def test_linear_fit(self):
''' Test of plotting fit
'''
X = e.MeasurementArray([1, 2, 3, 4, 5], [0.1])
Y = e.MeasurementArray([3, 5, 7, 9, 11], [0.05])
figure = p.MakePlot(xdata=X, ydata=Y)
slope, intercept = figure.fit('linear', print_results=False)
self.assertEqual(slope, 2)
self.assertEqual(intercept, 1)
def test5():
''' Test of plotting fit
'''
X = e.MeasurementArray([1, 2, 3, 4, 5], [0.1])
Y = e.MeasurementArray([3, 5, 7, 9, 11], [0.05])
figure = p.Plot(X, Y)
figure.fit('linear')
intercept, slope = figure.fit_parameters
assert slope.mean == 2
assert intercept.mean == 1
def test_delete(self):
'''Tests inserting new values into a MeasurementArray.
'''
x = e.MeasurementArray([3, 2, 1], 1)
x = x.delete(1)
self.assertEqual(len(x), 2)
def test_array_elementary(self):
'''Tests elementary operations on Measurement objects
'''
x = e.MeasurementArray([4, 9, 2], error=[0.1, 0.2, 0.3])
y = e.MeasurementArray([2, 3, 3], error=0.1)
self.assertListEqual((x + y).means.tolist(), [6, 12, 5])
self.assertListEqual((y + x).means.tolist(), [6, 12, 5])
self.assertListEqual((x - y).means.tolist(), [2, 6, -1])
self.assertListEqual((y - x).means.tolist(), [-2, -6, 1])
self.assertListEqual((x * y).means.tolist(), [8, 27, 6])
self.assertListEqual((y * x).means.tolist(), [8, 27, 6])
self.assertListEqual((x / y).means.tolist(), [2, 3, 2 / 3])
self.assertListEqual((y / x).means.tolist(), [0.5, 1 / 3, 3 / 2])
self.assertListEqual((x**y).means.tolist(), [16, 729, 8])
self.assertListEqual((y**x).means.tolist(), [16, 19683, 9])
def test_insert(self):
'''Tests inserting new values into a MeasurementArray.
'''
x = e.MeasurementArray([3, 1], 1)
x = x.insert(1, 2)
to_insert = e.Measurement(4, 1)
x = x.insert(2, to_insert)
self.assertEqual(x[1], 2)
self.assertEqual(x[2], to_insert)
def test_append(self):
'''Tests appending new values to a MeasurementArray.
'''
x = e.MeasurementArray([3, 2], 1)
x = x.append(1)
to_append = e.Measurement(4, 1)
x = x.append(to_append)
self.assertEqual(x[2], 1)
self.assertEqual(x[3], to_append)
def test_array_functions(self):
'''Tests mathematical functions on Measurement objects
'''
x = e.MeasurementArray([4, 9, 2], error=[0.1, 0.2, 0.3])
y = e.MeasurementArray([0.3, 0.56, 0.2], error=0.01)
self.assertEqual(e.sin(x).means.tolist(), np.sin(x.means).tolist())
self.assertEqual(e.cos(x).means.tolist(), np.cos(x.means).tolist())
self.assertEqual(e.tan(x).means.tolist(), np.tan(x.means).tolist())
self.assertEqual(
e.csc(x).means.tolist(), (1 / np.sin(x.means)).tolist())
self.assertEqual(
e.sec(x).means.tolist(), (1 / np.cos(x.means)).tolist())
self.assertEqual(
e.cot(x).means.tolist(), (1 / np.tan(x.means)).tolist())
self.assertEqual(e.exp(x).means.tolist(), np.exp(x.means).tolist())
self.assertEqual(e.log(x).means.tolist(), np.log(x.means).tolist())
self.assertEqual(e.asin(y).means.tolist(), np.arcsin(y.means).tolist())
self.assertEqual(e.acos(y).means.tolist(), np.arccos(y.means).tolist())
self.assertEqual(e.atan(x).means.tolist(), np.arctan(x.means).tolist())
def test_polynomial_fit(self):
''' Test of plotting fit
'''
X = e.MeasurementArray([-2, -1, 0, 1, 2], [0.1])
Y = 3 * X**2 + 2 * X + 1
figure = p.MakePlot(xdata=X, ydata=Y)
figure.fit('pol2', print_results=False)
par0 = figure.get_dataset().xyfitter[0].fit_pars[0]
par1 = figure.get_dataset().xyfitter[0].fit_pars[1]
par2 = figure.get_dataset().xyfitter[0].fit_pars[2]
self.assertAlmostEqual(par0, 1, places=7)
self.assertAlmostEqual(par1, 2, places=7)
self.assertAlmostEqual(par2, 3, places=7)
def test_gaussian_fit(self):
''' Test of plotting fit
'''
X = e.MeasurementArray([-1, -1 / 3, 1 / 3, 1], [0.1])
mean = 0.1
std = 0.5
norm = .5
Y = norm * (2 * m.pi * std**2)**(-0.5) * np.exp(-0.5 *
(X - mean)**2 / std**2)
figure = p.MakePlot(xdata=X, ydata=Y)
figure.fit('gauss', print_results=False)
par0 = figure.get_dataset().xyfitter[0].fit_pars[0]
par1 = figure.get_dataset().xyfitter[0].fit_pars[1]
par2 = figure.get_dataset().xyfitter[0].fit_pars[2]
self.assertAlmostEqual(par0, mean, places=7)
self.assertAlmostEqual(par1, std, places=7)
self.assertAlmostEqual(par2, norm, places=7)
def test_measurement_array(self):
'''Tests creating a MeasurementArray from multiple measurements
'''
x = e.MeasurementArray([9, 10, 11], error=1)
self.assertEqual(x.mean, 10)
self.assertEqual(x.std(), 1)
def __init__(self,
xdata,
ydata=None,
xerr=None,
yerr=None,
data_name=None,
xname=None,
xunits=None,
yname=None,
yunits=None,
is_histogram=False,
bins=50):
'''Use MeasurementArray() to initialize a dataset'''
if (data_name is None):
self.name = "dataset{}".format(XYDataSet.unnamed_data_counter)
'''A string of the name of the dataset.
.. code-block:: python
x = q.MeasurementArray([1, 2, 3, 4], error=0.5)
y = q.MeasurementArray([5, 6.2, 7, 7.8], error=0.1)
data = q.XYDataSet(x, y)
data.name = 'x vs. y'
print('Name:', data.name)
.. nboutput:: ipython3
Name = x vs. y
'''
XYDataSet.unnamed_data_counter += 1
else:
self.name = data_name
if ydata is None and not is_histogram:
print(
"Error, if ydata is not given, explicitly specify that this is a histogram"
)
elif ydata is None:
#this is a histogram
self.hist_data = xdata
hist, edges = np.histogram(xdata, bins=bins)
self.hist_bins = edges
_xdata = edges[:-1]
_xerr = np.zeros(_xdata.size)
_ydata = hist
_yerr = np.sqrt(hist)
else:
_xdata = xdata
_xerr = xerr
_ydata = ydata
_yerr = yerr
self.x = qe.MeasurementArray(_xdata,
error=_xerr,
name=xname,
units=xunits)
self.xdata = self.x.means
self.xerr = self.x.stds
self.xunits = self.x.get_units_str()
self.xname = self.x.name
self.y = qe.MeasurementArray(_ydata,
error=_yerr,
name=yname,
units=yunits)
self.ydata = self.y.means
self.yerr = self.y.stds
self.yunits = self.y.get_units_str()
self.yname = self.y.name
self.is_histogram = is_histogram
self.bins = bins
if self.x.size != self.y.size:
print("Error: x and y data should have the same number of points")
#TODO raise an error!
else:
self.npoints = self.x.size
self.xyfitter = []
self.fit_pars = [] #stored as Measurement_Array
self.fit_pcov = []
self.fit_pcorr = []
self.fit_function = []
self.fit_function_name = []
self.fit_npars = []
self.fit_yres = []
self.fit_chi2 = []
self.fit_ndof = []
self.fit_color = []
self.nfits = 0
def fit(self, dataset, fit_range=None, fit_count=0, name=None):
''' Perform a fit of the fit_function to a data set.
:param dataset: The dataset to be fit.
:type dataset: XYDataSet
:param fit_range: The range to plot the fit on.
:type fit_range: list
:param fit_count: The number of the fit.
:type fit_count: int
:param name: The name of the fit function.
:type name: str
:returns: The parameters of the fit.
:rtype: Measurement_Array
'''
if self.fit_function is None:
print("Error: fit function not set!")
return
#Grab the data
xdata = dataset.xdata
ydata = dataset.ydata
xerr = dataset.xerr
yerr = dataset.yerr
nz = np.count_nonzero(yerr)
if nz < ydata.size and nz != 0:
print(
"Warning: some errors on data are zero, switching to MC errors"
)
dataset.y.error_method = "MC"
yerr = dataset.y.stds
#now, check again
nz = np.count_nonzero(yerr)
if nz < ydata.size and nz != 0:
yerr[yerr == 0] = ydata[yerr == 0] / 1000000
#We're ok, modify the errors in the dataset to be the MC ones
else:
dataset.yerr = yerr
#If user specified a fit range, reduce the data:
if type(fit_range) in ARRAY and len(fit_range) is 2:
indices = np.where(
np.logical_and(xdata >= fit_range[0], xdata <= fit_range[1]))
xdata = xdata[indices]
ydata = ydata[indices]
xerr = xerr[indices]
yerr = yerr[indices]
#if the x errors are not zero, convert them to equivalent errors in y
#TODO: check the math on this...
#The maximum number of function evaluations
maxfev = 200 * (xdata.size + 1) if q.settings[
"fit_max_fcn_calls"] == -1 else q.settings["fit_max_fcn_calls"]
try:
warns = []
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", sp.OptimizeWarning)
self.fit_pars, self.fit_pcov = sp.curve_fit(self.fit_function,
xdata,
ydata,
sigma=yerr,
p0=self.parguess,
maxfev=maxfev)
warns = w
if len(warns) > 0 and (self.fit_function == Rlinear
or self.fit_function == Rpolynomial):
p, V = np.polyfit(x=xdata,
y=ydata,
deg=self.fit_npars - 1,
cov=True,
w=1 / yerr)
self.fit_pars = p[::-1]
self.fit_pcov = np.flipud(np.fliplr(V))
self.fit_pars_err = np.sqrt(np.diag(self.fit_pcov))
except RuntimeError:
print(
"Error: Fit could not converge; are the y errors too small? Is the function defined?"
)
print("Is the parameter guess good?")
return None
# Use derivative method to factor x error into fit
if xerr.nonzero()[0].size:
yerr_eff = np.sqrt((yerr**2 + np.multiply(
xerr,
num_der(lambda x: self.fit_function(x, *self.fit_pars), xdata))
**2))
try:
warns = []
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", sp.OptimizeWarning)
self.fit_pars, self.fit_pcov = sp.curve_fit(
self.fit_function,
xdata,
ydata,
sigma=yerr_eff,
p0=self.parguess,
maxfev=maxfev)
warns = w
if len(warns) == 1 and (self.fit_function == Rlinear
or self.fit_function == Rpolynomial):
p, V = np.polyfit(x=xdata,
y=ydata,
deg=self.fit_npars - 1,
cov=True,
w=1 / yerr)
self.fit_pars = p[::-1]
self.fit_pcov = np.flipud(np.fliplr(V))
self.fit_pars_err = np.sqrt(np.diag(self.fit_pcov))
except RuntimeError:
print(
"Error: Fit could not converge; are the y errors too small? Is the function defined?"
)
print("Is the parameter guess good?")
return None
#this should already be true, but let's be sure:
self.fit_npars = self.fit_pars.size
#This is to catch the case of scipy.optimize failing to determin
#the covariance matrix
for i in range(self.fit_npars):
if self.fit_pars_err[i] == float(
'inf') or self.fit_pars_err[i] == float('nan'):
#print("Warning: Error for fit parameter",i,"cannot be trusted")
self.fit_pars_err[i] = 0
for j in range(self.fit_npars):
if self.fit_pcov[i][j] == float(
'inf') or self.fit_pcov[i][j] == float('nan'):
#print("Warning: Covariance between parameters",i,j,"cannot be trusted")
self.fit_pcov[i][j] = 0.
parnames = dataset.name + "_" + self.fit_function_name + "_fit{}".format(
fit_count) + "_fitpars"
self.fit_parameters = qe.MeasurementArray(self.fit_npars,
name=parnames)
for i in range(self.fit_npars):
if self.fit_function_name is 'gaussian':
if i is 0:
name = 'mean'
elif i is 1:
name = 'sigma'
elif i == 2:
name = 'normalization'
elif self.fit_function_name is 'linear':
if i is 0:
name = 'intercept'
elif i is 1:
name = 'slope'
elif self.fit_function_name is 'exponential':
if i is 0:
name = 'amplitude'
elif i is 1:
name = 'decay-constant'
else:
name = 'par%d' % (i)
name = parnames + "_" + name
self.fit_parameters[i] = qe.Measurement(self.fit_pars[i],
self.fit_pars_err[i],
name=name)
for i in range(self.fit_npars):
for j in range(i + 1, self.fit_npars):
self.fit_parameters[i].set_covariance(self.fit_parameters[j],
self.fit_pcov[i][j])
#Calculate the residuals:
yfit = self.fit_function(dataset.xdata, *self.fit_pars)
self.fit_yres = qe.MeasurementArray((dataset.ydata - yfit),
dataset.yerr)
#Calculate the chi-squared:
self.fit_chi2 = 0
for i in range(xdata.size):
if self.fit_yres[i].std != 0:
self.fit_chi2 += (self.fit_yres[i].mean /
self.fit_yres[i].std)**2
self.fit_ndof = self.fit_yres.size - self.fit_npars - 1
return self.fit_parameters
def __init__(self,
xdata,
ydata=None,
xerr=None,
yerr=None,
data_name=None,
xname=None,
xunits=None,
yname=None,
yunits=None,
is_histogram=False,
bins=50):
'''Use MeasurementArray() to initialize a dataset'''
if (data_name is None):
self.name = "dataset{}".format(XYDataSet.unnamed_data_counter)
XYDataSet.unnamed_data_counter += 1
else:
self.name = data_name
if ydata is None and not is_histogram:
print(
"Error, if ydata is not given, explicitly specify that this is a histogram"
)
elif ydata is None:
#this is a histogram
self.hist_data = xdata
hist, edges = np.histogram(xdata, bins=bins)
self.hist_bins = edges
_xdata = edges[:-1]
_xerr = np.zeros(_xdata.size)
_ydata = hist
_yerr = np.sqrt(hist)
else:
_xdata = xdata
_xerr = xerr
_ydata = ydata
_yerr = yerr
self.x = qe.MeasurementArray(_xdata,
error=_xerr,
name=xname,
units=xunits)
self.xdata = self.x.get_means()
self.xerr = self.x.get_stds()
self.xunits = self.x.get_units_str()
self.xname = self.x.name
self.y = qe.MeasurementArray(_ydata,
error=_yerr,
name=yname,
units=yunits)
self.ydata = self.y.get_means()
self.yerr = self.y.get_stds()
self.yunits = self.y.get_units_str()
self.yname = self.y.name
self.is_histogram = is_histogram
if self.x.size != self.y.size:
print("Error: x and y data should have the same number of points")
#TODO raise an error!
else:
self.npoints = self.x.size
self.xyfitter = []
self.fit_pars = [] #stored as Measurement_Array
self.fit_pcov = []
self.fit_pcorr = []
self.fit_function = []
self.fit_function_name = []
self.fit_npars = []
self.fit_yres = []
self.fit_chi2 = []
self.fit_ndof = []
self.fit_color = []
self.nfits = 0