) | [
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Inputs:
-------
``q``: independent variable
``factor``: factor for the first branch
other arguments (*args): the defining arguments of the consecutive
parts: radius of gyration (``Rg``) and dimensionality
parameter (``s``) for Guinier and exponent (``alpha``) for
power-law parts.
supported keyword arguments:
``startswithguinier``: True if the first segment is a Guinier-type
scattering (this is the default) or False if it is a power-law
Formula:
--------
The intensity is a piecewise function with continuous first derivatives.
The separating points in ``q`` between the consecutive parts and the
intensity factors of them (except the first) are determined from
conditions of smoothness (continuity of the function and its first
derivative) at the border points of the intervals. Guinier-type
(``G*q**(3-s)*exp(-q^2*Rg1^2/s)``) and Power-law type (``A*q^alpha``)
parts follow each other in alternating sequence. The exact number of
parts is determined from the number of positional arguments (*args).
Literature:
-----------
B. Hammouda: A new Guinier-Porod model. J. Appl. Crystallogr. (2010) 43,
716-719. | [
"Empirical",
"generalized",
"multi",
"-",
"part",
"Guinier",
"-",
"Porod",
"scattering"
] | train | https://github.com/awacha/sastool/blob/deaddfa3002f3f6818697e36139633b7e30427a3/sastool/fitting/fitfunctions/sasbasic.py#L412-L472 |
awacha/sastool | sastool/fitting/fitfunctions/saspolymer.py | DebyeChain | def DebyeChain(q, Rg):
"""Scattering form-factor intensity of a Gaussian chain (Debye)
Inputs:
-------
``q``: independent variable
``Rg``: radius of gyration
Formula:
--------
``2*(exp(-a)-1+a)/a^2`` where ``a=(q*Rg)^2``
"""
a = (q * Rg) ** 2
return 2 * (np.exp(-a) - 1 + a) / a ** 2 | python | def DebyeChain(q, Rg):
"""Scattering form-factor intensity of a Gaussian chain (Debye)
Inputs:
-------
``q``: independent variable
``Rg``: radius of gyration
Formula:
--------
``2*(exp(-a)-1+a)/a^2`` where ``a=(q*Rg)^2``
"""
a = (q * Rg) ** 2
return 2 * (np.exp(-a) - 1 + a) / a ** 2 | [
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Inputs:
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``q``: independent variable
``Rg``: radius of gyration
Formula:
--------
``2*(exp(-a)-1+a)/a^2`` where ``a=(q*Rg)^2`` | [
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awacha/sastool | sastool/fitting/fitfunctions/saspolymer.py | ExcludedVolumeChain | def ExcludedVolumeChain(q, Rg, nu):
"""Scattering intensity of a generalized excluded-volume Gaussian chain
Inputs:
-------
``q``: independent variable
``Rg``: radius of gyration
``nu``: excluded volume exponent
Formula:
--------
``(u^(1/nu)*gamma(0.5/nu)*gammainc_lower(0.5/nu,u)-
gamma(1/nu)*gammainc_lower(1/nu,u)) / (nu*u^(1/nu))``
where ``u = q^2*Rg^2*(2*nu+1)*(2*nu+2)/6`` is the reduced scattering
variable, ``gamma(x)`` is the gamma function and ``gammainc_lower(x,t)``
is the lower incomplete gamma function.
Literature:
-----------
SASFit manual 6. nov. 2010. Equation (3.60b)
"""
u = (q * Rg) ** 2 * (2 * nu + 1) * (2 * nu + 2) / 6.
return (u ** (0.5 / nu) * gamma(0.5 / nu) * gammainc(0.5 / nu, u) -
gamma(1. / nu) * gammainc(1. / nu, u)) / (nu * u ** (1. / nu)) | python | def ExcludedVolumeChain(q, Rg, nu):
"""Scattering intensity of a generalized excluded-volume Gaussian chain
Inputs:
-------
``q``: independent variable
``Rg``: radius of gyration
``nu``: excluded volume exponent
Formula:
--------
``(u^(1/nu)*gamma(0.5/nu)*gammainc_lower(0.5/nu,u)-
gamma(1/nu)*gammainc_lower(1/nu,u)) / (nu*u^(1/nu))``
where ``u = q^2*Rg^2*(2*nu+1)*(2*nu+2)/6`` is the reduced scattering
variable, ``gamma(x)`` is the gamma function and ``gammainc_lower(x,t)``
is the lower incomplete gamma function.
Literature:
-----------
SASFit manual 6. nov. 2010. Equation (3.60b)
"""
u = (q * Rg) ** 2 * (2 * nu + 1) * (2 * nu + 2) / 6.
return (u ** (0.5 / nu) * gamma(0.5 / nu) * gammainc(0.5 / nu, u) -
gamma(1. / nu) * gammainc(1. / nu, u)) / (nu * u ** (1. / nu)) | [
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Inputs:
-------
``q``: independent variable
``Rg``: radius of gyration
``nu``: excluded volume exponent
Formula:
--------
``(u^(1/nu)*gamma(0.5/nu)*gammainc_lower(0.5/nu,u)-
gamma(1/nu)*gammainc_lower(1/nu,u)) / (nu*u^(1/nu))``
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Literature:
-----------
SASFit manual 6. nov. 2010. Equation (3.60b) | [
"Scattering",
"intensity",
"of",
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"generalized",
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"-",
"volume",
"Gaussian",
"chain"
] | train | https://github.com/awacha/sastool/blob/deaddfa3002f3f6818697e36139633b7e30427a3/sastool/fitting/fitfunctions/saspolymer.py#L21-L44 |
awacha/sastool | sastool/fitting/fitfunctions/saspolymer.py | BorueErukhimovich | def BorueErukhimovich(q, C, r0, s, t):
"""Borue-Erukhimovich model of microphase separation in polyelectrolytes
Inputs:
-------
``q``: independent variable
``C``: scaling factor
``r0``: typical el.stat. screening length
``s``: dimensionless charge concentration
``t``: dimensionless temperature
Formula:
--------
``C*(x^2+s)/((x^2+s)(x^2+t)+1)`` where ``x=q*r0``
Literature:
-----------
o Borue and Erukhimovich. Macromolecules (1988) 21 (11) 3240-3249
o Shibayama and Tanaka. J. Chem. Phys (1995) 102 (23) 9392
o Moussaid et. al. J. Phys II (France) (1993) 3 (4) 573-594
o Ermi and Amis. Macromolecules (1997) 30 (22) 6937-6942
"""
x = q * r0
return C * (x ** 2 + s) / ((x ** 2 + s) * (x ** 2 + t) + 1) | python | def BorueErukhimovich(q, C, r0, s, t):
"""Borue-Erukhimovich model of microphase separation in polyelectrolytes
Inputs:
-------
``q``: independent variable
``C``: scaling factor
``r0``: typical el.stat. screening length
``s``: dimensionless charge concentration
``t``: dimensionless temperature
Formula:
--------
``C*(x^2+s)/((x^2+s)(x^2+t)+1)`` where ``x=q*r0``
Literature:
-----------
o Borue and Erukhimovich. Macromolecules (1988) 21 (11) 3240-3249
o Shibayama and Tanaka. J. Chem. Phys (1995) 102 (23) 9392
o Moussaid et. al. J. Phys II (France) (1993) 3 (4) 573-594
o Ermi and Amis. Macromolecules (1997) 30 (22) 6937-6942
"""
x = q * r0
return C * (x ** 2 + s) / ((x ** 2 + s) * (x ** 2 + t) + 1) | [
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Inputs:
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``q``: independent variable
``C``: scaling factor
``r0``: typical el.stat. screening length
``s``: dimensionless charge concentration
``t``: dimensionless temperature
Formula:
--------
``C*(x^2+s)/((x^2+s)(x^2+t)+1)`` where ``x=q*r0``
Literature:
-----------
o Borue and Erukhimovich. Macromolecules (1988) 21 (11) 3240-3249
o Shibayama and Tanaka. J. Chem. Phys (1995) 102 (23) 9392
o Moussaid et. al. J. Phys II (France) (1993) 3 (4) 573-594
o Ermi and Amis. Macromolecules (1997) 30 (22) 6937-6942 | [
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awacha/sastool | sastool/fitting/fitfunctions/saspolymer.py | BorueErukhimovich_Powerlaw | def BorueErukhimovich_Powerlaw(q, C, r0, s, t, nu):
"""Borue-Erukhimovich model ending in a power-law.
Inputs:
-------
``q``: independent variable
``C``: scaling factor
``r0``: typical el.stat. screening length
``s``: dimensionless charge concentration
``t``: dimensionless temperature
``nu``: excluded volume parameter
Formula:
--------
``C*(x^2+s)/((x^2+s)(x^2+t)+1)`` where ``x=q*r0`` if ``q<qsep``
``A*q^(-1/nu)``if ``q>qsep``
``A`` and ``qsep`` are determined from conditions of smoothness at the
cross-over.
"""
def get_xsep(alpha, s, t):
A = alpha + 2
B = 2 * s * alpha + t * alpha + 4 * s
C = s * t * alpha + alpha + alpha * s ** 2 + alpha * s * t - 2 + 2 * s ** 2
D = alpha * s ** 2 * t + alpha * s
r = np.roots([A, B, C, D])
#print "get_xsep: ", alpha, s, t, r
return r[r > 0][0] ** 0.5
get_B = lambda C, xsep, s, t, nu:C * (xsep ** 2 + s) / ((xsep ** 2 + s) * (xsep ** 2 + t) + 1) * xsep ** (1.0 / nu)
x = q * r0
xsep = np.real_if_close(get_xsep(-1.0 / nu, s, t))
A = get_B(C, xsep, s, t, nu)
return np.piecewise(q, (x < xsep, x >= xsep),
(lambda a:BorueErukhimovich(a, C, r0, s, t),
lambda a:A * (a * r0) ** (-1.0 / nu))) | python | def BorueErukhimovich_Powerlaw(q, C, r0, s, t, nu):
"""Borue-Erukhimovich model ending in a power-law.
Inputs:
-------
``q``: independent variable
``C``: scaling factor
``r0``: typical el.stat. screening length
``s``: dimensionless charge concentration
``t``: dimensionless temperature
``nu``: excluded volume parameter
Formula:
--------
``C*(x^2+s)/((x^2+s)(x^2+t)+1)`` where ``x=q*r0`` if ``q<qsep``
``A*q^(-1/nu)``if ``q>qsep``
``A`` and ``qsep`` are determined from conditions of smoothness at the
cross-over.
"""
def get_xsep(alpha, s, t):
A = alpha + 2
B = 2 * s * alpha + t * alpha + 4 * s
C = s * t * alpha + alpha + alpha * s ** 2 + alpha * s * t - 2 + 2 * s ** 2
D = alpha * s ** 2 * t + alpha * s
r = np.roots([A, B, C, D])
#print "get_xsep: ", alpha, s, t, r
return r[r > 0][0] ** 0.5
get_B = lambda C, xsep, s, t, nu:C * (xsep ** 2 + s) / ((xsep ** 2 + s) * (xsep ** 2 + t) + 1) * xsep ** (1.0 / nu)
x = q * r0
xsep = np.real_if_close(get_xsep(-1.0 / nu, s, t))
A = get_B(C, xsep, s, t, nu)
return np.piecewise(q, (x < xsep, x >= xsep),
(lambda a:BorueErukhimovich(a, C, r0, s, t),
lambda a:A * (a * r0) ** (-1.0 / nu))) | [
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Inputs:
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``q``: independent variable
``C``: scaling factor
``r0``: typical el.stat. screening length
``s``: dimensionless charge concentration
``t``: dimensionless temperature
``nu``: excluded volume parameter
Formula:
--------
``C*(x^2+s)/((x^2+s)(x^2+t)+1)`` where ``x=q*r0`` if ``q<qsep``
``A*q^(-1/nu)``if ``q>qsep``
``A`` and ``qsep`` are determined from conditions of smoothness at the
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bmcfee/pumpp | pumpp/sampler.py | Sampler.sample | def sample(self, data, interval):
'''Sample a patch from the data object
Parameters
----------
data : dict
A data dict as produced by pumpp.Pump.transform
interval : slice
The time interval to sample
Returns
-------
data_slice : dict
`data` restricted to `interval`.
'''
data_slice = dict()
for key in data:
if '_valid' in key:
continue
index = [slice(None)] * data[key].ndim
# if we have multiple observations for this key, pick one
index[0] = self.rng.randint(0, data[key].shape[0])
index[0] = slice(index[0], index[0] + 1)
for tdim in self._time[key]:
index[tdim] = interval
data_slice[key] = data[key][tuple(index)]
return data_slice | python | def sample(self, data, interval):
'''Sample a patch from the data object
Parameters
----------
data : dict
A data dict as produced by pumpp.Pump.transform
interval : slice
The time interval to sample
Returns
-------
data_slice : dict
`data` restricted to `interval`.
'''
data_slice = dict()
for key in data:
if '_valid' in key:
continue
index = [slice(None)] * data[key].ndim
# if we have multiple observations for this key, pick one
index[0] = self.rng.randint(0, data[key].shape[0])
index[0] = slice(index[0], index[0] + 1)
for tdim in self._time[key]:
index[tdim] = interval
data_slice[key] = data[key][tuple(index)]
return data_slice | [
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bmcfee/pumpp | pumpp/sampler.py | Sampler.indices | def indices(self, data):
'''Generate patch indices
Parameters
----------
data : dict of np.ndarray
As produced by pumpp.transform
Yields
------
start : int >= 0
The start index of a sample patch
'''
duration = self.data_duration(data)
if self.duration > duration:
raise DataError('Data duration={} is less than '
'sample duration={}'.format(duration, self.duration))
while True:
# Generate a sampling interval
yield self.rng.randint(0, duration - self.duration + 1) | python | def indices(self, data):
'''Generate patch indices
Parameters
----------
data : dict of np.ndarray
As produced by pumpp.transform
Yields
------
start : int >= 0
The start index of a sample patch
'''
duration = self.data_duration(data)
if self.duration > duration:
raise DataError('Data duration={} is less than '
'sample duration={}'.format(duration, self.duration))
while True:
# Generate a sampling interval
yield self.rng.randint(0, duration - self.duration + 1) | [
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bmcfee/pumpp | pumpp/sampler.py | SequentialSampler.indices | def indices(self, data):
'''Generate patch start indices
Parameters
----------
data : dict of np.ndarray
As produced by pumpp.transform
Yields
------
start : int >= 0
The start index of a sample patch
'''
duration = self.data_duration(data)
for start in range(0, duration - self.duration, self.stride):
yield start | python | def indices(self, data):
'''Generate patch start indices
Parameters
----------
data : dict of np.ndarray
As produced by pumpp.transform
Yields
------
start : int >= 0
The start index of a sample patch
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bmcfee/pumpp | pumpp/sampler.py | VariableLengthSampler.indices | def indices(self, data):
'''Generate patch indices
Parameters
----------
data : dict of np.ndarray
As produced by pumpp.transform
Yields
------
start : int >= 0
The start index of a sample patch
'''
duration = self.data_duration(data)
while True:
# Generate a sampling interval
yield self.rng.randint(0, duration - self.min_duration + 1) | python | def indices(self, data):
'''Generate patch indices
Parameters
----------
data : dict of np.ndarray
As produced by pumpp.transform
Yields
------
start : int >= 0
The start index of a sample patch
'''
duration = self.data_duration(data)
while True:
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bmcfee/pumpp | pumpp/base.py | Scope.scope | def scope(self, key):
'''Apply the name scope to a key
Parameters
----------
key : string
Returns
-------
`name/key` if `name` is not `None`;
otherwise, `key`.
'''
if self.name is None:
return key
return '{:s}/{:s}'.format(self.name, key) | python | def scope(self, key):
'''Apply the name scope to a key
Parameters
----------
key : string
Returns
-------
`name/key` if `name` is not `None`;
otherwise, `key`.
'''
if self.name is None:
return key
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bmcfee/pumpp | pumpp/base.py | Scope.register | def register(self, field, shape, dtype):
'''Register a field as a tensor with specified shape and type.
A `Tensor` of the given shape and type will be registered in this
object's `fields` dict.
Parameters
----------
field : str
The name of the field
shape : iterable of `int` or `None`
The shape of the output variable.
This does not include a dimension for multiple outputs.
`None` may be used to indicate variable-length outputs
dtype : type
The data type of the field
Raises
------
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If dtype or shape are improperly specified
'''
if not isinstance(dtype, type):
raise ParameterError('dtype={} must be a type'.format(dtype))
if not (isinstance(shape, Iterable) and
all([s is None or isinstance(s, int) for s in shape])):
raise ParameterError('shape={} must be an iterable of integers'.format(shape))
self.fields[self.scope(field)] = Tensor(tuple(shape), dtype) | python | def register(self, field, shape, dtype):
'''Register a field as a tensor with specified shape and type.
A `Tensor` of the given shape and type will be registered in this
object's `fields` dict.
Parameters
----------
field : str
The name of the field
shape : iterable of `int` or `None`
The shape of the output variable.
This does not include a dimension for multiple outputs.
`None` may be used to indicate variable-length outputs
dtype : type
The data type of the field
Raises
------
ParameterError
If dtype or shape are improperly specified
'''
if not isinstance(dtype, type):
raise ParameterError('dtype={} must be a type'.format(dtype))
if not (isinstance(shape, Iterable) and
all([s is None or isinstance(s, int) for s in shape])):
raise ParameterError('shape={} must be an iterable of integers'.format(shape))
self.fields[self.scope(field)] = Tensor(tuple(shape), dtype) | [
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bmcfee/pumpp | pumpp/base.py | Scope.merge | def merge(self, data):
'''Merge an array of output dictionaries into a single dictionary
with properly scoped names.
Parameters
----------
data : list of dict
Output dicts as produced by `pumpp.task.BaseTaskTransformer.transform`
or `pumpp.feature.FeatureExtractor.transform`.
Returns
-------
data_out : dict
All elements of the input dicts are stacked along the 0 axis,
and keys are re-mapped by `scope`.
'''
data_out = dict()
# Iterate over all keys in data
for key in set().union(*data):
data_out[self.scope(key)] = np.stack([np.asarray(d[key]) for d in data],
axis=0)
return data_out | python | def merge(self, data):
'''Merge an array of output dictionaries into a single dictionary
with properly scoped names.
Parameters
----------
data : list of dict
Output dicts as produced by `pumpp.task.BaseTaskTransformer.transform`
or `pumpp.feature.FeatureExtractor.transform`.
Returns
-------
data_out : dict
All elements of the input dicts are stacked along the 0 axis,
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return data_out | [
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bmcfee/pumpp | pumpp/base.py | Slicer.add | def add(self, operator):
'''Add an operator to the Slicer
Parameters
----------
operator : Scope (TaskTransformer or FeatureExtractor)
The new operator to add
'''
if not isinstance(operator, Scope):
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for key in operator.fields:
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# We add 1 to the dimension here to account for batching
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'''Add an operator to the Slicer
Parameters
----------
operator : Scope (TaskTransformer or FeatureExtractor)
The new operator to add
'''
if not isinstance(operator, Scope):
raise ParameterError('Operator {} must be a TaskTransformer '
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self._time[key] = []
# We add 1 to the dimension here to account for batching
for tdim, idx in enumerate(operator.fields[key].shape, 1):
if idx is None:
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bmcfee/pumpp | pumpp/base.py | Slicer.data_duration | def data_duration(self, data):
'''Compute the valid data duration of a dict
Parameters
----------
data : dict
As produced by pumpp.transform
Returns
-------
length : int
The minimum temporal extent of a dynamic observation in data
'''
# Find all the time-like indices of the data
lengths = []
for key in self._time:
for idx in self._time.get(key, []):
lengths.append(data[key].shape[idx])
return min(lengths) | python | def data_duration(self, data):
'''Compute the valid data duration of a dict
Parameters
----------
data : dict
As produced by pumpp.transform
Returns
-------
length : int
The minimum temporal extent of a dynamic observation in data
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bmcfee/pumpp | pumpp/base.py | Slicer.crop | def crop(self, data):
'''Crop a data dictionary down to its common time
Parameters
----------
data : dict
As produced by pumpp.transform
Returns
-------
data_cropped : dict
Like `data` but with all time-like axes truncated to the
minimum common duration
'''
duration = self.data_duration(data)
data_out = dict()
for key in data:
idx = [slice(None)] * data[key].ndim
for tdim in self._time.get(key, []):
idx[tdim] = slice(duration)
data_out[key] = data[key][tuple(idx)]
return data_out | python | def crop(self, data):
'''Crop a data dictionary down to its common time
Parameters
----------
data : dict
As produced by pumpp.transform
Returns
-------
data_cropped : dict
Like `data` but with all time-like axes truncated to the
minimum common duration
'''
duration = self.data_duration(data)
data_out = dict()
for key in data:
idx = [slice(None)] * data[key].ndim
for tdim in self._time.get(key, []):
idx[tdim] = slice(duration)
data_out[key] = data[key][tuple(idx)]
return data_out | [
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bmcfee/pumpp | pumpp/feature/mel.py | Mel.transform_audio | def transform_audio(self, y):
'''Compute the Mel spectrogram
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, n_mels)
The Mel spectrogram
'''
n_frames = self.n_frames(get_duration(y=y, sr=self.sr))
mel = np.sqrt(melspectrogram(y=y, sr=self.sr,
n_fft=self.n_fft,
hop_length=self.hop_length,
n_mels=self.n_mels,
fmax=self.fmax)).astype(np.float32)
mel = fix_length(mel, n_frames)
if self.log:
mel = amplitude_to_db(mel, ref=np.max)
return {'mag': mel.T[self.idx]} | python | def transform_audio(self, y):
'''Compute the Mel spectrogram
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, n_mels)
The Mel spectrogram
'''
n_frames = self.n_frames(get_duration(y=y, sr=self.sr))
mel = np.sqrt(melspectrogram(y=y, sr=self.sr,
n_fft=self.n_fft,
hop_length=self.hop_length,
n_mels=self.n_mels,
fmax=self.fmax)).astype(np.float32)
mel = fix_length(mel, n_frames)
if self.log:
mel = amplitude_to_db(mel, ref=np.max)
return {'mag': mel.T[self.idx]} | [
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bmcfee/pumpp | pumpp/task/regression.py | VectorTransformer.empty | def empty(self, duration):
'''Empty vector annotations.
This returns an annotation with a single observation
vector consisting of all-zeroes.
Parameters
----------
duration : number >0
Length of the track
Returns
-------
ann : jams.Annotation
The empty annotation
'''
ann = super(VectorTransformer, self).empty(duration)
ann.append(time=0, duration=duration, confidence=0,
value=np.zeros(self.dimension, dtype=np.float32))
return ann | python | def empty(self, duration):
'''Empty vector annotations.
This returns an annotation with a single observation
vector consisting of all-zeroes.
Parameters
----------
duration : number >0
Length of the track
Returns
-------
ann : jams.Annotation
The empty annotation
'''
ann = super(VectorTransformer, self).empty(duration)
ann.append(time=0, duration=duration, confidence=0,
value=np.zeros(self.dimension, dtype=np.float32))
return ann | [
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bmcfee/pumpp | pumpp/task/regression.py | VectorTransformer.transform_annotation | def transform_annotation(self, ann, duration):
'''Apply the vector transformation.
Parameters
----------
ann : jams.Annotation
The input annotation
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['vector'] : np.ndarray, shape=(dimension,)
Raises
------
DataError
If the input dimension does not match
'''
_, values = ann.to_interval_values()
vector = np.asarray(values[0], dtype=self.dtype)
if len(vector) != self.dimension:
raise DataError('vector dimension({:0}) '
'!= self.dimension({:1})'
.format(len(vector), self.dimension))
return {'vector': vector} | python | def transform_annotation(self, ann, duration):
'''Apply the vector transformation.
Parameters
----------
ann : jams.Annotation
The input annotation
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['vector'] : np.ndarray, shape=(dimension,)
Raises
------
DataError
If the input dimension does not match
'''
_, values = ann.to_interval_values()
vector = np.asarray(values[0], dtype=self.dtype)
if len(vector) != self.dimension:
raise DataError('vector dimension({:0}) '
'!= self.dimension({:1})'
.format(len(vector), self.dimension))
return {'vector': vector} | [
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-------
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------
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bmcfee/pumpp | pumpp/task/regression.py | VectorTransformer.inverse | def inverse(self, vector, duration=None):
'''Inverse vector transformer'''
ann = jams.Annotation(namespace=self.namespace, duration=duration)
if duration is None:
duration = 0
ann.append(time=0, duration=duration, value=vector)
return ann | python | def inverse(self, vector, duration=None):
'''Inverse vector transformer'''
ann = jams.Annotation(namespace=self.namespace, duration=duration)
if duration is None:
duration = 0
ann.append(time=0, duration=duration, value=vector)
return ann | [
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bmcfee/pumpp | pumpp/task/tags.py | DynamicLabelTransformer.set_transition | def set_transition(self, p_self):
'''Set the transition matrix according to self-loop probabilities.
Parameters
----------
p_self : None, float in (0, 1), or np.ndarray [shape=(n_labels,)]
Optional self-loop probability(ies), used for Viterbi decoding
'''
if p_self is None:
self.transition = None
else:
self.transition = np.empty((len(self._classes), 2, 2))
if np.isscalar(p_self):
self.transition = transition_loop(2, p_self)
elif len(p_self) != len(self._classes):
raise ParameterError('Invalid p_self.shape={} for vocabulary size={}'.format(p_self.shape, len(self._classes)))
else:
for i in range(len(self._classes)):
self.transition[i] = transition_loop(2, p_self[i]) | python | def set_transition(self, p_self):
'''Set the transition matrix according to self-loop probabilities.
Parameters
----------
p_self : None, float in (0, 1), or np.ndarray [shape=(n_labels,)]
Optional self-loop probability(ies), used for Viterbi decoding
'''
if p_self is None:
self.transition = None
else:
self.transition = np.empty((len(self._classes), 2, 2))
if np.isscalar(p_self):
self.transition = transition_loop(2, p_self)
elif len(p_self) != len(self._classes):
raise ParameterError('Invalid p_self.shape={} for vocabulary size={}'.format(p_self.shape, len(self._classes)))
else:
for i in range(len(self._classes)):
self.transition[i] = transition_loop(2, p_self[i]) | [
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bmcfee/pumpp | pumpp/task/tags.py | DynamicLabelTransformer.empty | def empty(self, duration):
'''Empty label annotations.
Constructs a single observation with an empty value (None).
Parameters
----------
duration : number > 0
The duration of the annotation
'''
ann = super(DynamicLabelTransformer, self).empty(duration)
ann.append(time=0, duration=duration, value=None)
return ann | python | def empty(self, duration):
'''Empty label annotations.
Constructs a single observation with an empty value (None).
Parameters
----------
duration : number > 0
The duration of the annotation
'''
ann = super(DynamicLabelTransformer, self).empty(duration)
ann.append(time=0, duration=duration, value=None)
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bmcfee/pumpp | pumpp/task/tags.py | DynamicLabelTransformer.transform_annotation | def transform_annotation(self, ann, duration):
'''Transform an annotation to dynamic label encoding.
Parameters
----------
ann : jams.Annotation
The annotation to convert
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['tags'] : np.ndarray, shape=(n, n_labels)
A time-varying binary encoding of the labels
'''
intervals, values = ann.to_interval_values()
# Suppress all intervals not in the encoder
tags = []
for v in values:
if v in self._classes:
tags.extend(self.encoder.transform([[v]]))
else:
tags.extend(self.encoder.transform([[]]))
tags = np.asarray(tags)
target = self.encode_intervals(duration, intervals, tags)
return {'tags': target} | python | def transform_annotation(self, ann, duration):
'''Transform an annotation to dynamic label encoding.
Parameters
----------
ann : jams.Annotation
The annotation to convert
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['tags'] : np.ndarray, shape=(n, n_labels)
A time-varying binary encoding of the labels
'''
intervals, values = ann.to_interval_values()
# Suppress all intervals not in the encoder
tags = []
for v in values:
if v in self._classes:
tags.extend(self.encoder.transform([[v]]))
else:
tags.extend(self.encoder.transform([[]]))
tags = np.asarray(tags)
target = self.encode_intervals(duration, intervals, tags)
return {'tags': target} | [
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The duration of the track
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bmcfee/pumpp | pumpp/task/tags.py | DynamicLabelTransformer.inverse | def inverse(self, encoded, duration=None):
'''Inverse transformation'''
ann = jams.Annotation(namespace=self.namespace, duration=duration)
for start, end, value in self.decode_intervals(encoded,
duration=duration,
transition=self.transition,
p_init=self.p_init,
p_state=self.p_state):
# Map start:end to frames
f_start, f_end = time_to_frames([start, end],
sr=self.sr,
hop_length=self.hop_length)
confidence = np.mean(encoded[f_start:f_end+1, value])
value_dec = self.encoder.inverse_transform(np.atleast_2d(value))[0]
for vd in value_dec:
ann.append(time=start,
duration=end-start,
value=vd,
confidence=confidence)
return ann | python | def inverse(self, encoded, duration=None):
'''Inverse transformation'''
ann = jams.Annotation(namespace=self.namespace, duration=duration)
for start, end, value in self.decode_intervals(encoded,
duration=duration,
transition=self.transition,
p_init=self.p_init,
p_state=self.p_state):
# Map start:end to frames
f_start, f_end = time_to_frames([start, end],
sr=self.sr,
hop_length=self.hop_length)
confidence = np.mean(encoded[f_start:f_end+1, value])
value_dec = self.encoder.inverse_transform(np.atleast_2d(value))[0]
for vd in value_dec:
ann.append(time=start,
duration=end-start,
value=vd,
confidence=confidence)
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bmcfee/pumpp | pumpp/task/tags.py | StaticLabelTransformer.transform_annotation | def transform_annotation(self, ann, duration):
'''Transform an annotation to static label encoding.
Parameters
----------
ann : jams.Annotation
The annotation to convert
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['tags'] : np.ndarray, shape=(n_labels,)
A static binary encoding of the labels
'''
intervals = np.asarray([[0, 1]])
values = list([obs.value for obs in ann])
intervals = np.tile(intervals, [len(values), 1])
# Suppress all intervals not in the encoder
tags = [v for v in values if v in self._classes]
if len(tags):
target = self.encoder.transform([tags]).astype(np.bool).max(axis=0)
else:
target = np.zeros(len(self._classes), dtype=np.bool)
return {'tags': target} | python | def transform_annotation(self, ann, duration):
'''Transform an annotation to static label encoding.
Parameters
----------
ann : jams.Annotation
The annotation to convert
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['tags'] : np.ndarray, shape=(n_labels,)
A static binary encoding of the labels
'''
intervals = np.asarray([[0, 1]])
values = list([obs.value for obs in ann])
intervals = np.tile(intervals, [len(values), 1])
# Suppress all intervals not in the encoder
tags = [v for v in values if v in self._classes]
if len(tags):
target = self.encoder.transform([tags]).astype(np.bool).max(axis=0)
else:
target = np.zeros(len(self._classes), dtype=np.bool)
return {'tags': target} | [
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The duration of the track
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-------
data : dict
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bmcfee/pumpp | pumpp/task/tags.py | StaticLabelTransformer.inverse | def inverse(self, encoded, duration=None):
'''Inverse static tag transformation'''
ann = jams.Annotation(namespace=self.namespace, duration=duration)
if np.isrealobj(encoded):
detected = (encoded >= 0.5)
else:
detected = encoded
for vd in self.encoder.inverse_transform(np.atleast_2d(detected))[0]:
vid = np.flatnonzero(self.encoder.transform(np.atleast_2d(vd)))
ann.append(time=0,
duration=duration,
value=vd,
confidence=encoded[vid])
return ann | python | def inverse(self, encoded, duration=None):
'''Inverse static tag transformation'''
ann = jams.Annotation(namespace=self.namespace, duration=duration)
if np.isrealobj(encoded):
detected = (encoded >= 0.5)
else:
detected = encoded
for vd in self.encoder.inverse_transform(np.atleast_2d(detected))[0]:
vid = np.flatnonzero(self.encoder.transform(np.atleast_2d(vd)))
ann.append(time=0,
duration=duration,
value=vd,
confidence=encoded[vid])
return ann | [
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bmcfee/pumpp | pumpp/feature/time.py | TimePosition.transform_audio | def transform_audio(self, y):
'''Compute the time position encoding
Parameters
----------
y : np.ndarray
Audio buffer
Returns
-------
data : dict
data['relative'] = np.ndarray, shape=(n_frames, 2)
data['absolute'] = np.ndarray, shape=(n_frames, 2)
Relative and absolute time positional encodings.
'''
duration = get_duration(y=y, sr=self.sr)
n_frames = self.n_frames(duration)
relative = np.zeros((n_frames, 2), dtype=np.float32)
relative[:, 0] = np.cos(np.pi * np.linspace(0, 1, num=n_frames))
relative[:, 1] = np.sin(np.pi * np.linspace(0, 1, num=n_frames))
absolute = relative * np.sqrt(duration)
return {'relative': relative[self.idx],
'absolute': absolute[self.idx]} | python | def transform_audio(self, y):
'''Compute the time position encoding
Parameters
----------
y : np.ndarray
Audio buffer
Returns
-------
data : dict
data['relative'] = np.ndarray, shape=(n_frames, 2)
data['absolute'] = np.ndarray, shape=(n_frames, 2)
Relative and absolute time positional encodings.
'''
duration = get_duration(y=y, sr=self.sr)
n_frames = self.n_frames(duration)
relative = np.zeros((n_frames, 2), dtype=np.float32)
relative[:, 0] = np.cos(np.pi * np.linspace(0, 1, num=n_frames))
relative[:, 1] = np.sin(np.pi * np.linspace(0, 1, num=n_frames))
absolute = relative * np.sqrt(duration)
return {'relative': relative[self.idx],
'absolute': absolute[self.idx]} | [
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bmcfee/pumpp | pumpp/core.py | Pump.add | def add(self, operator):
'''Add an operation to this pump.
Parameters
----------
operator : BaseTaskTransformer, FeatureExtractor
The operation to add
Raises
------
ParameterError
if `op` is not of a correct type
'''
if not isinstance(operator, (BaseTaskTransformer, FeatureExtractor)):
raise ParameterError('operator={} must be one of '
'(BaseTaskTransformer, FeatureExtractor)'
.format(operator))
if operator.name in self.opmap:
raise ParameterError('Duplicate operator name detected: '
'{}'.format(operator))
super(Pump, self).add(operator)
self.opmap[operator.name] = operator
self.ops.append(operator) | python | def add(self, operator):
'''Add an operation to this pump.
Parameters
----------
operator : BaseTaskTransformer, FeatureExtractor
The operation to add
Raises
------
ParameterError
if `op` is not of a correct type
'''
if not isinstance(operator, (BaseTaskTransformer, FeatureExtractor)):
raise ParameterError('operator={} must be one of '
'(BaseTaskTransformer, FeatureExtractor)'
.format(operator))
if operator.name in self.opmap:
raise ParameterError('Duplicate operator name detected: '
'{}'.format(operator))
super(Pump, self).add(operator)
self.opmap[operator.name] = operator
self.ops.append(operator) | [
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The operation to add
Raises
------
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bmcfee/pumpp | pumpp/core.py | Pump.transform | def transform(self, audio_f=None, jam=None, y=None, sr=None, crop=False):
'''Apply the transformations to an audio file, and optionally JAMS object.
Parameters
----------
audio_f : str
Path to audio file
jam : optional, `jams.JAMS`, str or file-like
Optional JAMS object/path to JAMS file/open file descriptor.
If provided, this will provide data for task transformers.
y : np.ndarray
sr : number > 0
If provided, operate directly on an existing audio buffer `y` at
sampling rate `sr` rather than load from `audio_f`.
crop : bool
If `True`, then data are cropped to a common time index across all
fields. Otherwise, data may have different time extents.
Returns
-------
data : dict
Data dictionary containing the transformed audio (and annotations)
Raises
------
ParameterError
At least one of `audio_f` or `(y, sr)` must be provided.
'''
if y is None:
if audio_f is None:
raise ParameterError('At least one of `y` or `audio_f` '
'must be provided')
# Load the audio
y, sr = librosa.load(audio_f, sr=sr, mono=True)
if sr is None:
raise ParameterError('If audio is provided as `y`, you must '
'specify the sampling rate as sr=')
if jam is None:
jam = jams.JAMS()
jam.file_metadata.duration = librosa.get_duration(y=y, sr=sr)
# Load the jams
if not isinstance(jam, jams.JAMS):
jam = jams.load(jam)
data = dict()
for operator in self.ops:
if isinstance(operator, BaseTaskTransformer):
data.update(operator.transform(jam))
elif isinstance(operator, FeatureExtractor):
data.update(operator.transform(y, sr))
if crop:
data = self.crop(data)
return data | python | def transform(self, audio_f=None, jam=None, y=None, sr=None, crop=False):
'''Apply the transformations to an audio file, and optionally JAMS object.
Parameters
----------
audio_f : str
Path to audio file
jam : optional, `jams.JAMS`, str or file-like
Optional JAMS object/path to JAMS file/open file descriptor.
If provided, this will provide data for task transformers.
y : np.ndarray
sr : number > 0
If provided, operate directly on an existing audio buffer `y` at
sampling rate `sr` rather than load from `audio_f`.
crop : bool
If `True`, then data are cropped to a common time index across all
fields. Otherwise, data may have different time extents.
Returns
-------
data : dict
Data dictionary containing the transformed audio (and annotations)
Raises
------
ParameterError
At least one of `audio_f` or `(y, sr)` must be provided.
'''
if y is None:
if audio_f is None:
raise ParameterError('At least one of `y` or `audio_f` '
'must be provided')
# Load the audio
y, sr = librosa.load(audio_f, sr=sr, mono=True)
if sr is None:
raise ParameterError('If audio is provided as `y`, you must '
'specify the sampling rate as sr=')
if jam is None:
jam = jams.JAMS()
jam.file_metadata.duration = librosa.get_duration(y=y, sr=sr)
# Load the jams
if not isinstance(jam, jams.JAMS):
jam = jams.load(jam)
data = dict()
for operator in self.ops:
if isinstance(operator, BaseTaskTransformer):
data.update(operator.transform(jam))
elif isinstance(operator, FeatureExtractor):
data.update(operator.transform(y, sr))
if crop:
data = self.crop(data)
return data | [
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If provided, this will provide data for task transformers.
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If `True`, then data are cropped to a common time index across all
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Returns
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data : dict
Data dictionary containing the transformed audio (and annotations)
Raises
------
ParameterError
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bmcfee/pumpp | pumpp/core.py | Pump.sampler | def sampler(self, n_samples, duration, random_state=None):
'''Construct a sampler object for this pump's operators.
Parameters
----------
n_samples : None or int > 0
The number of samples to generate
duration : int > 0
The duration (in frames) of each sample patch
random_state : None, int, or np.random.RandomState
If int, random_state is the seed used by the random number
generator;
If RandomState instance, random_state is the random number
generator;
If None, the random number generator is the RandomState instance
used by np.random.
Returns
-------
sampler : pumpp.Sampler
The sampler object
See Also
--------
pumpp.sampler.Sampler
'''
return Sampler(n_samples, duration,
random_state=random_state,
*self.ops) | python | def sampler(self, n_samples, duration, random_state=None):
'''Construct a sampler object for this pump's operators.
Parameters
----------
n_samples : None or int > 0
The number of samples to generate
duration : int > 0
The duration (in frames) of each sample patch
random_state : None, int, or np.random.RandomState
If int, random_state is the seed used by the random number
generator;
If RandomState instance, random_state is the random number
generator;
If None, the random number generator is the RandomState instance
used by np.random.
Returns
-------
sampler : pumpp.Sampler
The sampler object
See Also
--------
pumpp.sampler.Sampler
'''
return Sampler(n_samples, duration,
random_state=random_state,
*self.ops) | [
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duration : int > 0
The duration (in frames) of each sample patch
random_state : None, int, or np.random.RandomState
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bmcfee/pumpp | pumpp/core.py | Pump.fields | def fields(self):
'''A dictionary of fields constructed by this pump'''
out = dict()
for operator in self.ops:
out.update(**operator.fields)
return out | python | def fields(self):
'''A dictionary of fields constructed by this pump'''
out = dict()
for operator in self.ops:
out.update(**operator.fields)
return out | [
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bmcfee/pumpp | pumpp/core.py | Pump.layers | def layers(self):
'''Construct Keras input layers for all feature transformers
in the pump.
Returns
-------
layers : {field: keras.layers.Input}
A dictionary of keras input layers, keyed by the corresponding
fields.
'''
layermap = dict()
for operator in self.ops:
if hasattr(operator, 'layers'):
layermap.update(operator.layers())
return layermap | python | def layers(self):
'''Construct Keras input layers for all feature transformers
in the pump.
Returns
-------
layers : {field: keras.layers.Input}
A dictionary of keras input layers, keyed by the corresponding
fields.
'''
layermap = dict()
for operator in self.ops:
if hasattr(operator, 'layers'):
layermap.update(operator.layers())
return layermap | [
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Returns
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A dictionary of keras input layers, keyed by the corresponding
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bmcfee/pumpp | pumpp/task/beat.py | BeatTransformer.set_transition_beat | def set_transition_beat(self, p_self):
'''Set the beat-tracking transition matrix according to
self-loop probabilities.
Parameters
----------
p_self : None, float in (0, 1), or np.ndarray [shape=(2,)]
Optional self-loop probability(ies), used for Viterbi decoding
'''
if p_self is None:
self.beat_transition = None
else:
self.beat_transition = transition_loop(2, p_self) | python | def set_transition_beat(self, p_self):
'''Set the beat-tracking transition matrix according to
self-loop probabilities.
Parameters
----------
p_self : None, float in (0, 1), or np.ndarray [shape=(2,)]
Optional self-loop probability(ies), used for Viterbi decoding
'''
if p_self is None:
self.beat_transition = None
else:
self.beat_transition = transition_loop(2, p_self) | [
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bmcfee/pumpp | pumpp/task/beat.py | BeatTransformer.set_transition_down | def set_transition_down(self, p_self):
'''Set the downbeat-tracking transition matrix according to
self-loop probabilities.
Parameters
----------
p_self : None, float in (0, 1), or np.ndarray [shape=(2,)]
Optional self-loop probability(ies), used for Viterbi decoding
'''
if p_self is None:
self.down_transition = None
else:
self.down_transition = transition_loop(2, p_self) | python | def set_transition_down(self, p_self):
'''Set the downbeat-tracking transition matrix according to
self-loop probabilities.
Parameters
----------
p_self : None, float in (0, 1), or np.ndarray [shape=(2,)]
Optional self-loop probability(ies), used for Viterbi decoding
'''
if p_self is None:
self.down_transition = None
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self.down_transition = transition_loop(2, p_self) | [
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bmcfee/pumpp | pumpp/task/beat.py | BeatTransformer.transform_annotation | def transform_annotation(self, ann, duration):
'''Apply the beat transformer
Parameters
----------
ann : jams.Annotation
The input annotation
duration : number > 0
The duration of the audio
Returns
-------
data : dict
data['beat'] : np.ndarray, shape=(n, 1)
Binary indicator of beat/non-beat
data['downbeat'] : np.ndarray, shape=(n, 1)
Binary indicator of downbeat/non-downbeat
mask_downbeat : bool
True if downbeat annotations are present
'''
mask_downbeat = False
intervals, values = ann.to_interval_values()
values = np.asarray(values)
beat_events = intervals[:, 0]
beat_labels = np.ones((len(beat_events), 1))
idx = (values == 1)
if np.any(idx):
downbeat_events = beat_events[idx]
downbeat_labels = np.ones((len(downbeat_events), 1))
mask_downbeat = True
else:
downbeat_events = np.zeros(0)
downbeat_labels = np.zeros((0, 1))
target_beat = self.encode_events(duration,
beat_events,
beat_labels)
target_downbeat = self.encode_events(duration,
downbeat_events,
downbeat_labels)
return {'beat': target_beat,
'downbeat': target_downbeat,
'mask_downbeat': mask_downbeat} | python | def transform_annotation(self, ann, duration):
'''Apply the beat transformer
Parameters
----------
ann : jams.Annotation
The input annotation
duration : number > 0
The duration of the audio
Returns
-------
data : dict
data['beat'] : np.ndarray, shape=(n, 1)
Binary indicator of beat/non-beat
data['downbeat'] : np.ndarray, shape=(n, 1)
Binary indicator of downbeat/non-downbeat
mask_downbeat : bool
True if downbeat annotations are present
'''
mask_downbeat = False
intervals, values = ann.to_interval_values()
values = np.asarray(values)
beat_events = intervals[:, 0]
beat_labels = np.ones((len(beat_events), 1))
idx = (values == 1)
if np.any(idx):
downbeat_events = beat_events[idx]
downbeat_labels = np.ones((len(downbeat_events), 1))
mask_downbeat = True
else:
downbeat_events = np.zeros(0)
downbeat_labels = np.zeros((0, 1))
target_beat = self.encode_events(duration,
beat_events,
beat_labels)
target_downbeat = self.encode_events(duration,
downbeat_events,
downbeat_labels)
return {'beat': target_beat,
'downbeat': target_downbeat,
'mask_downbeat': mask_downbeat} | [
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The duration of the audio
Returns
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bmcfee/pumpp | pumpp/task/beat.py | BeatTransformer.inverse | def inverse(self, encoded, downbeat=None, duration=None):
'''Inverse transformation for beats and optional downbeats'''
ann = jams.Annotation(namespace=self.namespace, duration=duration)
beat_times = np.asarray([t for t, _ in self.decode_events(encoded,
transition=self.beat_transition,
p_init=self.beat_p_init,
p_state=self.beat_p_state) if _])
beat_frames = time_to_frames(beat_times,
sr=self.sr,
hop_length=self.hop_length)
if downbeat is not None:
downbeat_times = set([t for t, _ in self.decode_events(downbeat,
transition=self.down_transition,
p_init=self.down_p_init,
p_state=self.down_p_state) if _])
pickup_beats = len([t for t in beat_times
if t < min(downbeat_times)])
else:
downbeat_times = set()
pickup_beats = 0
value = - pickup_beats - 1
for beat_t, beat_f in zip(beat_times, beat_frames):
if beat_t in downbeat_times:
value = 1
else:
value += 1
confidence = encoded[beat_f]
ann.append(time=beat_t,
duration=0,
value=value,
confidence=confidence)
return ann | python | def inverse(self, encoded, downbeat=None, duration=None):
'''Inverse transformation for beats and optional downbeats'''
ann = jams.Annotation(namespace=self.namespace, duration=duration)
beat_times = np.asarray([t for t, _ in self.decode_events(encoded,
transition=self.beat_transition,
p_init=self.beat_p_init,
p_state=self.beat_p_state) if _])
beat_frames = time_to_frames(beat_times,
sr=self.sr,
hop_length=self.hop_length)
if downbeat is not None:
downbeat_times = set([t for t, _ in self.decode_events(downbeat,
transition=self.down_transition,
p_init=self.down_p_init,
p_state=self.down_p_state) if _])
pickup_beats = len([t for t in beat_times
if t < min(downbeat_times)])
else:
downbeat_times = set()
pickup_beats = 0
value = - pickup_beats - 1
for beat_t, beat_f in zip(beat_times, beat_frames):
if beat_t in downbeat_times:
value = 1
else:
value += 1
confidence = encoded[beat_f]
ann.append(time=beat_t,
duration=0,
value=value,
confidence=confidence)
return ann | [
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bmcfee/pumpp | pumpp/task/beat.py | BeatPositionTransformer.transform_annotation | def transform_annotation(self, ann, duration):
'''Transform an annotation to the beat-position encoding
Parameters
----------
ann : jams.Annotation
The annotation to convert
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['position'] : np.ndarray, shape=(n, n_labels) or (n, 1)
A time-varying label encoding of beat position
'''
# 1. get all the events
# 2. find all the downbeats
# 3. map each downbeat to a subdivision counter
# number of beats until the next downbeat
# 4. pad out events to intervals
# 5. encode each beat interval to its position
boundaries, values = ann.to_interval_values()
# Convert to intervals and span the duration
# padding at the end of track does not propagate the right label
# this is an artifact of inferring end-of-track from boundaries though
boundaries = list(boundaries[:, 0])
if boundaries and boundaries[-1] < duration:
boundaries.append(duration)
intervals = boundaries_to_intervals(boundaries)
intervals, values = adjust_intervals(intervals, values,
t_min=0,
t_max=duration,
start_label=0,
end_label=0)
values = np.asarray(values, dtype=int)
downbeats = np.flatnonzero(values == 1)
position = []
for i, v in enumerate(values):
# If the value is a 0, mark it as X and move on
if v == 0:
position.extend(self.encoder.transform(['X']))
continue
# Otherwise, let's try to find the surrounding downbeats
prev_idx = np.searchsorted(downbeats, i, side='right') - 1
next_idx = 1 + prev_idx
if prev_idx >= 0 and next_idx < len(downbeats):
# In this case, the subdivision is well-defined
subdivision = downbeats[next_idx] - downbeats[prev_idx]
elif prev_idx < 0 and next_idx < len(downbeats):
subdivision = np.max(values[:downbeats[0]+1])
elif next_idx >= len(downbeats):
subdivision = len(values) - downbeats[prev_idx]
if subdivision > self.max_divisions or subdivision < 1:
position.extend(self.encoder.transform(['X']))
else:
position.extend(self.encoder.transform(['{:02d}/{:02d}'.format(subdivision, v)]))
dtype = self.fields[self.scope('position')].dtype
position = np.asarray(position)
if self.sparse:
position = position[:, np.newaxis]
target = self.encode_intervals(duration, intervals, position,
multi=False, dtype=dtype)
return {'position': target} | python | def transform_annotation(self, ann, duration):
'''Transform an annotation to the beat-position encoding
Parameters
----------
ann : jams.Annotation
The annotation to convert
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['position'] : np.ndarray, shape=(n, n_labels) or (n, 1)
A time-varying label encoding of beat position
'''
# 1. get all the events
# 2. find all the downbeats
# 3. map each downbeat to a subdivision counter
# number of beats until the next downbeat
# 4. pad out events to intervals
# 5. encode each beat interval to its position
boundaries, values = ann.to_interval_values()
# Convert to intervals and span the duration
# padding at the end of track does not propagate the right label
# this is an artifact of inferring end-of-track from boundaries though
boundaries = list(boundaries[:, 0])
if boundaries and boundaries[-1] < duration:
boundaries.append(duration)
intervals = boundaries_to_intervals(boundaries)
intervals, values = adjust_intervals(intervals, values,
t_min=0,
t_max=duration,
start_label=0,
end_label=0)
values = np.asarray(values, dtype=int)
downbeats = np.flatnonzero(values == 1)
position = []
for i, v in enumerate(values):
# If the value is a 0, mark it as X and move on
if v == 0:
position.extend(self.encoder.transform(['X']))
continue
# Otherwise, let's try to find the surrounding downbeats
prev_idx = np.searchsorted(downbeats, i, side='right') - 1
next_idx = 1 + prev_idx
if prev_idx >= 0 and next_idx < len(downbeats):
# In this case, the subdivision is well-defined
subdivision = downbeats[next_idx] - downbeats[prev_idx]
elif prev_idx < 0 and next_idx < len(downbeats):
subdivision = np.max(values[:downbeats[0]+1])
elif next_idx >= len(downbeats):
subdivision = len(values) - downbeats[prev_idx]
if subdivision > self.max_divisions or subdivision < 1:
position.extend(self.encoder.transform(['X']))
else:
position.extend(self.encoder.transform(['{:02d}/{:02d}'.format(subdivision, v)]))
dtype = self.fields[self.scope('position')].dtype
position = np.asarray(position)
if self.sparse:
position = position[:, np.newaxis]
target = self.encode_intervals(duration, intervals, position,
multi=False, dtype=dtype)
return {'position': target} | [
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bmcfee/pumpp | pumpp/feature/rhythm.py | Tempogram.transform_audio | def transform_audio(self, y):
'''Compute the tempogram
Parameters
----------
y : np.ndarray
Audio buffer
Returns
-------
data : dict
data['tempogram'] : np.ndarray, shape=(n_frames, win_length)
The tempogram
'''
n_frames = self.n_frames(get_duration(y=y, sr=self.sr))
tgram = tempogram(y=y, sr=self.sr,
hop_length=self.hop_length,
win_length=self.win_length).astype(np.float32)
tgram = fix_length(tgram, n_frames)
return {'tempogram': tgram.T[self.idx]} | python | def transform_audio(self, y):
'''Compute the tempogram
Parameters
----------
y : np.ndarray
Audio buffer
Returns
-------
data : dict
data['tempogram'] : np.ndarray, shape=(n_frames, win_length)
The tempogram
'''
n_frames = self.n_frames(get_duration(y=y, sr=self.sr))
tgram = tempogram(y=y, sr=self.sr,
hop_length=self.hop_length,
win_length=self.win_length).astype(np.float32)
tgram = fix_length(tgram, n_frames)
return {'tempogram': tgram.T[self.idx]} | [
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bmcfee/pumpp | pumpp/feature/rhythm.py | TempoScale.transform_audio | def transform_audio(self, y):
'''Apply the scale transform to the tempogram
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['temposcale'] : np.ndarray, shape=(n_frames, n_fmt)
The scale transform magnitude coefficients
'''
data = super(TempoScale, self).transform_audio(y)
data['temposcale'] = np.abs(fmt(data.pop('tempogram'),
axis=1,
n_fmt=self.n_fmt)).astype(np.float32)[self.idx]
return data | python | def transform_audio(self, y):
'''Apply the scale transform to the tempogram
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['temposcale'] : np.ndarray, shape=(n_frames, n_fmt)
The scale transform magnitude coefficients
'''
data = super(TempoScale, self).transform_audio(y)
data['temposcale'] = np.abs(fmt(data.pop('tempogram'),
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n_fmt=self.n_fmt)).astype(np.float32)[self.idx]
return data | [
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bmcfee/pumpp | pumpp/task/structure.py | StructureTransformer.transform_annotation | def transform_annotation(self, ann, duration):
'''Apply the structure agreement transformation.
Parameters
----------
ann : jams.Annotation
The segment annotation
duration : number > 0
The target duration
Returns
-------
data : dict
data['agree'] : np.ndarray, shape=(n, n), dtype=bool
'''
intervals, values = ann.to_interval_values()
intervals, values = adjust_intervals(intervals, values,
t_min=0, t_max=duration)
# Re-index the labels
ids, _ = index_labels(values)
rate = float(self.hop_length) / self.sr
# Sample segment labels on our frame grid
_, labels = intervals_to_samples(intervals, ids, sample_size=rate)
# Make the agreement matrix
return {'agree': np.equal.outer(labels, labels)} | python | def transform_annotation(self, ann, duration):
'''Apply the structure agreement transformation.
Parameters
----------
ann : jams.Annotation
The segment annotation
duration : number > 0
The target duration
Returns
-------
data : dict
data['agree'] : np.ndarray, shape=(n, n), dtype=bool
'''
intervals, values = ann.to_interval_values()
intervals, values = adjust_intervals(intervals, values,
t_min=0, t_max=duration)
# Re-index the labels
ids, _ = index_labels(values)
rate = float(self.hop_length) / self.sr
# Sample segment labels on our frame grid
_, labels = intervals_to_samples(intervals, ids, sample_size=rate)
# Make the agreement matrix
return {'agree': np.equal.outer(labels, labels)} | [
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bmcfee/pumpp | pumpp/feature/fft.py | STFT.transform_audio | def transform_audio(self, y):
'''Compute the STFT magnitude and phase.
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, 1 + n_fft//2)
STFT magnitude
data['phase'] : np.ndarray, shape=(n_frames, 1 + n_fft//2)
STFT phase
'''
n_frames = self.n_frames(get_duration(y=y, sr=self.sr))
D = stft(y, hop_length=self.hop_length,
n_fft=self.n_fft)
D = fix_length(D, n_frames)
mag, phase = magphase(D)
if self.log:
mag = amplitude_to_db(mag, ref=np.max)
return {'mag': mag.T[self.idx].astype(np.float32),
'phase': np.angle(phase.T)[self.idx].astype(np.float32)} | python | def transform_audio(self, y):
'''Compute the STFT magnitude and phase.
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, 1 + n_fft//2)
STFT magnitude
data['phase'] : np.ndarray, shape=(n_frames, 1 + n_fft//2)
STFT phase
'''
n_frames = self.n_frames(get_duration(y=y, sr=self.sr))
D = stft(y, hop_length=self.hop_length,
n_fft=self.n_fft)
D = fix_length(D, n_frames)
mag, phase = magphase(D)
if self.log:
mag = amplitude_to_db(mag, ref=np.max)
return {'mag': mag.T[self.idx].astype(np.float32),
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bmcfee/pumpp | pumpp/feature/fft.py | STFTPhaseDiff.transform_audio | def transform_audio(self, y):
'''Compute the STFT with phase differentials.
Parameters
----------
y : np.ndarray
the audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, 1 + n_fft//2)
The STFT magnitude
data['dphase'] : np.ndarray, shape=(n_frames, 1 + n_fft//2)
The unwrapped phase differential
'''
data = super(STFTPhaseDiff, self).transform_audio(y)
data['dphase'] = self.phase_diff(data.pop('phase'))
return data | python | def transform_audio(self, y):
'''Compute the STFT with phase differentials.
Parameters
----------
y : np.ndarray
the audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, 1 + n_fft//2)
The STFT magnitude
data['dphase'] : np.ndarray, shape=(n_frames, 1 + n_fft//2)
The unwrapped phase differential
'''
data = super(STFTPhaseDiff, self).transform_audio(y)
data['dphase'] = self.phase_diff(data.pop('phase'))
return data | [
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bmcfee/pumpp | pumpp/feature/fft.py | STFTMag.transform_audio | def transform_audio(self, y):
'''Compute the STFT
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, 1 + n_fft//2)
The STFT magnitude
'''
data = super(STFTMag, self).transform_audio(y)
data.pop('phase')
return data | python | def transform_audio(self, y):
'''Compute the STFT
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, 1 + n_fft//2)
The STFT magnitude
'''
data = super(STFTMag, self).transform_audio(y)
data.pop('phase')
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bmcfee/pumpp | pumpp/task/chord.py | _pad_nochord | def _pad_nochord(target, axis=-1):
'''Pad a chord annotation with no-chord flags.
Parameters
----------
target : np.ndarray
the input data
axis : int
the axis along which to pad
Returns
-------
target_pad
`target` expanded by 1 along the specified `axis`.
The expanded dimension will be 0 when `target` is non-zero
before padding, and 1 otherwise.
'''
ncmask = ~np.max(target, axis=axis, keepdims=True)
return np.concatenate([target, ncmask], axis=axis) | python | def _pad_nochord(target, axis=-1):
'''Pad a chord annotation with no-chord flags.
Parameters
----------
target : np.ndarray
the input data
axis : int
the axis along which to pad
Returns
-------
target_pad
`target` expanded by 1 along the specified `axis`.
The expanded dimension will be 0 when `target` is non-zero
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ncmask = ~np.max(target, axis=axis, keepdims=True)
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Parameters
----------
target : np.ndarray
the input data
axis : int
the axis along which to pad
Returns
-------
target_pad
`target` expanded by 1 along the specified `axis`.
The expanded dimension will be 0 when `target` is non-zero
before padding, and 1 otherwise. | [
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] | train | https://github.com/bmcfee/pumpp/blob/06a17b888271dd1f6cd41bddb22b0eb04d494056/pumpp/task/chord.py#L24-L44 |
bmcfee/pumpp | pumpp/task/chord.py | ChordTransformer.empty | def empty(self, duration):
'''Empty chord annotations
Parameters
----------
duration : number
The length (in seconds) of the empty annotation
Returns
-------
ann : jams.Annotation
A chord annotation consisting of a single `no-chord` observation.
'''
ann = super(ChordTransformer, self).empty(duration)
ann.append(time=0,
duration=duration,
value='N', confidence=0)
return ann | python | def empty(self, duration):
'''Empty chord annotations
Parameters
----------
duration : number
The length (in seconds) of the empty annotation
Returns
-------
ann : jams.Annotation
A chord annotation consisting of a single `no-chord` observation.
'''
ann = super(ChordTransformer, self).empty(duration)
ann.append(time=0,
duration=duration,
value='N', confidence=0)
return ann | [
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bmcfee/pumpp | pumpp/task/chord.py | ChordTransformer.transform_annotation | def transform_annotation(self, ann, duration):
'''Apply the chord transformation.
Parameters
----------
ann : jams.Annotation
The chord annotation
duration : number > 0
The target duration
Returns
-------
data : dict
data['pitch'] : np.ndarray, shape=(n, 12)
data['root'] : np.ndarray, shape=(n, 13) or (n, 1)
data['bass'] : np.ndarray, shape=(n, 13) or (n, 1)
`pitch` is a binary matrix indicating pitch class
activation at each frame.
`root` is a one-hot matrix indicating the chord
root's pitch class at each frame.
`bass` is a one-hot matrix indicating the chord
bass (lowest note) pitch class at each frame.
If sparsely encoded, `root` and `bass` are integers
in the range [0, 12] where 12 indicates no chord.
If densely encoded, `root` and `bass` have an extra
final dimension which is active when there is no chord
sounding.
'''
# Construct a blank annotation with mask = 0
intervals, chords = ann.to_interval_values()
# Get the dtype for root/bass
if self.sparse:
dtype = np.int
else:
dtype = np.bool
# If we don't have any labeled intervals, fill in a no-chord
if not chords:
intervals = np.asarray([[0, duration]])
chords = ['N']
# Suppress all intervals not in the encoder
pitches = []
roots = []
basses = []
# default value when data is missing
if self.sparse:
fill = 12
else:
fill = False
for chord in chords:
# Encode the pitches
root, semi, bass = mir_eval.chord.encode(chord)
pitches.append(np.roll(semi, root))
if self.sparse:
if root in self._classes:
roots.append([root])
basses.append([(root + bass) % 12])
else:
roots.append([fill])
basses.append([fill])
else:
if root in self._classes:
roots.extend(self.encoder.transform([[root]]))
basses.extend(self.encoder.transform([[(root + bass) % 12]]))
else:
roots.extend(self.encoder.transform([[]]))
basses.extend(self.encoder.transform([[]]))
pitches = np.asarray(pitches, dtype=np.bool)
roots = np.asarray(roots, dtype=dtype)
basses = np.asarray(basses, dtype=dtype)
target_pitch = self.encode_intervals(duration, intervals, pitches)
target_root = self.encode_intervals(duration, intervals, roots,
multi=False,
dtype=dtype,
fill=fill)
target_bass = self.encode_intervals(duration, intervals, basses,
multi=False,
dtype=dtype,
fill=fill)
if not self.sparse:
target_root = _pad_nochord(target_root)
target_bass = _pad_nochord(target_bass)
return {'pitch': target_pitch,
'root': target_root,
'bass': target_bass} | python | def transform_annotation(self, ann, duration):
'''Apply the chord transformation.
Parameters
----------
ann : jams.Annotation
The chord annotation
duration : number > 0
The target duration
Returns
-------
data : dict
data['pitch'] : np.ndarray, shape=(n, 12)
data['root'] : np.ndarray, shape=(n, 13) or (n, 1)
data['bass'] : np.ndarray, shape=(n, 13) or (n, 1)
`pitch` is a binary matrix indicating pitch class
activation at each frame.
`root` is a one-hot matrix indicating the chord
root's pitch class at each frame.
`bass` is a one-hot matrix indicating the chord
bass (lowest note) pitch class at each frame.
If sparsely encoded, `root` and `bass` are integers
in the range [0, 12] where 12 indicates no chord.
If densely encoded, `root` and `bass` have an extra
final dimension which is active when there is no chord
sounding.
'''
# Construct a blank annotation with mask = 0
intervals, chords = ann.to_interval_values()
# Get the dtype for root/bass
if self.sparse:
dtype = np.int
else:
dtype = np.bool
# If we don't have any labeled intervals, fill in a no-chord
if not chords:
intervals = np.asarray([[0, duration]])
chords = ['N']
# Suppress all intervals not in the encoder
pitches = []
roots = []
basses = []
# default value when data is missing
if self.sparse:
fill = 12
else:
fill = False
for chord in chords:
# Encode the pitches
root, semi, bass = mir_eval.chord.encode(chord)
pitches.append(np.roll(semi, root))
if self.sparse:
if root in self._classes:
roots.append([root])
basses.append([(root + bass) % 12])
else:
roots.append([fill])
basses.append([fill])
else:
if root in self._classes:
roots.extend(self.encoder.transform([[root]]))
basses.extend(self.encoder.transform([[(root + bass) % 12]]))
else:
roots.extend(self.encoder.transform([[]]))
basses.extend(self.encoder.transform([[]]))
pitches = np.asarray(pitches, dtype=np.bool)
roots = np.asarray(roots, dtype=dtype)
basses = np.asarray(basses, dtype=dtype)
target_pitch = self.encode_intervals(duration, intervals, pitches)
target_root = self.encode_intervals(duration, intervals, roots,
multi=False,
dtype=dtype,
fill=fill)
target_bass = self.encode_intervals(duration, intervals, basses,
multi=False,
dtype=dtype,
fill=fill)
if not self.sparse:
target_root = _pad_nochord(target_root)
target_bass = _pad_nochord(target_bass)
return {'pitch': target_pitch,
'root': target_root,
'bass': target_bass} | [
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The target duration
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data['root'] : np.ndarray, shape=(n, 13) or (n, 1)
data['bass'] : np.ndarray, shape=(n, 13) or (n, 1)
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`bass` is a one-hot matrix indicating the chord
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bmcfee/pumpp | pumpp/task/chord.py | SimpleChordTransformer.transform_annotation | def transform_annotation(self, ann, duration):
'''Apply the chord transformation.
Parameters
----------
ann : jams.Annotation
The chord annotation
duration : number > 0
The target duration
Returns
-------
data : dict
data['pitch'] : np.ndarray, shape=(n, 12)
`pitch` is a binary matrix indicating pitch class
activation at each frame.
'''
data = super(SimpleChordTransformer,
self).transform_annotation(ann, duration)
data.pop('root', None)
data.pop('bass', None)
return data | python | def transform_annotation(self, ann, duration):
'''Apply the chord transformation.
Parameters
----------
ann : jams.Annotation
The chord annotation
duration : number > 0
The target duration
Returns
-------
data : dict
data['pitch'] : np.ndarray, shape=(n, 12)
`pitch` is a binary matrix indicating pitch class
activation at each frame.
'''
data = super(SimpleChordTransformer,
self).transform_annotation(ann, duration)
data.pop('root', None)
data.pop('bass', None)
return data | [
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The target duration
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bmcfee/pumpp | pumpp/task/chord.py | ChordTagTransformer.set_transition | def set_transition(self, p_self):
'''Set the transition matrix according to self-loop probabilities.
Parameters
----------
p_self : None, float in (0, 1), or np.ndarray [shape=(n_labels,)]
Optional self-loop probability(ies), used for Viterbi decoding
'''
if p_self is None:
self.transition = None
else:
self.transition = transition_loop(len(self._classes), p_self) | python | def set_transition(self, p_self):
'''Set the transition matrix according to self-loop probabilities.
Parameters
----------
p_self : None, float in (0, 1), or np.ndarray [shape=(n_labels,)]
Optional self-loop probability(ies), used for Viterbi decoding
'''
if p_self is None:
self.transition = None
else:
self.transition = transition_loop(len(self._classes), p_self) | [
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bmcfee/pumpp | pumpp/task/chord.py | ChordTagTransformer.simplify | def simplify(self, chord):
'''Simplify a chord string down to the vocabulary space'''
# Drop inversions
chord = re.sub(r'/.*$', r'', chord)
# Drop any additional or suppressed tones
chord = re.sub(r'\(.*?\)', r'', chord)
# Drop dangling : indicators
chord = re.sub(r':$', r'', chord)
# Encode the chord
root, pitches, _ = mir_eval.chord.encode(chord)
# Build the query
# To map the binary vector pitches down to bit masked integer,
# we just dot against powers of 2
P = 2**np.arange(12, dtype=int)
query = self.mask_ & pitches[::-1].dot(P)
if root < 0 and chord[0].upper() == 'N':
return 'N'
if query not in QUALITIES:
return 'X'
return '{}:{}'.format(PITCHES[root], QUALITIES[query]) | python | def simplify(self, chord):
'''Simplify a chord string down to the vocabulary space'''
# Drop inversions
chord = re.sub(r'/.*$', r'', chord)
# Drop any additional or suppressed tones
chord = re.sub(r'\(.*?\)', r'', chord)
# Drop dangling : indicators
chord = re.sub(r':$', r'', chord)
# Encode the chord
root, pitches, _ = mir_eval.chord.encode(chord)
# Build the query
# To map the binary vector pitches down to bit masked integer,
# we just dot against powers of 2
P = 2**np.arange(12, dtype=int)
query = self.mask_ & pitches[::-1].dot(P)
if root < 0 and chord[0].upper() == 'N':
return 'N'
if query not in QUALITIES:
return 'X'
return '{}:{}'.format(PITCHES[root], QUALITIES[query]) | [
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bmcfee/pumpp | pumpp/task/chord.py | ChordTagTransformer.transform_annotation | def transform_annotation(self, ann, duration):
'''Transform an annotation to chord-tag encoding
Parameters
----------
ann : jams.Annotation
The annotation to convert
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['chord'] : np.ndarray, shape=(n, n_labels)
A time-varying binary encoding of the chords
'''
intervals, values = ann.to_interval_values()
chords = []
for v in values:
chords.extend(self.encoder.transform([self.simplify(v)]))
dtype = self.fields[self.scope('chord')].dtype
chords = np.asarray(chords)
if self.sparse:
chords = chords[:, np.newaxis]
target = self.encode_intervals(duration, intervals, chords,
multi=False, dtype=dtype)
return {'chord': target} | python | def transform_annotation(self, ann, duration):
'''Transform an annotation to chord-tag encoding
Parameters
----------
ann : jams.Annotation
The annotation to convert
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['chord'] : np.ndarray, shape=(n, n_labels)
A time-varying binary encoding of the chords
'''
intervals, values = ann.to_interval_values()
chords = []
for v in values:
chords.extend(self.encoder.transform([self.simplify(v)]))
dtype = self.fields[self.scope('chord')].dtype
chords = np.asarray(chords)
if self.sparse:
chords = chords[:, np.newaxis]
target = self.encode_intervals(duration, intervals, chords,
multi=False, dtype=dtype)
return {'chord': target} | [
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Parameters
----------
ann : jams.Annotation
The annotation to convert
duration : number > 0
The duration of the track
Returns
-------
data : dict
data['chord'] : np.ndarray, shape=(n, n_labels)
A time-varying binary encoding of the chords | [
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bmcfee/pumpp | pumpp/feature/cqt.py | CQT.transform_audio | def transform_audio(self, y):
'''Compute the CQT
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape = (n_frames, n_bins)
The CQT magnitude
data['phase']: np.ndarray, shape = mag.shape
The CQT phase
'''
n_frames = self.n_frames(get_duration(y=y, sr=self.sr))
C = cqt(y=y, sr=self.sr, hop_length=self.hop_length,
fmin=self.fmin,
n_bins=(self.n_octaves * self.over_sample * 12),
bins_per_octave=(self.over_sample * 12))
C = fix_length(C, n_frames)
cqtm, phase = magphase(C)
if self.log:
cqtm = amplitude_to_db(cqtm, ref=np.max)
return {'mag': cqtm.T.astype(np.float32)[self.idx],
'phase': np.angle(phase).T.astype(np.float32)[self.idx]} | python | def transform_audio(self, y):
'''Compute the CQT
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape = (n_frames, n_bins)
The CQT magnitude
data['phase']: np.ndarray, shape = mag.shape
The CQT phase
'''
n_frames = self.n_frames(get_duration(y=y, sr=self.sr))
C = cqt(y=y, sr=self.sr, hop_length=self.hop_length,
fmin=self.fmin,
n_bins=(self.n_octaves * self.over_sample * 12),
bins_per_octave=(self.over_sample * 12))
C = fix_length(C, n_frames)
cqtm, phase = magphase(C)
if self.log:
cqtm = amplitude_to_db(cqtm, ref=np.max)
return {'mag': cqtm.T.astype(np.float32)[self.idx],
'phase': np.angle(phase).T.astype(np.float32)[self.idx]} | [
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----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape = (n_frames, n_bins)
The CQT magnitude
data['phase']: np.ndarray, shape = mag.shape
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bmcfee/pumpp | pumpp/feature/cqt.py | CQTMag.transform_audio | def transform_audio(self, y):
'''Compute CQT magnitude.
Parameters
----------
y : np.ndarray
the audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, n_bins)
The CQT magnitude
'''
data = super(CQTMag, self).transform_audio(y)
data.pop('phase')
return data | python | def transform_audio(self, y):
'''Compute CQT magnitude.
Parameters
----------
y : np.ndarray
the audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, n_bins)
The CQT magnitude
'''
data = super(CQTMag, self).transform_audio(y)
data.pop('phase')
return data | [
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bmcfee/pumpp | pumpp/feature/cqt.py | CQTPhaseDiff.transform_audio | def transform_audio(self, y):
'''Compute the CQT with unwrapped phase
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, n_bins)
CQT magnitude
data['dphase'] : np.ndarray, shape=(n_frames, n_bins)
Unwrapped phase differential
'''
data = super(CQTPhaseDiff, self).transform_audio(y)
data['dphase'] = self.phase_diff(data.pop('phase'))
return data | python | def transform_audio(self, y):
'''Compute the CQT with unwrapped phase
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, n_bins)
CQT magnitude
data['dphase'] : np.ndarray, shape=(n_frames, n_bins)
Unwrapped phase differential
'''
data = super(CQTPhaseDiff, self).transform_audio(y)
data['dphase'] = self.phase_diff(data.pop('phase'))
return data | [
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CQT magnitude
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bmcfee/pumpp | pumpp/feature/cqt.py | HCQT.transform_audio | def transform_audio(self, y):
'''Compute the HCQT
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape = (n_frames, n_bins, n_harmonics)
The CQT magnitude
data['phase']: np.ndarray, shape = mag.shape
The CQT phase
'''
cqtm, phase = [], []
n_frames = self.n_frames(get_duration(y=y, sr=self.sr))
for h in self.harmonics:
C = cqt(y=y, sr=self.sr, hop_length=self.hop_length,
fmin=self.fmin * h,
n_bins=(self.n_octaves * self.over_sample * 12),
bins_per_octave=(self.over_sample * 12))
C = fix_length(C, n_frames)
C, P = magphase(C)
if self.log:
C = amplitude_to_db(C, ref=np.max)
cqtm.append(C)
phase.append(P)
cqtm = np.asarray(cqtm).astype(np.float32)
phase = np.angle(np.asarray(phase)).astype(np.float32)
return {'mag': self._index(cqtm),
'phase': self._index(phase)} | python | def transform_audio(self, y):
'''Compute the HCQT
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape = (n_frames, n_bins, n_harmonics)
The CQT magnitude
data['phase']: np.ndarray, shape = mag.shape
The CQT phase
'''
cqtm, phase = [], []
n_frames = self.n_frames(get_duration(y=y, sr=self.sr))
for h in self.harmonics:
C = cqt(y=y, sr=self.sr, hop_length=self.hop_length,
fmin=self.fmin * h,
n_bins=(self.n_octaves * self.over_sample * 12),
bins_per_octave=(self.over_sample * 12))
C = fix_length(C, n_frames)
C, P = magphase(C)
if self.log:
C = amplitude_to_db(C, ref=np.max)
cqtm.append(C)
phase.append(P)
cqtm = np.asarray(cqtm).astype(np.float32)
phase = np.angle(np.asarray(phase)).astype(np.float32)
return {'mag': self._index(cqtm),
'phase': self._index(phase)} | [
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y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape = (n_frames, n_bins, n_harmonics)
The CQT magnitude
data['phase']: np.ndarray, shape = mag.shape
The CQT phase | [
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bmcfee/pumpp | pumpp/feature/cqt.py | HCQT._index | def _index(self, value):
'''Rearrange a tensor according to the convolution mode
Input is assumed to be in (channels, bins, time) format.
'''
if self.conv in ('channels_last', 'tf'):
return np.transpose(value, (2, 1, 0))
else: # self.conv in ('channels_first', 'th')
return np.transpose(value, (0, 2, 1)) | python | def _index(self, value):
'''Rearrange a tensor according to the convolution mode
Input is assumed to be in (channels, bins, time) format.
'''
if self.conv in ('channels_last', 'tf'):
return np.transpose(value, (2, 1, 0))
else: # self.conv in ('channels_first', 'th')
return np.transpose(value, (0, 2, 1)) | [
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bmcfee/pumpp | pumpp/feature/cqt.py | HCQTMag.transform_audio | def transform_audio(self, y):
'''Compute HCQT magnitude.
Parameters
----------
y : np.ndarray
the audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, n_bins)
The CQT magnitude
'''
data = super(HCQTMag, self).transform_audio(y)
data.pop('phase')
return data | python | def transform_audio(self, y):
'''Compute HCQT magnitude.
Parameters
----------
y : np.ndarray
the audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, n_bins)
The CQT magnitude
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data = super(HCQTMag, self).transform_audio(y)
data.pop('phase')
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bmcfee/pumpp | pumpp/feature/cqt.py | HCQTPhaseDiff.transform_audio | def transform_audio(self, y):
'''Compute the HCQT with unwrapped phase
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, n_bins)
CQT magnitude
data['dphase'] : np.ndarray, shape=(n_frames, n_bins)
Unwrapped phase differential
'''
data = super(HCQTPhaseDiff, self).transform_audio(y)
data['dphase'] = self.phase_diff(data.pop('phase'))
return data | python | def transform_audio(self, y):
'''Compute the HCQT with unwrapped phase
Parameters
----------
y : np.ndarray
The audio buffer
Returns
-------
data : dict
data['mag'] : np.ndarray, shape=(n_frames, n_bins)
CQT magnitude
data['dphase'] : np.ndarray, shape=(n_frames, n_bins)
Unwrapped phase differential
'''
data = super(HCQTPhaseDiff, self).transform_audio(y)
data['dphase'] = self.phase_diff(data.pop('phase'))
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CQT magnitude
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bmcfee/pumpp | pumpp/task/base.py | fill_value | def fill_value(dtype):
'''Get a fill-value for a given dtype
Parameters
----------
dtype : type
Returns
-------
`np.nan` if `dtype` is real or complex
0 otherwise
'''
if np.issubdtype(dtype, np.floating) or np.issubdtype(dtype, np.complexfloating):
return dtype(np.nan)
return dtype(0) | python | def fill_value(dtype):
'''Get a fill-value for a given dtype
Parameters
----------
dtype : type
Returns
-------
`np.nan` if `dtype` is real or complex
0 otherwise
'''
if np.issubdtype(dtype, np.floating) or np.issubdtype(dtype, np.complexfloating):
return dtype(np.nan)
return dtype(0) | [
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bmcfee/pumpp | pumpp/task/base.py | BaseTaskTransformer.empty | def empty(self, duration):
'''Create an empty jams.Annotation for this task.
This method should be overridden by derived classes.
Parameters
----------
duration : int >= 0
Duration of the annotation
'''
return jams.Annotation(namespace=self.namespace, time=0, duration=0) | python | def empty(self, duration):
'''Create an empty jams.Annotation for this task.
This method should be overridden by derived classes.
Parameters
----------
duration : int >= 0
Duration of the annotation
'''
return jams.Annotation(namespace=self.namespace, time=0, duration=0) | [
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duration : int >= 0
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bmcfee/pumpp | pumpp/task/base.py | BaseTaskTransformer.transform | def transform(self, jam, query=None):
'''Transform jam object to make data for this task
Parameters
----------
jam : jams.JAMS
The jams container object
query : string, dict, or callable [optional]
An optional query to narrow the elements of `jam.annotations`
to be considered.
If not provided, all annotations are considered.
Returns
-------
data : dict
A dictionary of transformed annotations.
All annotations which can be converted to the target namespace
will be converted.
'''
anns = []
if query:
results = jam.search(**query)
else:
results = jam.annotations
# Find annotations that can be coerced to our target namespace
for ann in results:
try:
anns.append(jams.nsconvert.convert(ann, self.namespace))
except jams.NamespaceError:
pass
duration = jam.file_metadata.duration
# If none, make a fake one
if not anns:
anns = [self.empty(duration)]
# Apply transformations
results = []
for ann in anns:
results.append(self.transform_annotation(ann, duration))
# If the annotation range is None, it spans the entire track
if ann.time is None or ann.duration is None:
valid = [0, duration]
else:
valid = [ann.time, ann.time + ann.duration]
results[-1]['_valid'] = time_to_frames(valid, sr=self.sr,
hop_length=self.hop_length)
# Prefix and collect
return self.merge(results) | python | def transform(self, jam, query=None):
'''Transform jam object to make data for this task
Parameters
----------
jam : jams.JAMS
The jams container object
query : string, dict, or callable [optional]
An optional query to narrow the elements of `jam.annotations`
to be considered.
If not provided, all annotations are considered.
Returns
-------
data : dict
A dictionary of transformed annotations.
All annotations which can be converted to the target namespace
will be converted.
'''
anns = []
if query:
results = jam.search(**query)
else:
results = jam.annotations
# Find annotations that can be coerced to our target namespace
for ann in results:
try:
anns.append(jams.nsconvert.convert(ann, self.namespace))
except jams.NamespaceError:
pass
duration = jam.file_metadata.duration
# If none, make a fake one
if not anns:
anns = [self.empty(duration)]
# Apply transformations
results = []
for ann in anns:
results.append(self.transform_annotation(ann, duration))
# If the annotation range is None, it spans the entire track
if ann.time is None or ann.duration is None:
valid = [0, duration]
else:
valid = [ann.time, ann.time + ann.duration]
results[-1]['_valid'] = time_to_frames(valid, sr=self.sr,
hop_length=self.hop_length)
# Prefix and collect
return self.merge(results) | [
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query : string, dict, or callable [optional]
An optional query to narrow the elements of `jam.annotations`
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If not provided, all annotations are considered.
Returns
-------
data : dict
A dictionary of transformed annotations.
All annotations which can be converted to the target namespace
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bmcfee/pumpp | pumpp/task/base.py | BaseTaskTransformer.encode_events | def encode_events(self, duration, events, values, dtype=np.bool):
'''Encode labeled events as a time-series matrix.
Parameters
----------
duration : number
The duration of the track
events : ndarray, shape=(n,)
Time index of the events
values : ndarray, shape=(n, m)
Values array. Must have the same first index as `events`.
dtype : numpy data type
Returns
-------
target : ndarray, shape=(n_frames, n_values)
'''
frames = time_to_frames(events, sr=self.sr,
hop_length=self.hop_length)
n_total = int(time_to_frames(duration, sr=self.sr,
hop_length=self.hop_length))
n_alloc = n_total
if np.any(frames):
n_alloc = max(n_total, 1 + int(frames.max()))
target = np.empty((n_alloc, values.shape[1]),
dtype=dtype)
target.fill(fill_value(dtype))
values = values.astype(dtype)
for column, event in zip(values, frames):
target[event] += column
return target[:n_total] | python | def encode_events(self, duration, events, values, dtype=np.bool):
'''Encode labeled events as a time-series matrix.
Parameters
----------
duration : number
The duration of the track
events : ndarray, shape=(n,)
Time index of the events
values : ndarray, shape=(n, m)
Values array. Must have the same first index as `events`.
dtype : numpy data type
Returns
-------
target : ndarray, shape=(n_frames, n_values)
'''
frames = time_to_frames(events, sr=self.sr,
hop_length=self.hop_length)
n_total = int(time_to_frames(duration, sr=self.sr,
hop_length=self.hop_length))
n_alloc = n_total
if np.any(frames):
n_alloc = max(n_total, 1 + int(frames.max()))
target = np.empty((n_alloc, values.shape[1]),
dtype=dtype)
target.fill(fill_value(dtype))
values = values.astype(dtype)
for column, event in zip(values, frames):
target[event] += column
return target[:n_total] | [
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The duration of the track
events : ndarray, shape=(n,)
Time index of the events
values : ndarray, shape=(n, m)
Values array. Must have the same first index as `events`.
dtype : numpy data type
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bmcfee/pumpp | pumpp/task/base.py | BaseTaskTransformer.encode_intervals | def encode_intervals(self, duration, intervals, values, dtype=np.bool,
multi=True, fill=None):
'''Encode labeled intervals as a time-series matrix.
Parameters
----------
duration : number
The duration (in frames) of the track
intervals : np.ndarray, shape=(n, 2)
The list of intervals
values : np.ndarray, shape=(n, m)
The (encoded) values corresponding to each interval
dtype : np.dtype
The desired output type
multi : bool
If `True`, allow multiple labels per interval.
fill : dtype (optional)
Optional default fill value for missing data.
If not provided, the default is inferred from `dtype`.
Returns
-------
target : np.ndarray, shape=(duration * sr / hop_length, m)
The labeled interval encoding, sampled at the desired frame rate
'''
if fill is None:
fill = fill_value(dtype)
frames = time_to_frames(intervals, sr=self.sr,
hop_length=self.hop_length)
n_total = int(time_to_frames(duration, sr=self.sr,
hop_length=self.hop_length))
values = values.astype(dtype)
n_alloc = n_total
if np.any(frames):
n_alloc = max(n_total, 1 + int(frames.max()))
target = np.empty((n_alloc, values.shape[1]),
dtype=dtype)
target.fill(fill)
for column, interval in zip(values, frames):
if multi:
target[interval[0]:interval[1]] += column
else:
target[interval[0]:interval[1]] = column
return target[:n_total] | python | def encode_intervals(self, duration, intervals, values, dtype=np.bool,
multi=True, fill=None):
'''Encode labeled intervals as a time-series matrix.
Parameters
----------
duration : number
The duration (in frames) of the track
intervals : np.ndarray, shape=(n, 2)
The list of intervals
values : np.ndarray, shape=(n, m)
The (encoded) values corresponding to each interval
dtype : np.dtype
The desired output type
multi : bool
If `True`, allow multiple labels per interval.
fill : dtype (optional)
Optional default fill value for missing data.
If not provided, the default is inferred from `dtype`.
Returns
-------
target : np.ndarray, shape=(duration * sr / hop_length, m)
The labeled interval encoding, sampled at the desired frame rate
'''
if fill is None:
fill = fill_value(dtype)
frames = time_to_frames(intervals, sr=self.sr,
hop_length=self.hop_length)
n_total = int(time_to_frames(duration, sr=self.sr,
hop_length=self.hop_length))
values = values.astype(dtype)
n_alloc = n_total
if np.any(frames):
n_alloc = max(n_total, 1 + int(frames.max()))
target = np.empty((n_alloc, values.shape[1]),
dtype=dtype)
target.fill(fill)
for column, interval in zip(values, frames):
if multi:
target[interval[0]:interval[1]] += column
else:
target[interval[0]:interval[1]] = column
return target[:n_total] | [
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intervals : np.ndarray, shape=(n, 2)
The list of intervals
values : np.ndarray, shape=(n, m)
The (encoded) values corresponding to each interval
dtype : np.dtype
The desired output type
multi : bool
If `True`, allow multiple labels per interval.
fill : dtype (optional)
Optional default fill value for missing data.
If not provided, the default is inferred from `dtype`.
Returns
-------
target : np.ndarray, shape=(duration * sr / hop_length, m)
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bmcfee/pumpp | pumpp/task/base.py | BaseTaskTransformer.decode_events | def decode_events(self, encoded, transition=None, p_state=None, p_init=None):
'''Decode labeled events into (time, value) pairs
Real-valued inputs are thresholded at 0.5.
Optionally, viterbi decoding can be applied to each event class.
Parameters
----------
encoded : np.ndarray, shape=(n_frames, m)
Frame-level annotation encodings as produced by ``encode_events``.
transition : None or np.ndarray [shape=(2, 2) or (m, 2, 2)]
Optional transition matrix for each event, used for Viterbi
p_state : None or np.ndarray [shape=(m,)]
Optional marginal probability for each event
p_init : None or np.ndarray [shape=(m,)]
Optional marginal probability for each event
Returns
-------
[(time, value)] : iterable of tuples
where `time` is the event time and `value` is an
np.ndarray, shape=(m,) of the encoded value at that time
See Also
--------
librosa.sequence.viterbi_binary
'''
if np.isrealobj(encoded):
if transition is None:
encoded = (encoded >= 0.5)
else:
encoded = viterbi_binary(encoded.T, transition,
p_state=p_state,
p_init=p_init).T
times = times_like(encoded,
sr=self.sr,
hop_length=self.hop_length,
axis=0)
return zip(times, encoded) | python | def decode_events(self, encoded, transition=None, p_state=None, p_init=None):
'''Decode labeled events into (time, value) pairs
Real-valued inputs are thresholded at 0.5.
Optionally, viterbi decoding can be applied to each event class.
Parameters
----------
encoded : np.ndarray, shape=(n_frames, m)
Frame-level annotation encodings as produced by ``encode_events``.
transition : None or np.ndarray [shape=(2, 2) or (m, 2, 2)]
Optional transition matrix for each event, used for Viterbi
p_state : None or np.ndarray [shape=(m,)]
Optional marginal probability for each event
p_init : None or np.ndarray [shape=(m,)]
Optional marginal probability for each event
Returns
-------
[(time, value)] : iterable of tuples
where `time` is the event time and `value` is an
np.ndarray, shape=(m,) of the encoded value at that time
See Also
--------
librosa.sequence.viterbi_binary
'''
if np.isrealobj(encoded):
if transition is None:
encoded = (encoded >= 0.5)
else:
encoded = viterbi_binary(encoded.T, transition,
p_state=p_state,
p_init=p_init).T
times = times_like(encoded,
sr=self.sr,
hop_length=self.hop_length,
axis=0)
return zip(times, encoded) | [
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Frame-level annotation encodings as produced by ``encode_events``.
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Optional transition matrix for each event, used for Viterbi
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Optional marginal probability for each event
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-------
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bmcfee/pumpp | pumpp/task/base.py | BaseTaskTransformer.decode_intervals | def decode_intervals(self, encoded, duration=None, multi=True, sparse=False,
transition=None, p_state=None, p_init=None):
'''Decode labeled intervals into (start, end, value) triples
Parameters
----------
encoded : np.ndarray, shape=(n_frames, m)
Frame-level annotation encodings as produced by
``encode_intervals``
duration : None or float > 0
The max duration of the annotation (in seconds)
Must be greater than the length of encoded array.
multi : bool
If true, allow multiple labels per input frame.
If false, take the most likely label per input frame.
sparse : bool
If true, values are returned as indices, not one-hot.
If false, values are returned as one-hot encodings.
Only applies when `multi=False`.
transition : None or np.ndarray [shape=(m, m) or (2, 2) or (m, 2, 2)]
Optional transition matrix for each interval, used for Viterbi
decoding. If `multi=True`, then transition should be `(2, 2)` or
`(m, 2, 2)`-shaped. If `multi=False`, then transition should be
`(m, m)`-shaped.
p_state : None or np.ndarray [shape=(m,)]
Optional marginal probability for each label.
p_init : None or np.ndarray [shape=(m,)]
Optional marginal probability for each label.
Returns
-------
[(start, end, value)] : iterable of tuples
where `start` and `end` are the interval boundaries (in seconds)
and `value` is an np.ndarray, shape=(m,) of the encoded value
for this interval.
'''
if np.isrealobj(encoded):
if multi:
if transition is None:
encoded = encoded >= 0.5
else:
encoded = viterbi_binary(encoded.T, transition,
p_init=p_init, p_state=p_state).T
elif sparse and encoded.shape[1] > 1:
# map to argmax if it's densely encoded (logits)
if transition is None:
encoded = np.argmax(encoded, axis=1)[:, np.newaxis]
else:
encoded = viterbi_discriminative(encoded.T, transition,
p_init=p_init,
p_state=p_state)[:, np.newaxis]
elif not sparse:
# if dense and multi, map to one-hot encoding
if transition is None:
encoded = (encoded == np.max(encoded, axis=1, keepdims=True))
else:
encoded_ = viterbi_discriminative(encoded.T, transition,
p_init=p_init,
p_state=p_state)
# Map to one-hot encoding
encoded = np.zeros(encoded.shape, dtype=bool)
encoded[np.arange(len(encoded_)), encoded_] = True
if duration is None:
# 1+ is fair here, because encode_intervals already pads
duration = 1 + encoded.shape[0]
else:
duration = 1 + time_to_frames(duration,
sr=self.sr,
hop_length=self.hop_length)
# [0, duration] inclusive
times = times_like(duration + 1,
sr=self.sr, hop_length=self.hop_length)
# Find the change-points of the rows
if sparse:
idx = np.where(encoded[1:] != encoded[:-1])[0]
else:
idx = np.where(np.max(encoded[1:] != encoded[:-1], axis=-1))[0]
idx = np.unique(np.append(idx, encoded.shape[0]))
delta = np.diff(np.append(-1, idx))
# Starting positions can be integrated from changes
position = np.cumsum(np.append(0, delta))
return [(times[p], times[p + d], encoded[p])
for (p, d) in zip(position, delta)] | python | def decode_intervals(self, encoded, duration=None, multi=True, sparse=False,
transition=None, p_state=None, p_init=None):
'''Decode labeled intervals into (start, end, value) triples
Parameters
----------
encoded : np.ndarray, shape=(n_frames, m)
Frame-level annotation encodings as produced by
``encode_intervals``
duration : None or float > 0
The max duration of the annotation (in seconds)
Must be greater than the length of encoded array.
multi : bool
If true, allow multiple labels per input frame.
If false, take the most likely label per input frame.
sparse : bool
If true, values are returned as indices, not one-hot.
If false, values are returned as one-hot encodings.
Only applies when `multi=False`.
transition : None or np.ndarray [shape=(m, m) or (2, 2) or (m, 2, 2)]
Optional transition matrix for each interval, used for Viterbi
decoding. If `multi=True`, then transition should be `(2, 2)` or
`(m, 2, 2)`-shaped. If `multi=False`, then transition should be
`(m, m)`-shaped.
p_state : None or np.ndarray [shape=(m,)]
Optional marginal probability for each label.
p_init : None or np.ndarray [shape=(m,)]
Optional marginal probability for each label.
Returns
-------
[(start, end, value)] : iterable of tuples
where `start` and `end` are the interval boundaries (in seconds)
and `value` is an np.ndarray, shape=(m,) of the encoded value
for this interval.
'''
if np.isrealobj(encoded):
if multi:
if transition is None:
encoded = encoded >= 0.5
else:
encoded = viterbi_binary(encoded.T, transition,
p_init=p_init, p_state=p_state).T
elif sparse and encoded.shape[1] > 1:
# map to argmax if it's densely encoded (logits)
if transition is None:
encoded = np.argmax(encoded, axis=1)[:, np.newaxis]
else:
encoded = viterbi_discriminative(encoded.T, transition,
p_init=p_init,
p_state=p_state)[:, np.newaxis]
elif not sparse:
# if dense and multi, map to one-hot encoding
if transition is None:
encoded = (encoded == np.max(encoded, axis=1, keepdims=True))
else:
encoded_ = viterbi_discriminative(encoded.T, transition,
p_init=p_init,
p_state=p_state)
# Map to one-hot encoding
encoded = np.zeros(encoded.shape, dtype=bool)
encoded[np.arange(len(encoded_)), encoded_] = True
if duration is None:
# 1+ is fair here, because encode_intervals already pads
duration = 1 + encoded.shape[0]
else:
duration = 1 + time_to_frames(duration,
sr=self.sr,
hop_length=self.hop_length)
# [0, duration] inclusive
times = times_like(duration + 1,
sr=self.sr, hop_length=self.hop_length)
# Find the change-points of the rows
if sparse:
idx = np.where(encoded[1:] != encoded[:-1])[0]
else:
idx = np.where(np.max(encoded[1:] != encoded[:-1], axis=-1))[0]
idx = np.unique(np.append(idx, encoded.shape[0]))
delta = np.diff(np.append(-1, idx))
# Starting positions can be integrated from changes
position = np.cumsum(np.append(0, delta))
return [(times[p], times[p + d], encoded[p])
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Parameters
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encoded : np.ndarray, shape=(n_frames, m)
Frame-level annotation encodings as produced by
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duration : None or float > 0
The max duration of the annotation (in seconds)
Must be greater than the length of encoded array.
multi : bool
If true, allow multiple labels per input frame.
If false, take the most likely label per input frame.
sparse : bool
If true, values are returned as indices, not one-hot.
If false, values are returned as one-hot encodings.
Only applies when `multi=False`.
transition : None or np.ndarray [shape=(m, m) or (2, 2) or (m, 2, 2)]
Optional transition matrix for each interval, used for Viterbi
decoding. If `multi=True`, then transition should be `(2, 2)` or
`(m, 2, 2)`-shaped. If `multi=False`, then transition should be
`(m, m)`-shaped.
p_state : None or np.ndarray [shape=(m,)]
Optional marginal probability for each label.
p_init : None or np.ndarray [shape=(m,)]
Optional marginal probability for each label.
Returns
-------
[(start, end, value)] : iterable of tuples
where `start` and `end` are the interval boundaries (in seconds)
and `value` is an np.ndarray, shape=(m,) of the encoded value
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bmcfee/pumpp | pumpp/feature/base.py | FeatureExtractor.transform | def transform(self, y, sr):
'''Transform an audio signal
Parameters
----------
y : np.ndarray
The audio signal
sr : number > 0
The native sampling rate of y
Returns
-------
dict
Data dictionary containing features extracted from y
See Also
--------
transform_audio
'''
if sr != self.sr:
y = resample(y, sr, self.sr)
return self.merge([self.transform_audio(y)]) | python | def transform(self, y, sr):
'''Transform an audio signal
Parameters
----------
y : np.ndarray
The audio signal
sr : number > 0
The native sampling rate of y
Returns
-------
dict
Data dictionary containing features extracted from y
See Also
--------
transform_audio
'''
if sr != self.sr:
y = resample(y, sr, self.sr)
return self.merge([self.transform_audio(y)]) | [
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See Also
--------
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bmcfee/pumpp | pumpp/feature/base.py | FeatureExtractor.phase_diff | def phase_diff(self, phase):
'''Compute the phase differential along a given axis
Parameters
----------
phase : np.ndarray
Input phase (in radians)
Returns
-------
dphase : np.ndarray like `phase`
The phase differential.
'''
if self.conv is None:
axis = 0
elif self.conv in ('channels_last', 'tf'):
axis = 0
elif self.conv in ('channels_first', 'th'):
axis = 1
# Compute the phase differential
dphase = np.empty(phase.shape, dtype=phase.dtype)
zero_idx = [slice(None)] * phase.ndim
zero_idx[axis] = slice(1)
else_idx = [slice(None)] * phase.ndim
else_idx[axis] = slice(1, None)
zero_idx = tuple(zero_idx)
else_idx = tuple(else_idx)
dphase[zero_idx] = phase[zero_idx]
dphase[else_idx] = np.diff(np.unwrap(phase, axis=axis), axis=axis)
return dphase | python | def phase_diff(self, phase):
'''Compute the phase differential along a given axis
Parameters
----------
phase : np.ndarray
Input phase (in radians)
Returns
-------
dphase : np.ndarray like `phase`
The phase differential.
'''
if self.conv is None:
axis = 0
elif self.conv in ('channels_last', 'tf'):
axis = 0
elif self.conv in ('channels_first', 'th'):
axis = 1
# Compute the phase differential
dphase = np.empty(phase.shape, dtype=phase.dtype)
zero_idx = [slice(None)] * phase.ndim
zero_idx[axis] = slice(1)
else_idx = [slice(None)] * phase.ndim
else_idx[axis] = slice(1, None)
zero_idx = tuple(zero_idx)
else_idx = tuple(else_idx)
dphase[zero_idx] = phase[zero_idx]
dphase[else_idx] = np.diff(np.unwrap(phase, axis=axis), axis=axis)
return dphase | [
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Returns
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dphase : np.ndarray like `phase`
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bmcfee/pumpp | pumpp/feature/base.py | FeatureExtractor.layers | def layers(self):
'''Construct Keras input layers for the given transformer
Returns
-------
layers : {field: keras.layers.Input}
A dictionary of keras input layers, keyed by the corresponding
field keys.
'''
from keras.layers import Input
L = dict()
for key in self.fields:
L[key] = Input(name=key,
shape=self.fields[key].shape,
dtype=self.fields[key].dtype)
return L | python | def layers(self):
'''Construct Keras input layers for the given transformer
Returns
-------
layers : {field: keras.layers.Input}
A dictionary of keras input layers, keyed by the corresponding
field keys.
'''
from keras.layers import Input
L = dict()
for key in self.fields:
L[key] = Input(name=key,
shape=self.fields[key].shape,
dtype=self.fields[key].dtype)
return L | [
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A dictionary of keras input layers, keyed by the corresponding
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bmcfee/pumpp | pumpp/feature/base.py | FeatureExtractor.n_frames | def n_frames(self, duration):
'''Get the number of frames for a given duration
Parameters
----------
duration : number >= 0
The duration, in seconds
Returns
-------
n_frames : int >= 0
The number of frames at this extractor's sampling rate and
hop length
'''
return int(time_to_frames(duration, sr=self.sr,
hop_length=self.hop_length)) | python | def n_frames(self, duration):
'''Get the number of frames for a given duration
Parameters
----------
duration : number >= 0
The duration, in seconds
Returns
-------
n_frames : int >= 0
The number of frames at this extractor's sampling rate and
hop length
'''
return int(time_to_frames(duration, sr=self.sr,
hop_length=self.hop_length)) | [
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The duration, in seconds
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novopl/peltak | src/peltak/extra/gitflow/logic/release.py | start | def start(component, exact):
# type: (str, str) -> None
""" Create a new release branch.
Args:
component (str):
Version component to bump when creating the release. Can be *major*,
*minor* or *patch*.
exact (str):
The exact version to set for the release. Overrides the component
argument. This allows to re-release a version if something went
wrong with the release upload.
"""
version_file = conf.get_path('version_file', 'VERSION')
develop = conf.get('git.devel_branch', 'develop')
common.assert_on_branch(develop)
with conf.within_proj_dir():
out = shell.run('git status --porcelain', capture=True).stdout
lines = out.split(os.linesep)
has_changes = any(
not l.startswith('??') for l in lines if l.strip()
)
if has_changes:
log.info("Cannot release: there are uncommitted changes")
exit(1)
old_ver, new_ver = versioning.bump(component, exact)
log.info("Bumping package version")
log.info(" old version: <35>{}".format(old_ver))
log.info(" new version: <35>{}".format(new_ver))
with conf.within_proj_dir():
branch = 'release/' + new_ver
common.git_checkout(branch, create=True)
log.info("Creating commit for the release")
shell.run('git add {ver_file} && git commit -m "{msg}"'.format(
ver_file=version_file,
msg="Releasing v{}".format(new_ver)
)) | python | def start(component, exact):
# type: (str, str) -> None
""" Create a new release branch.
Args:
component (str):
Version component to bump when creating the release. Can be *major*,
*minor* or *patch*.
exact (str):
The exact version to set for the release. Overrides the component
argument. This allows to re-release a version if something went
wrong with the release upload.
"""
version_file = conf.get_path('version_file', 'VERSION')
develop = conf.get('git.devel_branch', 'develop')
common.assert_on_branch(develop)
with conf.within_proj_dir():
out = shell.run('git status --porcelain', capture=True).stdout
lines = out.split(os.linesep)
has_changes = any(
not l.startswith('??') for l in lines if l.strip()
)
if has_changes:
log.info("Cannot release: there are uncommitted changes")
exit(1)
old_ver, new_ver = versioning.bump(component, exact)
log.info("Bumping package version")
log.info(" old version: <35>{}".format(old_ver))
log.info(" new version: <35>{}".format(new_ver))
with conf.within_proj_dir():
branch = 'release/' + new_ver
common.git_checkout(branch, create=True)
log.info("Creating commit for the release")
shell.run('git add {ver_file} && git commit -m "{msg}"'.format(
ver_file=version_file,
msg="Releasing v{}".format(new_ver)
)) | [
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Args:
component (str):
Version component to bump when creating the release. Can be *major*,
*minor* or *patch*.
exact (str):
The exact version to set for the release. Overrides the component
argument. This allows to re-release a version if something went
wrong with the release upload. | [
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] | train | https://github.com/novopl/peltak/blob/b627acc019e3665875fe76cdca0a14773b69beaa/src/peltak/extra/gitflow/logic/release.py#L34-L78 |
novopl/peltak | src/peltak/extra/gitflow/logic/release.py | tag | def tag(message):
# type: () -> None
""" Tag the current commit with the current version. """
release_ver = versioning.current()
message = message or 'v{} release'.format(release_ver)
with conf.within_proj_dir():
log.info("Creating release tag")
git.tag(
author=git.latest_commit().author,
name='v{}'.format(release_ver),
message=message,
) | python | def tag(message):
# type: () -> None
""" Tag the current commit with the current version. """
release_ver = versioning.current()
message = message or 'v{} release'.format(release_ver)
with conf.within_proj_dir():
log.info("Creating release tag")
git.tag(
author=git.latest_commit().author,
name='v{}'.format(release_ver),
message=message,
) | [
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novopl/peltak | src/peltak/logic/lint.py | lint | def lint(exclude, skip_untracked, commit_only):
# type: (List[str], bool, bool) -> None
""" Lint python files.
Args:
exclude (list[str]):
A list of glob string patterns to test against. If the file/path
matches any of those patters, it will be filtered out.
skip_untracked (bool):
If set to **True** it will skip all files not tracked by git.
commit_only (bool):
Only lint files that are staged for commit.
"""
exclude = list(exclude) + conf.get('lint.exclude', [])
runner = LintRunner(exclude, skip_untracked, commit_only)
if not runner.run():
exit(1) | python | def lint(exclude, skip_untracked, commit_only):
# type: (List[str], bool, bool) -> None
""" Lint python files.
Args:
exclude (list[str]):
A list of glob string patterns to test against. If the file/path
matches any of those patters, it will be filtered out.
skip_untracked (bool):
If set to **True** it will skip all files not tracked by git.
commit_only (bool):
Only lint files that are staged for commit.
"""
exclude = list(exclude) + conf.get('lint.exclude', [])
runner = LintRunner(exclude, skip_untracked, commit_only)
if not runner.run():
exit(1) | [
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A list of glob string patterns to test against. If the file/path
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If set to **True** it will skip all files not tracked by git.
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novopl/peltak | src/peltak/logic/lint.py | tool | def tool(name):
# type: (str) -> FunctionType
""" Decorator for defining lint tools.
Args:
name (str):
The name of the tool. This name will be used to identify the tool
in `pelconf.yaml`.
"""
global g_tools
def decorator(fn): # pylint: disable=missing-docstring
# type: (FunctionType) -> FunctionType
g_tools[name] = fn
return fn
return decorator | python | def tool(name):
# type: (str) -> FunctionType
""" Decorator for defining lint tools.
Args:
name (str):
The name of the tool. This name will be used to identify the tool
in `pelconf.yaml`.
"""
global g_tools
def decorator(fn): # pylint: disable=missing-docstring
# type: (FunctionType) -> FunctionType
g_tools[name] = fn
return fn
return decorator | [
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novopl/peltak | src/peltak/logic/lint.py | pep8_check | def pep8_check(files):
# type: (List[str]) -> int
""" Run code checks using pep8.
Args:
files (list[str]):
A list of files to check
Returns:
bool: **True** if all files passed the checks, **False** otherwise.
pep8 tool is **very** fast. Especially compared to pylint and the bigger the
code base the bigger the difference. If you want to reduce check times you
might disable all pep8 checks in pylint and use pep8 for that. This way you
use pylint only for the more advanced checks (the number of checks enabled
in pylint will make a visible difference in it's run times).
"""
files = fs.wrap_paths(files)
cfg_path = conf.get_path('lint.pep8_cfg', 'ops/tools/pep8.ini')
pep8_cmd = 'pep8 --config {} {}'.format(cfg_path, files)
return shell.run(pep8_cmd, exit_on_error=False).return_code | python | def pep8_check(files):
# type: (List[str]) -> int
""" Run code checks using pep8.
Args:
files (list[str]):
A list of files to check
Returns:
bool: **True** if all files passed the checks, **False** otherwise.
pep8 tool is **very** fast. Especially compared to pylint and the bigger the
code base the bigger the difference. If you want to reduce check times you
might disable all pep8 checks in pylint and use pep8 for that. This way you
use pylint only for the more advanced checks (the number of checks enabled
in pylint will make a visible difference in it's run times).
"""
files = fs.wrap_paths(files)
cfg_path = conf.get_path('lint.pep8_cfg', 'ops/tools/pep8.ini')
pep8_cmd = 'pep8 --config {} {}'.format(cfg_path, files)
return shell.run(pep8_cmd, exit_on_error=False).return_code | [
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novopl/peltak | src/peltak/logic/lint.py | pylint_check | def pylint_check(files):
# type: (List[str]) -> int
""" Run code checks using pylint.
Args:
files (list[str]):
A list of files to check
Returns:
bool: **True** if all files passed the checks, **False** otherwise.
"""
files = fs.wrap_paths(files)
cfg_path = conf.get_path('lint.pylint_cfg', 'ops/tools/pylint.ini')
pylint_cmd = 'pylint --rcfile {} {}'.format(cfg_path, files)
return shell.run(pylint_cmd, exit_on_error=False).return_code | python | def pylint_check(files):
# type: (List[str]) -> int
""" Run code checks using pylint.
Args:
files (list[str]):
A list of files to check
Returns:
bool: **True** if all files passed the checks, **False** otherwise.
"""
files = fs.wrap_paths(files)
cfg_path = conf.get_path('lint.pylint_cfg', 'ops/tools/pylint.ini')
pylint_cmd = 'pylint --rcfile {} {}'.format(cfg_path, files)
return shell.run(pylint_cmd, exit_on_error=False).return_code | [
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novopl/peltak | src/peltak/logic/lint.py | LintRunner.run | def run(self):
# type: () -> bool
""" Run all linters and report results.
Returns:
bool: **True** if all checks were successful, **False** otherwise.
"""
with util.timed_block() as t:
files = self._collect_files()
log.info("Collected <33>{} <32>files in <33>{}s".format(
len(files), t.elapsed_s
))
if self.verbose:
for p in files:
log.info(" <0>{}", p)
# No files to lint - return success if empty runs are allowed.
if not files:
return self.allow_empty
with util.timed_block() as t:
results = self._run_checks(files)
log.info("Code checked in <33>{}s", t.elapsed_s)
success = True
for name, retcodes in results.items():
if any(x != 0 for x in retcodes):
success = False
log.err("<35>{} <31>failed with: <33>{}".format(
name, retcodes
))
return success | python | def run(self):
# type: () -> bool
""" Run all linters and report results.
Returns:
bool: **True** if all checks were successful, **False** otherwise.
"""
with util.timed_block() as t:
files = self._collect_files()
log.info("Collected <33>{} <32>files in <33>{}s".format(
len(files), t.elapsed_s
))
if self.verbose:
for p in files:
log.info(" <0>{}", p)
# No files to lint - return success if empty runs are allowed.
if not files:
return self.allow_empty
with util.timed_block() as t:
results = self._run_checks(files)
log.info("Code checked in <33>{}s", t.elapsed_s)
success = True
for name, retcodes in results.items():
if any(x != 0 for x in retcodes):
success = False
log.err("<35>{} <31>failed with: <33>{}".format(
name, retcodes
))
return success | [
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dacker-team/pyzure | pyzure/send/send.py | send_to_azure | def send_to_azure(instance, data, replace=True, types=None, primary_key=(), sub_commit=True):
"""
data = {
"table_name" : 'name_of_the_azure_schema' + '.' + 'name_of_the_azure_table' #Must already exist,
"columns_name" : [first_column_name,second_column_name,...,last_column_name],
"rows" : [[first_raw_value,second_raw_value,...,last_raw_value],...]
}
"""
# Time initialization
start = datetime.datetime.now()
# Extract info
rows = data["rows"]
if not rows:
return 0
table_name = data["table_name"]
columns_name = data["columns_name"]
total_len_data = len(rows)
# Create table if needed
if not existing_test(instance, table_name) or (types is not None) or (primary_key != ()):
create.create_table(instance, data, primary_key, types)
# Clean table if needed
if replace:
cleaning_function(instance, table_name)
connection_kwargs = credential(instance)
# Create an SSH tunnel
ssh_host = os.environ.get("SSH_%s_HOST" % instance)
ssh_user = os.environ.get("SSH_%s_USER" % instance)
ssh_path_private_key = os.environ.get("SSH_%s_PATH_PRIVATE_KEY" % instance)
if ssh_host:
tunnel = SSHTunnelForwarder(
(ssh_host, 22),
ssh_username=ssh_user,
ssh_private_key=ssh_path_private_key,
remote_bind_address=(
os.environ.get("AZURE_%s_HOST" % instance), int(os.environ.get("AZURE_%s_PORT" % instance))),
local_bind_address=('localhost', 1433), # could be any available port
)
# Start the tunnel
try:
tunnel.start()
print("Tunnel opened!")
except sshtunnel.HandlerSSHTunnelForwarderError:
pass
connection_kwargs["host"] = "localhost,1433"
connection_kwargs["port"] = 1433
cnxn = pyodbc.connect(**connection_kwargs)
cursor = cnxn.cursor()
small_batch_size = int(2099 / len(columns_name))
print("Initiate send_to_azure...")
# Initialize counters
boolean = True
question_mark_pattern = "(%s)" % ",".join(["?" for i in range(len(rows[0]))])
counter = 0
while boolean:
temp_row = []
question_mark_list = []
for i in range(small_batch_size):
if rows:
temp_row.append(rows.pop())
question_mark_list.append(question_mark_pattern)
else:
boolean = False
continue
counter = counter + len(temp_row)
# percent = round(float(counter * 100) / total_len_data)
if sub_commit:
suffix = "%% rows sent"
print_progress_bar(counter, total_len_data, suffix=suffix)
# print("%s %% rows sent" % str(percent))
else:
suffix = "% rows prepared to be sent"
print_progress_bar(counter, total_len_data, suffix=suffix)
# print("%s %% rows prepared to be sent" % str(percent))
data_values_str = ','.join(question_mark_list)
columns_name_str = ", ".join(columns_name)
inserting_request = '''INSERT INTO %s (%s) VALUES %s ;''' % (table_name, columns_name_str, data_values_str)
final_data = [y for x in temp_row for y in x]
if final_data:
cursor.execute(inserting_request, final_data)
if sub_commit:
commit_function(cnxn)
if not sub_commit:
commit_function(cnxn)
cursor.close()
cnxn.close()
if ssh_host:
tunnel.close()
print("Tunnel closed!")
print("data sent to azure")
print("Total rows: %s" % str(total_len_data))
print(C.BOLD + "Total time in seconds : %s" % str((datetime.datetime.now() - start).seconds) + C.ENDC)
return 0 | python | def send_to_azure(instance, data, replace=True, types=None, primary_key=(), sub_commit=True):
"""
data = {
"table_name" : 'name_of_the_azure_schema' + '.' + 'name_of_the_azure_table' #Must already exist,
"columns_name" : [first_column_name,second_column_name,...,last_column_name],
"rows" : [[first_raw_value,second_raw_value,...,last_raw_value],...]
}
"""
# Time initialization
start = datetime.datetime.now()
# Extract info
rows = data["rows"]
if not rows:
return 0
table_name = data["table_name"]
columns_name = data["columns_name"]
total_len_data = len(rows)
# Create table if needed
if not existing_test(instance, table_name) or (types is not None) or (primary_key != ()):
create.create_table(instance, data, primary_key, types)
# Clean table if needed
if replace:
cleaning_function(instance, table_name)
connection_kwargs = credential(instance)
# Create an SSH tunnel
ssh_host = os.environ.get("SSH_%s_HOST" % instance)
ssh_user = os.environ.get("SSH_%s_USER" % instance)
ssh_path_private_key = os.environ.get("SSH_%s_PATH_PRIVATE_KEY" % instance)
if ssh_host:
tunnel = SSHTunnelForwarder(
(ssh_host, 22),
ssh_username=ssh_user,
ssh_private_key=ssh_path_private_key,
remote_bind_address=(
os.environ.get("AZURE_%s_HOST" % instance), int(os.environ.get("AZURE_%s_PORT" % instance))),
local_bind_address=('localhost', 1433), # could be any available port
)
# Start the tunnel
try:
tunnel.start()
print("Tunnel opened!")
except sshtunnel.HandlerSSHTunnelForwarderError:
pass
connection_kwargs["host"] = "localhost,1433"
connection_kwargs["port"] = 1433
cnxn = pyodbc.connect(**connection_kwargs)
cursor = cnxn.cursor()
small_batch_size = int(2099 / len(columns_name))
print("Initiate send_to_azure...")
# Initialize counters
boolean = True
question_mark_pattern = "(%s)" % ",".join(["?" for i in range(len(rows[0]))])
counter = 0
while boolean:
temp_row = []
question_mark_list = []
for i in range(small_batch_size):
if rows:
temp_row.append(rows.pop())
question_mark_list.append(question_mark_pattern)
else:
boolean = False
continue
counter = counter + len(temp_row)
# percent = round(float(counter * 100) / total_len_data)
if sub_commit:
suffix = "%% rows sent"
print_progress_bar(counter, total_len_data, suffix=suffix)
# print("%s %% rows sent" % str(percent))
else:
suffix = "% rows prepared to be sent"
print_progress_bar(counter, total_len_data, suffix=suffix)
# print("%s %% rows prepared to be sent" % str(percent))
data_values_str = ','.join(question_mark_list)
columns_name_str = ", ".join(columns_name)
inserting_request = '''INSERT INTO %s (%s) VALUES %s ;''' % (table_name, columns_name_str, data_values_str)
final_data = [y for x in temp_row for y in x]
if final_data:
cursor.execute(inserting_request, final_data)
if sub_commit:
commit_function(cnxn)
if not sub_commit:
commit_function(cnxn)
cursor.close()
cnxn.close()
if ssh_host:
tunnel.close()
print("Tunnel closed!")
print("data sent to azure")
print("Total rows: %s" % str(total_len_data))
print(C.BOLD + "Total time in seconds : %s" % str((datetime.datetime.now() - start).seconds) + C.ENDC)
return 0 | [
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"table_name" : 'name_of_the_azure_schema' + '.' + 'name_of_the_azure_table' #Must already exist,
"columns_name" : [first_column_name,second_column_name,...,last_column_name],
"rows" : [[first_raw_value,second_raw_value,...,last_raw_value],...]
} | [
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cons3rt/pycons3rt | pycons3rt/dyndict.py | getdict | def getdict(source):
"""Returns a standard python Dict with computed values
from the DynDict
:param source: (DynDict) input
:return: (dict) Containing computed values
"""
std_dict = {}
for var, val in source.iteritems():
std_dict[var] = source[var]
return std_dict | python | def getdict(source):
"""Returns a standard python Dict with computed values
from the DynDict
:param source: (DynDict) input
:return: (dict) Containing computed values
"""
std_dict = {}
for var, val in source.iteritems():
std_dict[var] = source[var]
return std_dict | [
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Varkal/chuda | chuda/plugins.py | Plugin.enrich_app | def enrich_app(self, name, value):
'''
Add a new property to the app (with setattr)
Args:
name (str): the name of the new property
value (any): the value of the new property
'''
#Method shouldn't be added: https://stackoverflow.com/a/28060251/3042398
if type(value) == type(self.enrich_app):
raise ValueError("enrich_app can't add method")
setattr(self.app, name, value) | python | def enrich_app(self, name, value):
'''
Add a new property to the app (with setattr)
Args:
name (str): the name of the new property
value (any): the value of the new property
'''
#Method shouldn't be added: https://stackoverflow.com/a/28060251/3042398
if type(value) == type(self.enrich_app):
raise ValueError("enrich_app can't add method")
setattr(self.app, name, value) | [
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Vital-Fernandez/dazer | bin/lib/Math_Libraries/fitting_methods.py | linfit | def linfit(x_true, y, sigmay=None, relsigma=True, cov=False, chisq=False, residuals=False):
"""
Least squares linear fit.
Fit a straight line `f(x_true) = a + bx` to points `(x_true, y)`. Returns
coefficients `a` and `b` that minimize the squared error.
Parameters
----------
x_true : array_like
one dimensional array of `x_true` data with `n`>2 data points.
y : array_like
one dimensional array of `y` data with `n`>2 data points.
sigmay : NoneType or float or array_like, optional
one dimensional array of uncertainties (errors) in `y` data or a single
positive number if all uncertainties are the same. `sigmay` determines
the weighting in the least squares minimization. Leaving `sigmay=None`
uses no weighting and is equivalent to `sigmay=1`.
relsigma : bool, optional
If `relsigma` is True, the residuals are used to scale the covariance
matrix. Use this option if you do not know the absolute uncertainties
(`sigmay`) in the data but still want a covariance matrix whose entries
give meaningful estimates of the uncertainties in the fitting parameters
`a` and `b` (from `f = a + bx`). If `relsigma` is False, the covariance
matrix is calculated (provided `cov` = True) using sigmay assuming
sigmay represents absolute undertainties.
cov : bool, optional
If True, calculate and return the 2x2 covarience matrix of the fitting
parameters.
chisq : bool, optional
If True, calculate and return redchisq.
residuals : bool, optional
If True, calculate and return residuals.
Returns
-------
fit : array([a,b]) ndarray of floats
The best fit model parameters `a` (the slope) and `b` (the
`y`-intercept) for the input data arrays `x_true` and `y`
cvm : array, shape (2,2) : returned only if cov=True
Covarience matrix of the fitting parameters. Diagonal elements are
estimated variances of the fitting parameters a and b; square roots of
the diagonal elements thus provide estimates of the uncertainties in the
fitting parameters `a` and `b`. Off diagonal elements (equal to each
other) are the covarience between the fitting parameters `a` and `b`.
redchisq : float : returned only if chisq=True
Reduced chi-squared goodness of fit parameter.
residuals : ndarray of floats : returned only if residuals=True
Length n array of the differences `y-(ax+b)` between `y`-data and the
fitted data `ax + b`.
Raises
------
TypeError : if `x_true` and `y` have different lengths
TypeError : If `x_true` and `y` have 2 or fewer elements
TypeError : If `sigmay` length is not 1 or the same as `y`
See Also
--------
polyfit : Least squares fit to polynomial.
linalg.lstsq : Least-squares solution to a linear matrix equation.
Notes
-----
By default, ``linfit`` returns optimal fitting parameters `a` and `b` without
weighting of the data. In that case, linfit minimizes the squared error
.. math ::
E = \\sum_{i=0}^n [y_i - (a x_i + b)]^2
If `sigmay` is set equal to the uncertainties in the `y` data points, then
linfit minimizes the `chi-squared` sum
.. math ::
\chi^2 = \\sum_{i=0}^n \\left[ \\frac{y_i-(a x_i + b)}{\\sigma_i} \\right]^2
where :math:`\sigma_i` is given by `sigmay`, the "error" or standard
deviation of :math:`y_i`. `sigmay` can be either a single number that gives the
uncertainty for all elements of `y`, or it can be an array of the same
length as `y` that gives the "error" for each element of `y`.
`redchisq` is :math:`\chi^2/(n-2)` where :math:`n` is the number of data
points (the length of `x_true` or `y`).
If `relsigma` is False, then the uncertainties `sigmay` in `y` are
assumed to be the absolute one-standard-deviation uncertainties in `y`.
In this case, the reduced chi-squared value :math:`\chi^2/(n-2)` provides a
measure of the goodness of the fit. If it is near 1, then the linear
fitting model is considered to be good and the values of the covariance
matrix are appropriately scaled. In particular, the square root of the
diagonal elements of the covariance matrix give the estimated uncertainty
in the fitting parameters `a` and `b`. See Refernece [2] below for more
information.
If `relsigma` is True, then the uncertainties `sigmay` in `y` are
considered to be only relative uncertainties. They are used to weight
the data for the fit, but in this case, the covariance matrix is rescaled
using the residuals between the fit and the data. In this case, the reduced
chi-squared value :math:`\chi^2/(n-2)` does not provide a measure of the
goodness of the fit. Nevertheless, the diagonal elements of the rescaled
covariance matrix (returned by linfit) give the estimated uncertainty in the
fitting parameters `a` and `b`.
The covariance matrix is a 2x2 symmetric matrix where the diagonal elements
are the variance of the fitting parameters. Their square roots provide
estimates of the uncertainties in the fitting parameters. The off-diagonal
elements are equal and give the cross correlation between the two fitting
parameters `a` and `b`.
linfit runs faster, by a factor of 2 to 3, if calculation of the residuals
is suppressed letting `cov`, `chisq`, and `residuals` remain False (the
default setting).
Fitting a straight line to a single set of `(x_true, y)` data using ``linfit`` is
typically 2 to 10 times faster than using either ``polyfit`` or
``linalg.lstsq``, especially when weighting is used and for very large data
sets.
References
----------
.. [1] An Introduction to Error Analysis, 2nd Ed. by John R. Taylor
(University Science Books, 1997)
.. [2] Numerical Recipes, The Art of Scientific Computing, 3rd Edition
by W.H. Press, S. A. Teukolsky, W. T. Vetterling, & B. P. Flannery
(Cambridge University Press, 2007)
Examples
--------
Fit a line, `y = ax + b`, through some noisy `(x_true, y)` data-points without
any weighting (`sigmay` = None) to obtain fitting parameters `a` and `b`:
>>> x_true = np.array([0, 1, 2, 3])
>>> y = np.array([-1, 0.2, 0.9, 2.1])
>>> fit = linfit(x_true, y)
>>> print("a = {0:0.2f}, b = {1:0.2f}".format(fit[0], fit[1]))
a = 1.00, b = -0.95
Setting `cov` = True in the input, returns the covariance matrix `cvm`.
When uncertainties `sigmay` are left unspecified, meaningful estimates of
the uncertainties `da` and `db` in the fitting parameters `a` and `b`
are given by the square roots of the diagonals of the covariance matrix
`cvm`, provided `relsigma` = True (the default state).
>>> fit, cvm = linfit(x_true, y, cov=True)
>>> dfit = [np.sqrt(cvm[i,i]) for i in range(2)]
>>> print("da = {0:0.2f}, db = {1:0.2f}".format(dfit[0], dfit[1]))
da = 0.07, db = 0.13
A better practice is to supply estimates of the uncertainties in the
input argument `sigmay`. `sigmay` can be a single float, if the
uncertainties are the same for all data points, or it can be an array, if
the uncertainties for different data points are different. Here we
enter sigmay as an array.
>>> dy = np.array([0.18, 0.13, 0.15, 0.17])
>>> fit, cvm, redchisq, resids = linfit(x_true, y, cov=True, sigmay=dy, relsigma=False, chisq=True, residuals=True)
>>> print("a = {0:0.2f}, b = {1:0.2f}".format(fit[0], fit[1]))
a = 0.98, b = -0.91
>>> dfit = [np.sqrt(cvm[i,i]) for i in range(2)]
>>> print("da = {0:0.2f}, db = {1:0.2f}".format(dfit[0], dfit[1]))
da = 0.08, db = 0.14
>>> print("reduced chi-squared = {0:0.2f}".format(redchisq))
reduced chi-squared = 1.21
>>> print(resids)
[-0.08856653 0.12781099 -0.1558115 0.06056602]
The value of reduced chi-squared `redchisq` is 1.21 indicating that a
linear model is valid for these data. The residuals :math:`y_i - (a+bx_i)`
are given by the output `resids`.
If absolute estimates of the uncertainties are not available, but relative
estimates of the uncertainties are known, a fit can be obtained with
reasonable estimates of the uncertainties in the fitting parameters by
setting `relsigma` = True.
>>> dy = np.array([1.0, 0.75, 0.75, 1.25])
>>> fit, cvm, redchisq = linfit(x_true, y, cov=True, sigmay=dy, relsigma=True, chisq=True)
>>> print("a = {0:0.2f}, b = {1:0.2f}".format(fit[0], fit[1]))
a = 0.97, b = -0.91
>>> dfit = [np.sqrt(cvm[i,i]) for i in range(2)]
>>> print("da = {0:0.2f}, db = {1:0.2f}".format(dfit[0], dfit[1]))
da = 0.09, db = 0.16
>>> print("reduced chi-squared = {0:0.2f}".format(redchisq))
reduced chi-squared = 0.04
In this case, the value `redchisq` is meaningless, because only the
relative, rather than the absolute uncertainties are known. Nevertheless,
by setting `relsigma` = True, reasonable estimates for the uncertainties
in the fitting parameters are obtained.
Illustration:
.. image:: example.png
:scale: 75 %
"""
x_true = asarray(x_true)
y = asarray(y)
if x_true.size != y.size:
raise TypeError('Expected x_true and y to have same length')
if x_true.size <= 2:
raise TypeError('Expected x_true and y length > 2')
if sigmay is None: sigmay = 1.0
sigmay = asarray(sigmay)
if sigmay.size == 1:
sigy = float(sigmay) # convert 0-d array to a float
wt = 1./(sigy*sigy)
s = wt * y.size
sx = wt * x_true.sum()
sy = wt * y.sum()
t = x_true-sx/s
stt = wt * (t*t).sum()
slope = wt * (t*y).sum()/stt
yint = (sy - sx * slope)/s
else:
if sigmay.size != y.size:
raise TypeError('Expected sigmay size to be 1 or same as y')
wt = 1./(sigmay*sigmay)
s = wt.sum()
sx = (x_true*wt).sum()
sy = (y*wt).sum()
t = (x_true-sx/s)/sigmay
stt = (t*t).sum()
slope = (t*y/sigmay).sum()/stt
yint = (sy - sx * slope)/s
returns = array([slope, yint])
if cov is True:
cvm00 = 1./stt
cvm01 = -sx/(s*stt)
cvm11 = (1.0-sx*cvm01)/s
if relsigma is True:
redchisq, resids = _resids(x_true, y, sigmay, slope, yint)
cvm00 *= redchisq
cvm01 *= redchisq
cvm11 *= redchisq
returns = [returns] + [array([[cvm00, cvm01],
[cvm01, cvm11]])]
if residuals or chisq is True:
if relsigma is False:
redchisq, resids = _resids(x_true, y, sigmay, slope, yint)
if type(returns) is not list:
returns = [returns]
if chisq is True:
returns += [redchisq]
if residuals is True:
returns += [resids]
return returns | python | def linfit(x_true, y, sigmay=None, relsigma=True, cov=False, chisq=False, residuals=False):
"""
Least squares linear fit.
Fit a straight line `f(x_true) = a + bx` to points `(x_true, y)`. Returns
coefficients `a` and `b` that minimize the squared error.
Parameters
----------
x_true : array_like
one dimensional array of `x_true` data with `n`>2 data points.
y : array_like
one dimensional array of `y` data with `n`>2 data points.
sigmay : NoneType or float or array_like, optional
one dimensional array of uncertainties (errors) in `y` data or a single
positive number if all uncertainties are the same. `sigmay` determines
the weighting in the least squares minimization. Leaving `sigmay=None`
uses no weighting and is equivalent to `sigmay=1`.
relsigma : bool, optional
If `relsigma` is True, the residuals are used to scale the covariance
matrix. Use this option if you do not know the absolute uncertainties
(`sigmay`) in the data but still want a covariance matrix whose entries
give meaningful estimates of the uncertainties in the fitting parameters
`a` and `b` (from `f = a + bx`). If `relsigma` is False, the covariance
matrix is calculated (provided `cov` = True) using sigmay assuming
sigmay represents absolute undertainties.
cov : bool, optional
If True, calculate and return the 2x2 covarience matrix of the fitting
parameters.
chisq : bool, optional
If True, calculate and return redchisq.
residuals : bool, optional
If True, calculate and return residuals.
Returns
-------
fit : array([a,b]) ndarray of floats
The best fit model parameters `a` (the slope) and `b` (the
`y`-intercept) for the input data arrays `x_true` and `y`
cvm : array, shape (2,2) : returned only if cov=True
Covarience matrix of the fitting parameters. Diagonal elements are
estimated variances of the fitting parameters a and b; square roots of
the diagonal elements thus provide estimates of the uncertainties in the
fitting parameters `a` and `b`. Off diagonal elements (equal to each
other) are the covarience between the fitting parameters `a` and `b`.
redchisq : float : returned only if chisq=True
Reduced chi-squared goodness of fit parameter.
residuals : ndarray of floats : returned only if residuals=True
Length n array of the differences `y-(ax+b)` between `y`-data and the
fitted data `ax + b`.
Raises
------
TypeError : if `x_true` and `y` have different lengths
TypeError : If `x_true` and `y` have 2 or fewer elements
TypeError : If `sigmay` length is not 1 or the same as `y`
See Also
--------
polyfit : Least squares fit to polynomial.
linalg.lstsq : Least-squares solution to a linear matrix equation.
Notes
-----
By default, ``linfit`` returns optimal fitting parameters `a` and `b` without
weighting of the data. In that case, linfit minimizes the squared error
.. math ::
E = \\sum_{i=0}^n [y_i - (a x_i + b)]^2
If `sigmay` is set equal to the uncertainties in the `y` data points, then
linfit minimizes the `chi-squared` sum
.. math ::
\chi^2 = \\sum_{i=0}^n \\left[ \\frac{y_i-(a x_i + b)}{\\sigma_i} \\right]^2
where :math:`\sigma_i` is given by `sigmay`, the "error" or standard
deviation of :math:`y_i`. `sigmay` can be either a single number that gives the
uncertainty for all elements of `y`, or it can be an array of the same
length as `y` that gives the "error" for each element of `y`.
`redchisq` is :math:`\chi^2/(n-2)` where :math:`n` is the number of data
points (the length of `x_true` or `y`).
If `relsigma` is False, then the uncertainties `sigmay` in `y` are
assumed to be the absolute one-standard-deviation uncertainties in `y`.
In this case, the reduced chi-squared value :math:`\chi^2/(n-2)` provides a
measure of the goodness of the fit. If it is near 1, then the linear
fitting model is considered to be good and the values of the covariance
matrix are appropriately scaled. In particular, the square root of the
diagonal elements of the covariance matrix give the estimated uncertainty
in the fitting parameters `a` and `b`. See Refernece [2] below for more
information.
If `relsigma` is True, then the uncertainties `sigmay` in `y` are
considered to be only relative uncertainties. They are used to weight
the data for the fit, but in this case, the covariance matrix is rescaled
using the residuals between the fit and the data. In this case, the reduced
chi-squared value :math:`\chi^2/(n-2)` does not provide a measure of the
goodness of the fit. Nevertheless, the diagonal elements of the rescaled
covariance matrix (returned by linfit) give the estimated uncertainty in the
fitting parameters `a` and `b`.
The covariance matrix is a 2x2 symmetric matrix where the diagonal elements
are the variance of the fitting parameters. Their square roots provide
estimates of the uncertainties in the fitting parameters. The off-diagonal
elements are equal and give the cross correlation between the two fitting
parameters `a` and `b`.
linfit runs faster, by a factor of 2 to 3, if calculation of the residuals
is suppressed letting `cov`, `chisq`, and `residuals` remain False (the
default setting).
Fitting a straight line to a single set of `(x_true, y)` data using ``linfit`` is
typically 2 to 10 times faster than using either ``polyfit`` or
``linalg.lstsq``, especially when weighting is used and for very large data
sets.
References
----------
.. [1] An Introduction to Error Analysis, 2nd Ed. by John R. Taylor
(University Science Books, 1997)
.. [2] Numerical Recipes, The Art of Scientific Computing, 3rd Edition
by W.H. Press, S. A. Teukolsky, W. T. Vetterling, & B. P. Flannery
(Cambridge University Press, 2007)
Examples
--------
Fit a line, `y = ax + b`, through some noisy `(x_true, y)` data-points without
any weighting (`sigmay` = None) to obtain fitting parameters `a` and `b`:
>>> x_true = np.array([0, 1, 2, 3])
>>> y = np.array([-1, 0.2, 0.9, 2.1])
>>> fit = linfit(x_true, y)
>>> print("a = {0:0.2f}, b = {1:0.2f}".format(fit[0], fit[1]))
a = 1.00, b = -0.95
Setting `cov` = True in the input, returns the covariance matrix `cvm`.
When uncertainties `sigmay` are left unspecified, meaningful estimates of
the uncertainties `da` and `db` in the fitting parameters `a` and `b`
are given by the square roots of the diagonals of the covariance matrix
`cvm`, provided `relsigma` = True (the default state).
>>> fit, cvm = linfit(x_true, y, cov=True)
>>> dfit = [np.sqrt(cvm[i,i]) for i in range(2)]
>>> print("da = {0:0.2f}, db = {1:0.2f}".format(dfit[0], dfit[1]))
da = 0.07, db = 0.13
A better practice is to supply estimates of the uncertainties in the
input argument `sigmay`. `sigmay` can be a single float, if the
uncertainties are the same for all data points, or it can be an array, if
the uncertainties for different data points are different. Here we
enter sigmay as an array.
>>> dy = np.array([0.18, 0.13, 0.15, 0.17])
>>> fit, cvm, redchisq, resids = linfit(x_true, y, cov=True, sigmay=dy, relsigma=False, chisq=True, residuals=True)
>>> print("a = {0:0.2f}, b = {1:0.2f}".format(fit[0], fit[1]))
a = 0.98, b = -0.91
>>> dfit = [np.sqrt(cvm[i,i]) for i in range(2)]
>>> print("da = {0:0.2f}, db = {1:0.2f}".format(dfit[0], dfit[1]))
da = 0.08, db = 0.14
>>> print("reduced chi-squared = {0:0.2f}".format(redchisq))
reduced chi-squared = 1.21
>>> print(resids)
[-0.08856653 0.12781099 -0.1558115 0.06056602]
The value of reduced chi-squared `redchisq` is 1.21 indicating that a
linear model is valid for these data. The residuals :math:`y_i - (a+bx_i)`
are given by the output `resids`.
If absolute estimates of the uncertainties are not available, but relative
estimates of the uncertainties are known, a fit can be obtained with
reasonable estimates of the uncertainties in the fitting parameters by
setting `relsigma` = True.
>>> dy = np.array([1.0, 0.75, 0.75, 1.25])
>>> fit, cvm, redchisq = linfit(x_true, y, cov=True, sigmay=dy, relsigma=True, chisq=True)
>>> print("a = {0:0.2f}, b = {1:0.2f}".format(fit[0], fit[1]))
a = 0.97, b = -0.91
>>> dfit = [np.sqrt(cvm[i,i]) for i in range(2)]
>>> print("da = {0:0.2f}, db = {1:0.2f}".format(dfit[0], dfit[1]))
da = 0.09, db = 0.16
>>> print("reduced chi-squared = {0:0.2f}".format(redchisq))
reduced chi-squared = 0.04
In this case, the value `redchisq` is meaningless, because only the
relative, rather than the absolute uncertainties are known. Nevertheless,
by setting `relsigma` = True, reasonable estimates for the uncertainties
in the fitting parameters are obtained.
Illustration:
.. image:: example.png
:scale: 75 %
"""
x_true = asarray(x_true)
y = asarray(y)
if x_true.size != y.size:
raise TypeError('Expected x_true and y to have same length')
if x_true.size <= 2:
raise TypeError('Expected x_true and y length > 2')
if sigmay is None: sigmay = 1.0
sigmay = asarray(sigmay)
if sigmay.size == 1:
sigy = float(sigmay) # convert 0-d array to a float
wt = 1./(sigy*sigy)
s = wt * y.size
sx = wt * x_true.sum()
sy = wt * y.sum()
t = x_true-sx/s
stt = wt * (t*t).sum()
slope = wt * (t*y).sum()/stt
yint = (sy - sx * slope)/s
else:
if sigmay.size != y.size:
raise TypeError('Expected sigmay size to be 1 or same as y')
wt = 1./(sigmay*sigmay)
s = wt.sum()
sx = (x_true*wt).sum()
sy = (y*wt).sum()
t = (x_true-sx/s)/sigmay
stt = (t*t).sum()
slope = (t*y/sigmay).sum()/stt
yint = (sy - sx * slope)/s
returns = array([slope, yint])
if cov is True:
cvm00 = 1./stt
cvm01 = -sx/(s*stt)
cvm11 = (1.0-sx*cvm01)/s
if relsigma is True:
redchisq, resids = _resids(x_true, y, sigmay, slope, yint)
cvm00 *= redchisq
cvm01 *= redchisq
cvm11 *= redchisq
returns = [returns] + [array([[cvm00, cvm01],
[cvm01, cvm11]])]
if residuals or chisq is True:
if relsigma is False:
redchisq, resids = _resids(x_true, y, sigmay, slope, yint)
if type(returns) is not list:
returns = [returns]
if chisq is True:
returns += [redchisq]
if residuals is True:
returns += [resids]
return returns | [
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] | Least squares linear fit.
Fit a straight line `f(x_true) = a + bx` to points `(x_true, y)`. Returns
coefficients `a` and `b` that minimize the squared error.
Parameters
----------
x_true : array_like
one dimensional array of `x_true` data with `n`>2 data points.
y : array_like
one dimensional array of `y` data with `n`>2 data points.
sigmay : NoneType or float or array_like, optional
one dimensional array of uncertainties (errors) in `y` data or a single
positive number if all uncertainties are the same. `sigmay` determines
the weighting in the least squares minimization. Leaving `sigmay=None`
uses no weighting and is equivalent to `sigmay=1`.
relsigma : bool, optional
If `relsigma` is True, the residuals are used to scale the covariance
matrix. Use this option if you do not know the absolute uncertainties
(`sigmay`) in the data but still want a covariance matrix whose entries
give meaningful estimates of the uncertainties in the fitting parameters
`a` and `b` (from `f = a + bx`). If `relsigma` is False, the covariance
matrix is calculated (provided `cov` = True) using sigmay assuming
sigmay represents absolute undertainties.
cov : bool, optional
If True, calculate and return the 2x2 covarience matrix of the fitting
parameters.
chisq : bool, optional
If True, calculate and return redchisq.
residuals : bool, optional
If True, calculate and return residuals.
Returns
-------
fit : array([a,b]) ndarray of floats
The best fit model parameters `a` (the slope) and `b` (the
`y`-intercept) for the input data arrays `x_true` and `y`
cvm : array, shape (2,2) : returned only if cov=True
Covarience matrix of the fitting parameters. Diagonal elements are
estimated variances of the fitting parameters a and b; square roots of
the diagonal elements thus provide estimates of the uncertainties in the
fitting parameters `a` and `b`. Off diagonal elements (equal to each
other) are the covarience between the fitting parameters `a` and `b`.
redchisq : float : returned only if chisq=True
Reduced chi-squared goodness of fit parameter.
residuals : ndarray of floats : returned only if residuals=True
Length n array of the differences `y-(ax+b)` between `y`-data and the
fitted data `ax + b`.
Raises
------
TypeError : if `x_true` and `y` have different lengths
TypeError : If `x_true` and `y` have 2 or fewer elements
TypeError : If `sigmay` length is not 1 or the same as `y`
See Also
--------
polyfit : Least squares fit to polynomial.
linalg.lstsq : Least-squares solution to a linear matrix equation.
Notes
-----
By default, ``linfit`` returns optimal fitting parameters `a` and `b` without
weighting of the data. In that case, linfit minimizes the squared error
.. math ::
E = \\sum_{i=0}^n [y_i - (a x_i + b)]^2
If `sigmay` is set equal to the uncertainties in the `y` data points, then
linfit minimizes the `chi-squared` sum
.. math ::
\chi^2 = \\sum_{i=0}^n \\left[ \\frac{y_i-(a x_i + b)}{\\sigma_i} \\right]^2
where :math:`\sigma_i` is given by `sigmay`, the "error" or standard
deviation of :math:`y_i`. `sigmay` can be either a single number that gives the
uncertainty for all elements of `y`, or it can be an array of the same
length as `y` that gives the "error" for each element of `y`.
`redchisq` is :math:`\chi^2/(n-2)` where :math:`n` is the number of data
points (the length of `x_true` or `y`).
If `relsigma` is False, then the uncertainties `sigmay` in `y` are
assumed to be the absolute one-standard-deviation uncertainties in `y`.
In this case, the reduced chi-squared value :math:`\chi^2/(n-2)` provides a
measure of the goodness of the fit. If it is near 1, then the linear
fitting model is considered to be good and the values of the covariance
matrix are appropriately scaled. In particular, the square root of the
diagonal elements of the covariance matrix give the estimated uncertainty
in the fitting parameters `a` and `b`. See Refernece [2] below for more
information.
If `relsigma` is True, then the uncertainties `sigmay` in `y` are
considered to be only relative uncertainties. They are used to weight
the data for the fit, but in this case, the covariance matrix is rescaled
using the residuals between the fit and the data. In this case, the reduced
chi-squared value :math:`\chi^2/(n-2)` does not provide a measure of the
goodness of the fit. Nevertheless, the diagonal elements of the rescaled
covariance matrix (returned by linfit) give the estimated uncertainty in the
fitting parameters `a` and `b`.
The covariance matrix is a 2x2 symmetric matrix where the diagonal elements
are the variance of the fitting parameters. Their square roots provide
estimates of the uncertainties in the fitting parameters. The off-diagonal
elements are equal and give the cross correlation between the two fitting
parameters `a` and `b`.
linfit runs faster, by a factor of 2 to 3, if calculation of the residuals
is suppressed letting `cov`, `chisq`, and `residuals` remain False (the
default setting).
Fitting a straight line to a single set of `(x_true, y)` data using ``linfit`` is
typically 2 to 10 times faster than using either ``polyfit`` or
``linalg.lstsq``, especially when weighting is used and for very large data
sets.
References
----------
.. [1] An Introduction to Error Analysis, 2nd Ed. by John R. Taylor
(University Science Books, 1997)
.. [2] Numerical Recipes, The Art of Scientific Computing, 3rd Edition
by W.H. Press, S. A. Teukolsky, W. T. Vetterling, & B. P. Flannery
(Cambridge University Press, 2007)
Examples
--------
Fit a line, `y = ax + b`, through some noisy `(x_true, y)` data-points without
any weighting (`sigmay` = None) to obtain fitting parameters `a` and `b`:
>>> x_true = np.array([0, 1, 2, 3])
>>> y = np.array([-1, 0.2, 0.9, 2.1])
>>> fit = linfit(x_true, y)
>>> print("a = {0:0.2f}, b = {1:0.2f}".format(fit[0], fit[1]))
a = 1.00, b = -0.95
Setting `cov` = True in the input, returns the covariance matrix `cvm`.
When uncertainties `sigmay` are left unspecified, meaningful estimates of
the uncertainties `da` and `db` in the fitting parameters `a` and `b`
are given by the square roots of the diagonals of the covariance matrix
`cvm`, provided `relsigma` = True (the default state).
>>> fit, cvm = linfit(x_true, y, cov=True)
>>> dfit = [np.sqrt(cvm[i,i]) for i in range(2)]
>>> print("da = {0:0.2f}, db = {1:0.2f}".format(dfit[0], dfit[1]))
da = 0.07, db = 0.13
A better practice is to supply estimates of the uncertainties in the
input argument `sigmay`. `sigmay` can be a single float, if the
uncertainties are the same for all data points, or it can be an array, if
the uncertainties for different data points are different. Here we
enter sigmay as an array.
>>> dy = np.array([0.18, 0.13, 0.15, 0.17])
>>> fit, cvm, redchisq, resids = linfit(x_true, y, cov=True, sigmay=dy, relsigma=False, chisq=True, residuals=True)
>>> print("a = {0:0.2f}, b = {1:0.2f}".format(fit[0], fit[1]))
a = 0.98, b = -0.91
>>> dfit = [np.sqrt(cvm[i,i]) for i in range(2)]
>>> print("da = {0:0.2f}, db = {1:0.2f}".format(dfit[0], dfit[1]))
da = 0.08, db = 0.14
>>> print("reduced chi-squared = {0:0.2f}".format(redchisq))
reduced chi-squared = 1.21
>>> print(resids)
[-0.08856653 0.12781099 -0.1558115 0.06056602]
The value of reduced chi-squared `redchisq` is 1.21 indicating that a
linear model is valid for these data. The residuals :math:`y_i - (a+bx_i)`
are given by the output `resids`.
If absolute estimates of the uncertainties are not available, but relative
estimates of the uncertainties are known, a fit can be obtained with
reasonable estimates of the uncertainties in the fitting parameters by
setting `relsigma` = True.
>>> dy = np.array([1.0, 0.75, 0.75, 1.25])
>>> fit, cvm, redchisq = linfit(x_true, y, cov=True, sigmay=dy, relsigma=True, chisq=True)
>>> print("a = {0:0.2f}, b = {1:0.2f}".format(fit[0], fit[1]))
a = 0.97, b = -0.91
>>> dfit = [np.sqrt(cvm[i,i]) for i in range(2)]
>>> print("da = {0:0.2f}, db = {1:0.2f}".format(dfit[0], dfit[1]))
da = 0.09, db = 0.16
>>> print("reduced chi-squared = {0:0.2f}".format(redchisq))
reduced chi-squared = 0.04
In this case, the value `redchisq` is meaningless, because only the
relative, rather than the absolute uncertainties are known. Nevertheless,
by setting `relsigma` = True, reasonable estimates for the uncertainties
in the fitting parameters are obtained.
Illustration:
.. image:: example.png
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".",
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"of",
"(",
"x_true",
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")",
"data",
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"References",
"----------",
"..",
"[",
"1",
"]",
"An",
"Introduction",
"to",
"Error",
"Analysis",
"2nd",
"Ed",
".",
"by",
"John",
"R",
".",
"Taylor",
"(",
"University",
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"Books",
"1997",
")",
"..",
"[",
"2",
"]",
"Numerical",
"Recipes",
"The",
"Art",
"of",
"Scientific",
"Computing",
"3rd",
"Edition",
"by",
"W",
".",
"H",
".",
"Press",
"S",
".",
"A",
".",
"Teukolsky",
"W",
".",
"T",
".",
"Vetterling",
"&",
"B",
".",
"P",
".",
"Flannery",
"(",
"Cambridge",
"University",
"Press",
"2007",
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] | train | https://github.com/Vital-Fernandez/dazer/blob/3c9ae8ae6d40ea33f22cc20dc11365d6d6e65244/bin/lib/Math_Libraries/fitting_methods.py#L53-L305 |
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