def plot_model_full(self,
model,
data,
labels=True,
paramvalues=None,
offset=0,
**kw):
if self.no_fits:
return
if paramvalues is None:
paramvalues = prepare_params(model.params, data.meta)[3]
nsamples = self._get_samples(model, data)
imin, imax = data.x_plot.argmin(), data.x_plot.argmax()
xx = multi_linspace(data.x[imin], data.x[imax], nsamples)
xxp = linspace(data.x_plot[imin], data.x_plot[imax], nsamples)
yy = model.fcn(paramvalues, xx)
if 'label' not in kw:
kw['label'] = labels and 'fit' or ''
self.axes.plot(xxp, yy + offset, 'g', lw=kw.pop('kw', 2), **kw)
for comp in model.get_components():
if comp is model:
continue
yy = comp.fcn(paramvalues, xx)
kw['label'] = labels and comp.name or ''
self.axes.plot(xxp, yy + offset, '-.', **kw)
def simulate(self, data):
varying, varynames, dependent, _ = prepare_params(
self.params, data.meta)
pd = dict((p.name, p.value) for p in self.params)
update_params(dependent, data.meta, pd)
yy = self.fcn(pd, data.x)
new = data.copy()
new.y = yy
new.dy = zeros(len(yy))
return new
def export_fits(self, filename):
xx = linspace(self.data.x.min(), self.data.x.max(), 1000)
paramvalues = prepare_params(self.model.params, self.data.meta)[3]
yy = self.model.fcn(paramvalues, xx)
yys = []
for comp in self.model.get_components():
if comp is self.model:
continue
yys.append(comp.fcn(paramvalues, xx))
savetxt(filename, array([xx, yy] + yys).T)
def do_fit(data, fcn, params, add_kw):
x, y, dy = data.fit_columns
meta = data.meta
varying, varynames, dependent, _ = prepare_params(params, meta)
def leastsqfcn(params, data):
pd = dict(zip(varynames, params))
update_params(dependent, meta, pd)
return (fcn(pd, x) - y) / dy
initpars = []
warned = False
for p in varying:
initpars.append(p.value)
if (p.pmin is not None or p.pmax is not None) and not warned:
print('Sorry, scipy backend cannot handle parameter bounds.')
warned = True
try:
res = leastsq(leastsqfcn,
initpars,
args=(data, ),
full_output=1,
**add_kw)
except Exception as e:
return False, str(e), 0
popt, pcov, infodict, errmsg, ier = res
success = (ier in [1, 2, 3, 4])
nfree = len(y) - len(varying)
if nfree > 0 and pcov is not None:
s_sq = (leastsqfcn(popt, data)**2).sum() / nfree
pcov = pcov * s_sq
else:
pcov = inf
pd = {}
for i, p in enumerate(varying):
pd[p.name] = popt[i]
if pcov is not inf:
p.error = sqrt(pcov[i, i])
else:
p.error = 0
p.correl = {} # XXX
update_params(dependent, meta, pd)
for p in params:
p.value = pd[p.name]
return success, errmsg, get_chisqr(fcn, x, y, dy, params)
def do_fit(data, fcn, params, add_kw):
# lmfit can handle expression-based parameters itself, but that is
# a) buggy (cannot pass custom items into namespace without subclass)
# and b) it is better to use the same mechanism in all backends
x, y, dy = data.fit_columns
meta = data.meta
varying, varynames, dependent, _ = prepare_params(params, meta)
lmfparams = Parameters()
for p in varying:
lmfparams.add(p.name, p.value, min=p.pmin, max=p.pmax)
def lmfitfcn(lmfparams, data):
pd = dict((pn, lmfparams[pn].value) for pn in varynames)
update_params(dependent, meta, pd)
return (fcn(pd, x) - y) / dy
printReport = add_kw.pop('printReport', False)
try:
out = minimize(lmfitfcn, lmfparams, args=(data,), **add_kw)
except Exception as e:
print(str(e))
return False, str(e), 0
if printReport:
report_fit(out.params)
pd = dict((pn, out.params[pn].value) for pn in varynames)
update_params(dependent, meta, pd)
for p in params:
p.value = pd[p.name]
if p.name in lmfparams:
p.error = out.params[p.name].stderr
p.correl = out.params[p.name].correl
else:
p.error = 0
p.correl = {}
# sadly, out.message is a bit buggy
message = ''
if not out.success:
message = out.lmdif_message
if not out.errorbars:
message += ' Could not estimate error bars.'
return out.success, message, out.redchi
def do_fit(data, fcn, params, add_kw):
x, y, dy = data.fit_columns
meta = data.meta
varying, varynames, dependent, _ = prepare_params(params, meta)
def minuitfcn(*args):
pd = dict(zip(varynames, args))
update_params(dependent, meta, pd)
return ((fcn(pd, x) - y)**2 / dy**2).sum()
printReport = add_kw.pop('printReport', False)
marg = dict(
print_level=int(printReport),
forced_parameters=varynames,
)
marg.update(add_kw)
if 'errordef' not in marg:
marg['errordef'] = 1
for p in varying:
marg[p.name] = p.value
marg['error_' + p.name] = 100*p.delta or p.value/100. or 0.01
if p.pmin is not None or p.pmax is not None:
marg['limit_' + p.name] = (p.pmin is None and -1e8 or p.pmin,
p.pmax is None and +1e8 or p.pmax)
m = Minuit(minuitfcn, **marg)
try:
m.migrad()
m.hesse()
except Exception as e:
return False, str(e), 0
# m.minos() -> would calculate more exact and asymmetric errors
pd = dict((pn, m.values[pn]) for pn in varynames)
update_params(dependent, meta, pd)
for p in params:
p.value = pd[p.name]
if p.name in varynames:
p.error = m.errors[p.name]
p.correl = {} # XXX
else:
p.error = 0
p.correl = {}
return True, '', get_chisqr(fcn, x, y, dy, params)
def plot_model_components(self,
model,
data,
labels=True,
paramvalues=None,
offset=0,
**kw):
if self.no_fits:
return
if paramvalues is None:
paramvalues = prepare_params(model.params, data.meta)[3]
nsamples = self._get_samples(model, data)
imin, imax = data.x_plot.argmin(), data.x_plot.argmax()
xx = multi_linspace(data.x[imin], data.x[imax], nsamples)
xxp = linspace(data.x_plot[imin], data.x_plot[imax], nsamples)
for comp in model.get_components():
yy = comp.fcn(paramvalues, xx)
kw['label'] = labels and comp.name or ''
self.axes.plot(xxp, yy + offset, kw.pop('fmt', '-.'), **kw)
def do_fit(data, fcn, params, add_kw):
x, y, dy = data.fit_columns
meta = data.meta
varying, varynames, dependent, _ = prepare_params(params, meta)
def leastsqfcn(x, params):
pd = dict(zip(varynames, params))
update_params(dependent, meta, pd)
return fcn(pd, x)
initpars = []
initdp = []
warned = False
for p in varying:
initpars.append(p.value)
initdp.append(p.delta or p.value / 10. or 0.01)
if (p.pmin is not None or p.pmax is not None) and not warned:
print('Sorry, unifit backend cannot handle parameter bounds.')
warned = True
try:
res = __leastsq((x, y, dy), leastsqfcn, initpars, initdp, **add_kw)
except Exception as e:
raise
return False, str(e), 0
success = res['converged']
errmsg = res['errmsg']
pd = {}
for i, p in enumerate(varying):
pd[p.name] = res['values'][i]
p.error = res['errors'][i]
p.correl = {} # XXX
update_params(dependent, meta, pd)
for p in params:
p.value = pd[p.name]
return success, errmsg, get_chisqr(fcn, x, y, dy, params)
def plot_model(self,
model,
data,
labels=True,
paramvalues=None,
offset=0,
**kw):
if self.no_fits:
return
if paramvalues is None:
paramvalues = prepare_params(model.params, data.meta)[3]
nsamples = self._get_samples(model, data)
imin, imax = data.x_plot.argmin(), data.x_plot.argmax()
xx = multi_linspace(data.x[imin], data.x[imax], nsamples)
xxp = linspace(data.x_plot[imin], data.x_plot[imax], nsamples)
yy = model.fcn(paramvalues, xx)
if 'label' not in kw:
kw['label'] = labels and 'fit' or ''
self.axes.plot(xxp,
yy + offset,
kw.pop('fmt', 'g'),
lw=kw.pop('lw', 2),
**kw)