class TestObjective(object):
def setup_method(self):
# Choose the "true" parameters.
# Reproducible results!
np.random.seed(123)
self.m_true = -0.9594
self.b_true = 4.294
self.f_true = 0.534
self.m_ls = -1.1040757010910947
self.b_ls = 5.4405552502319505
# Generate some synthetic data from the model.
N = 50
x = np.sort(10 * np.random.rand(N))
y_err = 0.1 + 0.5 * np.random.rand(N)
y = self.m_true * x + self.b_true
y += np.abs(self.f_true * y) * np.random.randn(N)
y += y_err * np.random.randn(N)
self.data = Data1D(data=(x, y, y_err))
self.p = Parameter(self.b_ls, 'b') | Parameter(self.m_ls, 'm')
self.model = Model(self.p, fitfunc=line)
self.objective = Objective(self.model, self.data)
# want b and m
self.p[0].vary = True
self.p[1].vary = True
mod = np.array([
4.78166609, 4.42364699, 4.16404064, 3.50343504, 3.4257084,
2.93594347, 2.92035638, 2.67533842, 2.28136038, 2.19772983,
1.99295496, 1.93748334, 1.87484436, 1.65161016, 1.44613461,
1.11128101, 1.04584535, 0.86055984, 0.76913963, 0.73906649,
0.73331407, 0.68350418, 0.65216599, 0.59838566, 0.13070299,
0.10749131, -0.01010195, -0.10010155, -0.29495372, -0.42817431,
-0.43122391, -0.64637715, -1.30560686, -1.32626428, -1.44835768,
-1.52589881, -1.56371158, -2.12048349, -2.24899179, -2.50292682,
-2.53576659, -2.55797996, -2.60870542, -2.7074727, -3.93781479,
-4.12415366, -4.42313742, -4.98368609, -5.38782395, -5.44077086
])
self.mod = mod
def test_model(self):
# test that the line data produced by our model is the same as the
# test data
assert_almost_equal(self.model(self.data.x), self.mod)
def test_synthetic_data(self):
# test that we create the correct synthetic data by performing a least
# squares fit on it
assert_(self.data.y_err is not None)
x, y, y_err, _ = self.data.data
A = np.vstack((np.ones_like(x), x)).T
C = np.diag(y_err * y_err)
cov = np.linalg.inv(np.dot(A.T, np.linalg.solve(C, A)))
b_ls, m_ls = np.dot(cov, np.dot(A.T, np.linalg.solve(C, y)))
assert_almost_equal(b_ls, self.b_ls)
assert_almost_equal(m_ls, self.m_ls)
def test_setp(self):
# check that we can set parameters
self.p[0].vary = False
assert_(len(self.objective.varying_parameters()) == 1)
self.objective.setp(np.array([1.23]))
assert_equal(self.p[1].value, 1.23)
self.objective.setp(np.array([1.234, 1.23]))
assert_equal(np.array(self.p), [1.234, 1.23])
def test_pvals(self):
assert_equal(self.objective.parameters.pvals, [self.b_ls, self.m_ls])
self.objective.parameters.pvals = [1, 2]
assert_equal(self.objective.parameters.pvals, [1, 2.])
def test_lnprior(self):
self.p[0].range(0, 10)
assert_almost_equal(self.objective.lnprior(), np.log(0.1))
# lnprior should set parameters
self.objective.lnprior([8, 2])
assert_equal(np.array(self.objective.parameters), [8, 2])
# if we supply a value outside the range it should return -inf
assert_equal(self.objective.lnprior([-1, 2]), -np.inf)
def test_lnprob(self):
# http://dan.iel.fm/emcee/current/user/line/
assert_almost_equal(self.objective.lnprior(), 0)
# the uncertainties are underestimated in this example...
assert_almost_equal(self.objective.lnlike(), -559.01078135444595)
assert_almost_equal(self.objective.lnprob(), -559.01078135444595)
def test_chisqr(self):
assert_almost_equal(self.objective.chisqr(), 1231.1096772954229)
def test_residuals(self):
# weighted, with and without transform
assert_almost_equal(self.objective.residuals(),
(self.data.y - self.mod) / self.data.y_err)
objective = Objective(self.model,
self.data,
transform=Transform('lin'))
assert_almost_equal(objective.residuals(),
(self.data.y - self.mod) / self.data.y_err)
# unweighted, with and without transform
objective = Objective(self.model, self.data, use_weights=False)
assert_almost_equal(objective.residuals(), self.data.y - self.mod)
objective = Objective(self.model,
self.data,
use_weights=False,
transform=Transform('lin'))
assert_almost_equal(objective.residuals(), self.data.y - self.mod)
def test_lnprob_extra(self):
self.objective.lnprob_extra = lnprob_extra
# repeat lnprior test
self.p[0].range(0, 10)
assert_almost_equal(self.objective.lnprior(), np.log(0.1) + 1)
def test_objective_pickle(self):
# can you pickle the objective function?
pkl = pickle.dumps(self.objective)
pickle.loads(pkl)
# check the ForkingPickler as well.
if hasattr(ForkingPickler, 'dumps'):
pkl = ForkingPickler.dumps(self.objective)
pickle.loads(pkl)
# can you pickle with an extra function present?
self.objective.lnprob_extra = lnprob_extra
pkl = pickle.dumps(self.objective)
pickle.loads(pkl)
# check the ForkingPickler as well.
if hasattr(ForkingPickler, 'dumps'):
pkl = ForkingPickler.dumps(self.objective)
pickle.loads(pkl)
def test_transform_pickle(self):
# can you pickle the Transform object?
pkl = pickle.dumps(Transform('logY'))
pickle.loads(pkl)
def test_transform(self):
pth = os.path.dirname(os.path.abspath(__file__))
fname = os.path.join(pth, 'c_PLP0011859_q.txt')
data = ReflectDataset(fname)
t = Transform('logY')
yt, et = t(data.x, data.y, y_err=data.y_err)
assert_equal(yt, np.log10(data.y))
yt, _ = t(data.x, data.y, y_err=None)
assert_equal(yt, np.log10(data.y))
EPy, EPe = EP.EPlog10(data.y, data.y_err)
assert_equal(yt, EPy)
assert_equal(et, EPe)
def test_lnsigma(self):
# check that lnsigma works correctly
def lnprior(theta, x, y, yerr):
m, b, lnf = theta
if -5.0 < m < 0.5 and 0.0 < b < 10.0 and -10.0 < lnf < 1.0:
return 0.0
return -np.inf
def lnlike(theta, x, y, yerr):
m, b, lnf = theta
model = m * x + b
inv_sigma2 = 1.0 / (yerr**2 + model**2 * np.exp(2 * lnf))
print(inv_sigma2)
return -0.5 * (np.sum((y - model)**2 * inv_sigma2 -
np.log(inv_sigma2)))
x, y, yerr, _ = self.data.data
theta = [self.m_true, self.b_true, np.log(self.f_true)]
bo = BaseObjective(theta,
lnlike,
lnprior=lnprior,
fcn_args=(x, y, yerr))
lnsigma = Parameter(np.log(self.f_true),
'lnsigma',
bounds=(-10, 1),
vary=True)
self.objective.setp(np.array([self.b_true, self.m_true]))
self.objective.lnsigma = lnsigma
assert_allclose(self.objective.lnlike(), bo.lnlike())
def test_base_emcee(self):
# check that the base objective works against the emcee example.
def lnprior(theta, x, y, yerr):
m, b, lnf = theta
if -5.0 < m < 0.5 and 0.0 < b < 10.0 and -10.0 < lnf < 1.0:
return 0.0
return -np.inf
def lnlike(theta, x, y, yerr):
m, b, lnf = theta
model = m * x + b
inv_sigma2 = 1.0 / (yerr**2 + model**2 * np.exp(2 * lnf))
return -0.5 * (np.sum((y - model)**2 * inv_sigma2 -
np.log(inv_sigma2)))
x, y, yerr, _ = self.data.data
theta = [self.m_true, self.b_true, np.log(self.f_true)]
bo = BaseObjective(theta,
lnlike,
lnprior=lnprior,
fcn_args=(x, y, yerr))
# test that the wrapper gives the same lnlike as the direct function
assert_almost_equal(bo.lnlike(theta), lnlike(theta, x, y, yerr))
assert_almost_equal(bo.lnlike(theta), -bo.nll(theta))
assert_almost_equal(bo.nll(theta), 12.8885352412)
# Find the maximum likelihood value.
result = minimize(bo.nll, theta)
# for repeatable sampling
np.random.seed(1)
ndim, nwalkers = 3, 100
pos = [
result["x"] + 1e-4 * np.random.randn(ndim) for i in range(nwalkers)
]
sampler = emcee.EnsembleSampler(nwalkers, ndim, bo.lnprob)
sampler.run_mcmc(pos, 800, rstate0=np.random.get_state())
burnin = 200
samples = sampler.chain[:, burnin:, :].reshape((-1, ndim))
samples[:, 2] = np.exp(samples[:, 2])
m_mc, b_mc, f_mc = map(
lambda v: (v[1], v[2] - v[1], v[1] - v[0]),
zip(*np.percentile(samples, [16, 50, 84], axis=0)))
assert_allclose(m_mc, (-1.0071664, 0.0809444, 0.0784894), rtol=0.04)
assert_allclose(b_mc, (4.5428107, 0.3549174, 0.3673304), rtol=0.04)
assert_allclose(f_mc, (0.4610898, 0.0823304, 0.0640812), rtol=0.06)
# # smoke test for covariance matrix
bo.parameters = np.array(result['x'])
covar1 = bo.covar()
uncertainties = np.sqrt(np.diag(covar1))
# covariance from objective._covar should be almost equal to
# the covariance matrix from sampling
covar2 = np.cov(samples.T)
assert_almost_equal(np.sqrt(np.diag(covar2))[:2], uncertainties[:2], 2)
# check covariance of self.objective
# TODO
var_arr = result['x'][:]
var_arr[0], var_arr[1], var_arr[2] = var_arr[2], var_arr[1], var_arr[0]
# assert_(self.objective.data.weighted)
# self.objective.parameters.pvals = var_arr
# covar3 = self.objective.covar()
# uncertainties3 = np.sqrt(np.diag(covar3))
# assert_almost_equal(uncertainties3, uncertainties)
# assert(False)
def test_covar(self):
# checks objective.covar against optimize.least_squares covariance.
path = os.path.dirname(os.path.abspath(__file__))
theoretical = np.loadtxt(os.path.join(path, 'gauss_data.txt'))
xvals, yvals, evals = np.hsplit(theoretical, 3)
xvals = xvals.flatten()
yvals = yvals.flatten()
evals = evals.flatten()
p0 = np.array([0.1, 20., 0.1, 0.1])
names = ['bkg', 'A', 'x0', 'width']
bounds = [(-1, 1), (0, 30), (-5., 5.), (0.001, 2)]
params = Parameters(name="gauss_params")
for p, name, bound in zip(p0, names, bounds):
param = Parameter(p, name=name)
param.range(*bound)
param.vary = True
params.append(param)
model = Model(params, fitfunc=gauss)
data = Data1D((xvals, yvals, evals))
objective = Objective(model, data)
# first calculate least_squares jac/hess/covariance matrices
res = least_squares(objective.residuals,
np.array(params),
jac='3-point')
hess_least_squares = np.matmul(res.jac.T, res.jac)
covar_least_squares = np.linalg.inv(hess_least_squares)
# now calculate corresponding matrices by hand, to see if the approach
# concurs with least_squares
objective.setp(res.x)
_pvals = np.array(res.x)
def residuals_scaler(vals):
return np.squeeze(objective.residuals(_pvals * vals))
jac = approx_derivative(residuals_scaler, np.ones_like(_pvals))
hess = np.matmul(jac.T, jac)
covar = np.linalg.inv(hess)
covar = covar * np.atleast_2d(_pvals) * np.atleast_2d(_pvals).T
assert_allclose(covar, covar_least_squares)
# check that objective.covar corresponds to the least_squares
# covariance matrix
objective.setp(res.x)
_pvals = np.array(res.x)
covar_objective = objective.covar()
assert_allclose(covar_objective, covar_least_squares)
# now see what happens with a parameter that has no effect on residuals
param = Parameter(1.234, name='dummy')
param.vary = True
params.append(param)
from pytest import raises
with raises(LinAlgError):
objective.covar()
class Motofit(object):
"""
An interactive slab modeller (Jupyter/ipywidgets based) for Neutron and
X-ray reflectometry data.
The interactive modeller is designed to be used in a Jupyter notebook.
Usage
-----
>>> # specify that plots are in a separate graph window
>>> %matplotlib qt
>>> # alternately if you want the graph to be embedded in the notebook use
>>> # %matplotlib notebook
>>> from refnx.reflect import Motofit
>>> # create an instance of the modeller
>>> app = Motofit()
>>> # display it in the notebook by calling the object with a datafile.
>>> app('dataset1.txt')
>>> # lets fit a different dataset
>>> app2 = Motofit()
>>> app2('dataset2.txt')
The `Motofit` instance has several useful attributes that can be used in
other cells. For example, one can access the `objective` and `curvefitter`
attributes for more advanced fitting functionality than is available in the
GUI. A `code` attribute can be used to retrieve a Python code fragment that
can be used as a basis for developing more complicated models, such as
interparameter constraints, global fitting, etc.
Attributes
----------
dataset: refnx.reflect.Data1D
The dataset associated with the modeller
model: refnx.reflect.ReflectModel
Calculates a theoretical model, from an interfacial structure
(`model.Structure`).
objective: refnx.analysis.Objective
The Objective that allows one to compare the model against the data.
curvefitter: refnx.analysis.CurveFitter
Object for fitting the data based on the objective.
fig: matplotlib.Figure
Graph displaying the data.
code: str
A Python code fragment capable of fitting the data.
Methods
-------
__call__ - display the GUI in a Jupyter cell
save_model - save the current model to a pickle file
load_model - load a pickle file and set it as the current file
set_model - use an existing `refnx.reflect.ReflectModel` to set the GUI
model
load_data - load a dataset
do_fit - do a fit
redraw - Update the notebook cell containing the GUI
"""
def __init__(self):
# attributes for the graph
# for the graph
self.qmin = 0.005
self.qmax = 0.5
self.qpnt = 1000
self.fig = None
self.ax_data = None
self.ax_residual = None
self.ax_sld = None
# gridspecs specify how the plots are laid out. Gridspec1 is when the
# residuals plot is displayed. Gridspec2 is when it's not visible
self._gridspec1 = gridspec.GridSpec(2,
2,
height_ratios=[5, 1],
width_ratios=[1, 1],
hspace=0.01)
self._gridspec2 = gridspec.GridSpec(1, 2)
self.theoretical_plot = None
self.theoretical_plot_sld = None
# attributes for a user dataset
self.dataset = None
self.objective = None
self._curvefitter = None
self.data_plot = None
self.residuals_plot = None
self.data_plot_sld = None
self.dataset_name = widgets.Text(description='dataset:')
self.dataset_name.disabled = True
self.chisqr = widgets.FloatText(description='chi-squared:')
self.chisqr.disabled = True
# fronting
slab0 = Slab(0, 0, 0)
slab1 = Slab(25, 3.47, 3)
slab2 = Slab(0, 2.07, 3)
structure = slab0 | slab1 | slab2
rename_params(structure)
self.model = ReflectModel(structure)
structure = slab0 | slab1 | slab2
self.model = ReflectModel(structure)
# give some default parameter limits
self.model.scale.bounds = (0.1, 2)
self.model.bkg.bounds = (1e-8, 2e-5)
self.model.dq.bounds = (0, 20)
for slab in self.model.structure:
slab.thick.bounds = (0, 2 * slab.thick.value)
slab.sld.real.bounds = (0, 2 * slab.sld.real.value)
slab.sld.imag.bounds = (0, 2 * slab.sld.imag.value)
slab.rough.bounds = (0, 2 * slab.rough.value)
# the main GUI widget
self.display_box = widgets.VBox()
self.tab = widgets.Tab()
self.tab.set_title(0, 'Model')
self.tab.set_title(1, 'Limits')
self.tab.set_title(2, 'Options')
self.tab.observe(self._on_tab_changed, names='selected_index')
# an output area for messages.
self.output = widgets.Output()
# options tab
self.plot_type = widgets.Dropdown(
options=['lin', 'logY', 'YX4', 'YX2'],
value='lin',
description='Plot Type:',
disabled=False)
self.plot_type.observe(self._on_plot_type_changed, names='value')
self.use_weights = widgets.RadioButtons(
options=['Yes', 'No'],
value='Yes',
description='use dataset weights?',
style={'description_width': 'initial'})
self.use_weights.observe(self._on_use_weights_changed, names='value')
self.transform = Transform('lin')
self.display_residuals = widgets.Checkbox(
value=False, description='Display residuals')
self.display_residuals.observe(self._on_display_residuals_changed,
names='value')
self.model_view = None
self.set_model(self.model)
def save_model(self, f=None):
"""
Serialise a model to a pickle file.
Parameters
----------
f: file like or str
File to save model to.
"""
if f is None:
f = 'model_' + datetime.datetime.now().isoformat() + '.pkl'
if self.dataset is not None:
f = 'model_' + self.dataset.name + '.pkl'
with possibly_open_file(f) as g:
pickle.dump(self.model, g)
def load_model(self, f):
"""
Load a serialised model.
Parameters
----------
f: file like or str
pickle file to load model from.
"""
with possibly_open_file(f) as g:
reflect_model = pickle.load(g)
self.set_model(reflect_model)
self._print(repr(self.objective))
def set_model(self, model):
"""
Change the `refnx.reflect.ReflectModel` associated with the `Motofit`
instance.
Parameters
----------
model: refnx.reflect.ReflectModel
"""
if self.model_view is not None:
self.model_view.unobserve_all()
# figure out if the reflect_model is a different instance. If it is
# then the objective has to be updated.
if model is not self.model:
self.model = model
self._update_analysis_objects()
self.model = model
self.model_view = ReflectModelView(self.model)
self.model_view.observe(self.update_model, names=['view_changed'])
self.model_view.observe(self.redraw, names=['view_redraw'])
# observe when the number of varying parameters changed. This
# invalidates a curvefitter, and a new one has to be produced.
self.model_view.observe(self._on_num_varying_changed,
names=['num_varying'])
self.model_view.do_fit_button.on_click(self.do_fit)
self.model_view.to_code_button.on_click(self._to_code)
self.redraw(None)
def update_model(self, change):
"""
Updates the plots when the parameters change
Parameters
----------
change
"""
if not self.fig:
return
q = np.linspace(self.qmin, self.qmax, self.qpnt)
theoretical = self.model.model(q)
yt, _ = self.transform(q, theoretical)
sld_profile = self.model.structure.sld_profile()
z, sld = sld_profile
if self.theoretical_plot is not None:
self.theoretical_plot.set_xdata(q)
self.theoretical_plot.set_ydata(yt)
self.theoretical_plot_sld.set_xdata(z)
self.theoretical_plot_sld.set_ydata(sld)
self.ax_sld.relim()
self.ax_sld.autoscale_view()
if self.dataset is not None:
# if there's a dataset loaded then residuals_plot
# should exist
residuals = self.objective.residuals()
self.chisqr.value = np.sum(residuals**2)
self.residuals_plot.set_xdata(self.dataset.x)
self.residuals_plot.set_ydata(residuals)
self.ax_residual.relim()
self.ax_residual.autoscale_view()
self.fig.canvas.draw()
def _on_num_varying_changed(self, change):
# observe when the number of varying parameters changed. This
# invalidates a curvefitter, and a new one has to be produced.
if change['new'] != change['old']:
self._curvefitter = None
def _update_analysis_objects(self):
use_weights = self.use_weights.value == 'Yes'
self.objective = Objective(self.model,
self.dataset,
transform=self.transform,
use_weights=use_weights)
self._curvefitter = None
def __call__(self, data=None, model=None):
"""
Display the `Motofit` GUI in a Jupyter notebook cell.
Parameters
----------
data: refnx.dataset.Data1D
The dataset to associate with the `Motofit` instance.
model: refnx.reflect.ReflectModel or str or file-like
A model to associate with the data.
If `model` is a `str` or `file`-like then the `load_model` method
will be used to try and load the model from file. This assumes that
the file is a pickle of a `ReflectModel`
"""
# the theoretical model
# display the main graph
self.fig = plt.figure(figsize=(9, 4))
# grid specs depending on whether the residuals are displayed
if self.display_residuals.value:
d_gs = self._gridspec1[0, 0]
sld_gs = self._gridspec1[:, 1]
else:
d_gs = self._gridspec2[0, 0]
sld_gs = self._gridspec2[0, 1]
self.ax_data = self.fig.add_subplot(d_gs)
self.ax_data.set_xlabel('$Q/\AA^{-1}$')
self.ax_data.set_ylabel('Reflectivity')
self.ax_data.grid(True, color='b', linestyle='--', linewidth=0.1)
self.ax_sld = self.fig.add_subplot(sld_gs)
self.ax_sld.set_ylabel('$\\rho/10^{-6}\AA^{-2}$')
self.ax_sld.set_xlabel('$z/\AA$')
self.ax_residual = self.fig.add_subplot(self._gridspec1[1, 0],
sharex=self.ax_data)
self.ax_residual.set_xlabel('$Q/\AA^{-1}$')
self.ax_residual.grid(True, color='b', linestyle='--', linewidth=0.1)
self.ax_residual.set_visible(self.display_residuals.value)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
self.fig.tight_layout()
q = np.linspace(self.qmin, self.qmax, self.qpnt)
theoretical = self.model.model(q)
yt, _ = self.transform(q, theoretical)
self.theoretical_plot = self.ax_data.plot(q, yt, zorder=2)[0]
self.ax_data.set_yscale('log')
z, sld = self.model.structure.sld_profile()
self.theoretical_plot_sld = self.ax_sld.plot(z, sld)[0]
# the figure has been reset, so remove ref to the data_plot,
# residual_plot
self.data_plot = None
self.residuals_plot = None
self.dataset = None
if data is not None:
self.load_data(data)
if isinstance(model, ReflectModel):
self.set_model(model)
return self.display_box
elif model is not None:
self.load_model(model)
return self.display_box
self.redraw(None)
return self.display_box
def load_data(self, data):
"""
Load a dataset into the `Motofit` instance.
Parameters
----------
data: refnx.dataset.Data1D, or str, or file-like
"""
if isinstance(data, ReflectDataset):
self.dataset = data
else:
self.dataset = ReflectDataset(data)
self.dataset_name.value = self.dataset.name
# loading a dataset changes the objective and curvefitter
self._update_analysis_objects()
self.qmin = np.min(self.dataset.x)
self.qmax = np.max(self.dataset.x)
if self.fig is not None:
yt, et = self.transform(self.dataset.x, self.dataset.y)
if self.data_plot is None:
self.data_plot, = self.ax_data.plot(self.dataset.x,
yt,
label=self.dataset.name,
ms=2,
marker='o',
ls='',
zorder=1)
self.data_plot.set_label(self.dataset.name)
self.ax_data.legend()
# no need to calculate residuals here, that'll be updated in
# the redraw method
self.residuals_plot, = self.ax_residual.plot(self.dataset.x)
else:
self.data_plot.set_xdata(self.dataset.x)
self.data_plot.set_ydata(yt)
# calculate theoretical model over same range as data
# use redraw over update_model because it ensures chi2 widget gets
# displayed
self.redraw(None)
self.ax_data.relim()
self.ax_data.autoscale_view()
self.ax_residual.relim()
self.ax_residual.autoscale_view()
self.fig.canvas.draw()
def redraw(self, change):
"""
Redraw the Jupyter GUI associated with the `Motofit` instance.
"""
self._update_display_box(self.display_box)
self.update_model(None)
@property
def curvefitter(self):
if self.objective is not None and self._curvefitter is None:
self._curvefitter = CurveFitter(self.objective)
return self._curvefitter
def _print(self, string):
"""
Print to the output widget
"""
with self.output:
clear_output()
print(string)
def do_fit(self, change=None):
"""
Ask the Motofit object to perform a fit (differential evolution).
Parameters
----------
change
Notes
-----
After performing the fit the Jupyter display is updated.
"""
if self.dataset is None:
return
if not self.model.parameters.varying_parameters():
self._print("No parameters are being varied")
return
try:
lnprior = self.objective.lnprior()
if not np.isfinite(lnprior):
self._print("One of your parameter values lies outside its"
" bounds. Please adjust the value, or the bounds.")
return
except ZeroDivisionError:
self._print("One parameter has equal lower and upper bounds."
" Either alter the bounds, or don't let that"
" parameter vary.")
return
def callback(xk, convergence):
self.chisqr.value = self.objective.chisqr(xk)
self.curvefitter.fit('differential_evolution', callback=callback)
# need to update the widgets as the model will be updated.
# this also redraws GUI.
# self.model_view.refresh()
self.set_model(self.model)
self._print(repr(self.objective))
def _to_code(self, change=None):
self._print(self.code)
@property
def code(self):
"""
Executable Python code fragment for the GUI model.
"""
if self.objective is None:
self._update_analysis_objects()
return to_code(self.objective)
def _on_tab_changed(self, change):
pass
def _on_plot_type_changed(self, change):
"""
User would like to plot and fit as logR/linR/RQ4/RQ2, etc
"""
self.transform = Transform(change['new'])
if self.objective is not None:
self.objective.transform = self.transform
if self.dataset is not None:
yt, _ = self.transform(self.dataset.x, self.dataset.y)
self.data_plot.set_xdata(self.dataset.x)
self.data_plot.set_ydata(yt)
self.update_model(None)
# probably have to change LHS axis of the data plot when
# going between different plot types.
if change['new'] == 'logY':
self.ax_data.set_yscale('linear')
else:
self.ax_data.set_yscale('log')
self.ax_data.relim()
self.ax_data.autoscale_view()
self.fig.canvas.draw()
def _on_use_weights_changed(self, change):
self._update_analysis_objects()
self.update_model(None)
def _on_display_residuals_changed(self, change):
if change['new']:
self.ax_residual.set_visible(True)
self.ax_data.set_position(self._gridspec1[0, 0].get_position(
self.fig))
self.ax_sld.set_position(self._gridspec1[:,
1].get_position(self.fig))
plt.setp(self.ax_data.get_xticklabels(), visible=False)
else:
self.ax_residual.set_visible(False)
self.ax_data.set_position(self._gridspec2[:, 0].get_position(
self.fig))
self.ax_sld.set_position(self._gridspec2[:,
1].get_position(self.fig))
plt.setp(self.ax_data.get_xticklabels(), visible=True)
@property
def _options_box(self):
return widgets.VBox(
[self.plot_type, self.use_weights, self.display_residuals])
def _update_display_box(self, box):
"""
Redraw the Jupyter GUI associated with the `Motofit` instance
"""
vbox_widgets = []
if self.dataset is not None:
vbox_widgets.append(widgets.HBox([self.dataset_name, self.chisqr]))
self.tab.children = [
self.model_view.model_box, self.model_view.limits_box,
self._options_box
]
vbox_widgets.append(self.tab)
vbox_widgets.append(self.output)
box.children = tuple(vbox_widgets)