def plot(self, *expr_pairs, save=None, xunit=None, yunit=None, xrange=None, yrange=None, ignore_dim=False):
""" Plots data or functions
Args:
expr_pairs: one or more pair of quantity on x-axis and on y-axis. e.g. ["p","V"]
y-axis can also be a function. e.g. ["t", "7*exp(t/t0)"]
save: string of file name without extension. if specified, plot will be saved to '<save>.png'
xunit: unit on x-axis. if not given, will find unit on its own
yunit: unit on y-axis. if not given, will find unit on its own
xrange: pair of x-axis range, e.g. [-5,10]
yrange: pair of y-axis range
ignore_dim: if True, will skip dimension check
"""
if len(expr_pairs) == 0:#
raise ValueError("nothing to plot specified.")
expr_pairs_obj = []
for expr_pair in expr_pairs:
# parse expressions
expr_pairs_obj.append( (quantities.parse_expr(expr_pair[0], self.data), quantities.parse_expr(expr_pair[1], self.data)) )
if not xunit is None:
xunit = units.parse_unit(xunit)[2]
if not yunit is None:
yunit = units.parse_unit(yunit)[2]
if not xrange is None:
xrange = [quantities.get_value(quantities.parse_expr(xrange[0], self.data)),
quantities.get_value(quantities.parse_expr(xrange[1], self.data))]
if not yrange is None:
yrange = [quantities.get_value(quantities.parse_expr(yrange[0], self.data)),
quantities.get_value(quantities.parse_expr(yrange[1], self.data))]
return plotting.plot(expr_pairs_obj, self.config, save=save, xunit=xunit, yunit=yunit, xrange=xrange, yrange=yrange, ignore_dim=ignore_dim)
def plot(self,
*expr_pairs,
save=None,
xunit=None,
yunit=None,
xrange=None,
yrange=None,
ignore_dim=False):
""" Plots data or functions
Args:
expr_pairs: one or more pair of quantity on x-axis and on y-axis. e.g. ["p","V"]
y-axis can also be a function. e.g. ["t", "7*exp(t/t0)"]
save: string of file name without extension. if specified, plot will be saved to '<save>.png'
xunit: unit on x-axis. if not given, will find unit on its own
yunit: unit on y-axis. if not given, will find unit on its own
xrange: pair of x-axis range, e.g. [-5,10]
yrange: pair of y-axis range
ignore_dim: if True, will skip dimension check
"""
if len(expr_pairs) == 0: #
raise ValueError("nothing to plot specified.")
expr_pairs_obj = []
for expr_pair in expr_pairs:
# parse expressions
expr_pairs_obj.append(
(quantities.parse_expr(expr_pair[0], self.data),
quantities.parse_expr(expr_pair[1], self.data)))
if not xunit is None:
xunit = units.parse_unit(xunit)[2]
if not yunit is None:
yunit = units.parse_unit(yunit)[2]
if not xrange is None:
xrange = [
quantities.get_value(
quantities.parse_expr(xrange[0], self.data)),
quantities.get_value(
quantities.parse_expr(xrange[1], self.data))
]
if not yrange is None:
yrange = [
quantities.get_value(
quantities.parse_expr(yrange[0], self.data)),
quantities.get_value(
quantities.parse_expr(yrange[1], self.data))
]
return plotting.plot(expr_pairs_obj,
self.config,
save=save,
xunit=xunit,
yunit=yunit,
xrange=xrange,
yrange=yrange,
ignore_dim=ignore_dim)
def plot(expr_pairs, config, save=None, xunit=None, yunit=None, xrange=None, yrange=None, ignore_dim=False):
# TODO it should be possible to e.g. plot the function [t,2*r] if r depends on t
# one or multiple things to plot
if len(expr_pairs) > 1:
single_plot = False
else:
single_plot = True
x_dim = None
y_dim = None
data_sets = []
functions = []
if ignore_dim:
xunit = S.One
yunit = S.One
for expr_pair in expr_pairs:
x = expr_pair[0]
y = expr_pair[1]
if not ignore_dim:
# check dimensions
if x_dim is None:
x_dim = get_dimension(x)
else:
if not x_dim == get_dimension(x):
raise RuntimeError("dimension mismatch\n%s != %s" % (x_dim, get_dimension(x)))
if y_dim is None:
y_dim = get_dimension(y)
else:
if not y_dim == get_dimension(y):
raise RuntimeError("dimension mismatch\n%s != %s" % (y_dim, get_dimension(y)))
# if y contains x, it must be a function
dummy = Quantity()
rep_y = y.subs(x,dummy)
if rep_y.has(dummy):
# get titles
if isinstance(x, Quantity):
x_title = ((x.longname + " ") if x.longname else "") + str(x)
else:
x_title = str(x)
y_title = str(y)
# check if x not only quantity but more complicated expression
if not isinstance(x,Quantity):
# replace by Dummy
y = rep_y
x = dummy
if not ignore_dim:
# get factors
x_factor, xunit = convert_to_unit(x_dim, outputUnit=xunit)
y_factor, yunit = convert_to_unit(y_dim, outputUnit=yunit)
# scale function to units
y = y.subs(x,x*x_factor) / y_factor
# if only one thing on plot, write labels to x-axis and y-axis
if single_plot:
title = None
x_label = x_title + ("" if xunit == S.One else " [" + str(xunit) + "]")
y_label = y_title + ("" if yunit == S.One else " [" + str(yunit) + "]")
# if more than one thing, use legend for title
else:
title = y_title
functions.append({"x":x,"term":y,"title":title})
# if y doesn't contain x, it must be a data set
else:
# calculate expressions first if necessary
if isinstance(expr_pair[0], Quantity):
x = expr_pair[0]
x_title = ((x.longname + " ") if x.longname else "") + str(x)
else:
# dummy quantity for calculation
x = Quantity()
x.value = get_value(expr_pair[0])
x.error = get_error(expr_pair[0])[0]
x.dim = x_dim
x_title = str(expr_pair[0])
if isinstance(expr_pair[1], Quantity):
y = expr_pair[1]
y_title = ((y.longname + " ") if y.longname else "") + str(y)
else:
# dummy quantity for calculation
y = Quantity()
y.value = get_value(expr_pair[1])
y.error = get_error(expr_pair[1])[0]
y.dim = y_dim
y_title = str(expr_pair[1])
if ignore_dim:
x_values = x.value
x_errors = x.error
y_values = y.value
y_errors = y.error
else:
# get values and errors all in one unit
x_values, x_errors, xunit = adjust_to_unit(x, unit = xunit)
y_values, y_errors, yunit = adjust_to_unit(y, unit = yunit)
# if only one thing on plot, write labels to x-axis and y-axis
if single_plot:
title = None
x_label = x_title + ("" if xunit == S.One else " [" + str(xunit) + "]")
y_label = y_title + ("" if yunit == S.One else " [" + str(yunit) + "]")
# if more than one thing, use legend for title
else:
title = y_title
data_sets.append({"x_values": x_values, "y_values": y_values, "x_errors": x_errors, "y_errors":y_errors, "title": title})
# if more than one thing on plot, write only units to axes
if not single_plot:
x_label = ("" if xunit == S.One else "[" + str(xunit) + "]")
y_label = ("" if yunit == S.One else "[" + str(yunit) + "]")
# plot
if config["plot_module"] == "matplotlib":
from errorpro import plot_mat
return plot_mat.plot(data_sets, functions, save=save, xrange=xrange, yrange=yrange, x_label=x_label, y_label=y_label)
elif config["plot_module"] == "gnuplot":
from errorpro import plot_gnu
return plot_gnu.plot(data_sets, functions, save=save, xrange=xrange, yrange=yrange, x_label=x_label, y_label=y_label)
else:
raise ValueError("There is not plot module called '%s'" % config["plot_module"])
def assign(value, error=None, unit=None, name=None, longname=None, value_unit=None, error_unit=None, ignore_dim=False):
""" function to create a new quantity
Args:
value: number or string that can be parsed by numpy, or sympy
expression. If it's a sympy expression containing quantities, it
will perform the calculation, otherwise it just saves the value.
error: number that is saved as the value's uncertainty. this will replace
any error coming from a calculation.
unit: sympy expression of Unit objects. This is used to convert and save
value and error in base units. Replaces value_unit and error_unit if
specified.
name: short name of the quantity (usually one letter). If not specified,
quantity will get a dummy name.
longname: optional additional description of the quantity
value_unit: unit of value. Use this if value and error have different units.
error_unit: unit of error.
ignore_dim: bool. Keeps function from raising an error even if calculated
and given unit don't match. Then given unit is used instead.
"""
value_formula = None
value_factor = 1
value_dim = Dimension()
error_formula = None
error_factor = 1
error_dim = Dimension()
# parse units
if unit is not None:
# if one general unit is given
value_factor, value_dim, value_unit = parse_unit(unit)
error_factor = value_factor
error_dim = value_dim
error_unit = value_unit
else:
# if value unit is given
if value_unit is not None:
value_factor, value_dim, value_unit = parse_unit(value_unit)
# if error unit is given
if error_unit is not None:
error_factor, error_dim, error_unit = parse_unit(error_unit)
# check dimension consistency between value_dim and error_dim
if value_unit is not None and not value_dim == error_dim:
raise RuntimeError("dimension mismatch\n%s != %s" % (value_dim, error_dim))
# process value
# if it's a calculation
if isinstance(value, Expr) and not value.is_number:
value_formula = value
value = get_value(value_formula)
if ignore_dim:
# with ignore_dim=True, calculated value is converted to given unit
value = np.float_(value_factor)*np.float_(value)
else:
# calculate dimension from dependency
calculated_dim = get_dimension(value_formula)
if value_unit is None:
value_dim = calculated_dim
else:
if not calculated_dim == value_dim:
raise RuntimeError("dimension mismatch \n%s != %s" % (value_dim, calculated_dim))
# if it's a number
else:
value=np.float_(value_factor)*np.float_(value)
# process error
if error is not None:
error=np.float_(error_factor)*np.float_(error)
# check value and error shapes and duplicate error in case
if error.shape == () or value.shape[-len(error.shape):] == error.shape:
error = np.resize(error, value.shape)
else:
raise RuntimeError("length of value and error don't match and "\
"can't be adjusted by duplicating.\n"\
"%s and %s" % (value.shape, error.shape))
# if error can be calculated
elif value_formula is not None:
error, error_formula = get_error(value_formula)
if ignore_dim:
# with ignore_dim=True, calculated error is converted to given unit
error = np.float_(error_factor)*np.float_(error)
q = Quantity(name, longname)
q.value = value
q.value_formula = value_formula
q.error = error
q.error_formula = error_formula
if value_unit is not None:
q.prefer_unit = value_unit
else:
q.prefer_unit = error_unit
q.dim = value_dim
return q
def assign(self, name, value=None, error=None, unit=None, longname=None, value_unit=None, error_unit=None, replace=False, ignore_dim=False):
""" Assigns value and/or error to quantity
Args:
name: quantity name
longname: description of quantity
value: value to assign, can be expression, string, list or number
error: error to assign, can be expression, string, list or number, but mustn't depend on other quantities
unit: unit of both value and error, replaces 'value_unit' and 'error_unit' if given
value_unit: value unit expression or string
error_unit: error unit expression or string
replace: if True, will replace quantity instead of trying to keep data
ignore_dim: if True, will ignore calculated dimension and use given unit instead
"""
if not unit is None:
value_unit = unit
error_unit = unit
if value is None and error is None:
raise ValueError("At least either value or error must be specified.")
value_len = None
value_dim = None
value_formula = None
error_len = None
error_dim = None
error_formula = None
# if value is given
if not value is None:
# parse unit if given
if not value_unit is None:
factor, value_dim, value_unit = units.parse_unit(value_unit)
# parse value
if isinstance(value, list) or isinstance(value, tuple):
# if it's a list, parse each element
parsed_list = []
for v in value:
parsed_list.append(quantities.parse_expr(v, self.data))
elif isinstance(value, str) or isinstance(value, Expr):
# if it's not a list, parse once
value = quantities.parse_expr(value, self.data)
# if it's a calculation
if isinstance(value, Expr) and not value.is_number:
# calculate value from dependency
value_formula = value
value = quantities.get_value(value_formula)
# calculate dimension from dependency
if not ignore_dim:
calculated_dim = quantities.get_dimension(value_formula)
if not value_dim is None and not calculated_dim == value_dim:
raise RuntimeError("dimension mismatch for '%s'\n%s != %s" % (name, value_dim, calculated_dim))
elif value_dim is None:
value_dim = calculated_dim
else:
# if ignore_dim is True and there's no unit given -> dimensionless
if value_dim is None:
factor=1
value_dim = Dimension()
value_unit = S.One
# calculated value must be converted to given unit (ignore_dim=True)
value = np.float_(factor)*value
# if it's a number
else:
# if no unit given, set dimensionless
if value_unit is None:
factor = 1
value_dim = Dimension()
value_unit = S.One
value=np.float_(factor)*np.float_(value)
# calculate value length
if isinstance(value,np.ndarray):
value_len = len(value)
else:
value_len = 1
# if error is given
if not error is None:
# parse unit if given
if not error_unit is None:
factor, error_dim, error_unit = units.parse_unit(error_unit)
# parse value
if isinstance(error, list) or isinstance(error, tuple):
# if it's a list, parse each element
parsed_list = []
for u in error:
parsed_list.append(quantities.parse_expr(u, self.data))
elif isinstance(error, str) or isinstance(error, Expr):
# if it's not a list, parse once
error = quantities.parse_expr(error, self.data)
# make sure error is a number
if isinstance(error, Expr) and not error.is_number:
raise RuntimeError("error '%s' is not a number" % error)
# if no unit given, set dimensionless
if error_unit is None:
factor = 1
error_dim = Dimension()
error_unit = S.One
error=np.float_(factor)*np.float_(error)
# calculate error length, ignore len(error)==1 because it can be duplicated to fit any value length
if isinstance(error,np.ndarray):
error_len = len(error)
# if error can be calculated
elif not value_formula is None:
error, error_formula = quantities.get_error(value_formula)
# merge dimensions
dim = value_dim
if not dim is None and not error_dim is None and not dim == error_dim:
raise RuntimeError("value dimension and error dimension are not the same\n%s != %s" % (dim, error_dim))
if not error_dim is None:
dim = error_dim
# merge lengths
new_len = value_len
if not new_len is None and not error_len is None and not new_len == error_len:
raise RuntimeError("value length doesn't fit error length for '%s':\n%s != %s" % (name, new_len, error_len))
if not error_len is None:
new_len = error_len
# if quantity didn't exist
if not name in self.data or replace:
self.data[name] = quantities.Quantity(name)
# if it did exist
else:
# get old length, len(error)=1 is not a length, because it can be duplicated to fit any value length
old_len = None
if not self.data[name].value is None:
if isinstance(self.data[name].value, np.ndarray):
old_len = len(self.data[name].value)
else:
old_len = 1
if not self.data[name].error is None and isinstance(self.data[name].error, np.ndarray):
old_len = len(self.data[name].error)
# if new dimension or new length, create new quantity
if (not self.data[name].dim == dim or
(not old_len is None and not new_len is None and not old_len == new_len)):
self.data[name] = quantities.Quantity(name)
# save stuff
if not longname is None:
self.data[name].longname = longname
if not value is None:
self.data[name].value = value
self.data[name].value_formula = value_formula
if not value_unit is None:
self.data[name].prefer_unit = value_unit
elif not error_unit is None:
self.data[name].prefer_unit = error_unit
if not error is None:
self.data[name].error = error
self.data[name].error_formula = error_formula
self.data[name].dim = dim
# check if error must be duplicated to adjust to value length
if isinstance(self.data[name].value, np.ndarray) and isinstance(self.data[name].error, np.float_):
error_arr = np.full(len(self.data[name].value),self.data[name].error)
self.data[name].error = error_arr
def fit(self, fit_function, xydata, parameters, weighted=None, plot=False, ignore_dim=False):
""" fits function to data
Args:
fit_function: function to fit, e.g. "n*t**2 + m*t + b"
xydata: pair of x-quantity and y-quantity of data to fit to, e.g. ["t","U"]
parameters: list of parameters in fit function, e.g. ["n","m","b"]
weighted: if True, will weight fit by errors (returns error if not possible)
if False, will not weight fit by errors
if None, will try to weight fit, but if at least one error is not given, will not weight it
plot: Bool, if data and fit function should be plotted
ignore_dim: if True, will ignore dimensions and just calculate in base units instead
"""
if self.config["fit_module"] == "scipy":
import errorpro.fit_scipy as fit_module
else:
raise ValueError("no fit module called '%s'." % self.config["fit_module"])
# get parameter quantities
parameters_obj = []
for p in parameters:
if isinstance(p, str):
if not p in self.data:
self.data[p] = quantities.Quantity(p)
self.data[p].dim = Dimension()
parameters_obj.append(self.data[p])
elif isinstance(p, quantities.Quantity):
parameters_obj.append(p)
else:
raise TypeError("parameters can only be strings or Quantity objects")
# parse fit function
fit_function = quantities.parse_expr(fit_function, self.data)
# get data quantities
x_data = quantities.parse_expr(xydata[0], self.data)
# if x-data is an expression
if not isinstance(x_data, quantities.Quantity):
dummy = quantities.Quantity()
fit_function = fit_function.subs(x_data,dummy)
dummy.value = quantities.get_value(x_data)
dummy.error = quantities.get_error(x_data)[0]
dummy.dim = quantities.get_dimension(x_data)
x_data = dummy
y_data = quantities.parse_expr(xydata[1], self.data)
# if y-data is an expression
if not isinstance(y_data, quantities.Quantity):
dummy = quantities.Quantity()
dummy.value = quantities.get_value(y_data)
dummy.error = quantities.get_error(y_data)[0]
dummy.dim = quantities.get_dimension(y_data)
y_data = dummy
# check if dimension fits
if not ignore_dim:
try:
dim_func = quantities.get_dimension(fit_function)
except ValueError:
dim_func = None
if not dim_func == y_data.dim:
# try to solve for dimensionless parameters
known_dimensions = {x_data.name: x_data.dim}
known_dimensions = dim_solve(fit_function, y_data.dim, known_dimensions)
for q_name in known_dimensions:
if q_name in self.data:
if not self.data[q_name].dim == known_dimensions[q_name]:
self.data[q_name].dim = known_dimensions[q_name]
self.data[q_name].prefer_unit = None
dim_func = quantities.get_dimension(fit_function)
# if it still doesn't work, raise error
if not dim_func == y_data.dim:
raise RuntimeError("Finding dimensions of fit parameters was not sucessful.\n"\
"Check fit function or specify parameter units manually.\n"\
"This error will occur until dimensions are right.")
# fit
values, errors = fit_module.fit(x_data, y_data, fit_function, parameters_obj, weighted)
# save results
i = 0
for p in parameters_obj:
p.value = values[i]
p.value_formula = "fit"
p.error = errors[i]
p.error_formula = "fit"
i += 1
# plot
if plot:
return plotting.plot([(x_data, y_data), (x_data, fit_function)], self.config, ignore_dim=ignore_dim)
else:
return self.table(*parameters_obj)
def plot(expr_pairs,
config,
save=None,
xunit=None,
yunit=None,
xrange=None,
yrange=None,
ignore_dim=False):
# TODO it should be possible to e.g. plot the function [t,2*r] if r depends on t
# one or multiple things to plot
if len(expr_pairs) > 1:
single_plot = False
else:
single_plot = True
x_dim = None
y_dim = None
data_sets = []
functions = []
if ignore_dim:
xunit = S.One
yunit = S.One
for expr_pair in expr_pairs:
x = expr_pair[0]
y = expr_pair[1]
if not ignore_dim:
# check dimensions
if x_dim is None:
x_dim = get_dimension(x)
else:
if not x_dim == get_dimension(x):
raise RuntimeError("dimension mismatch\n%s != %s" %
(x_dim, get_dimension(x)))
if y_dim is None:
y_dim = get_dimension(y)
else:
if not y_dim == get_dimension(y):
raise RuntimeError("dimension mismatch\n%s != %s" %
(y_dim, get_dimension(y)))
# if y contains x, it must be a function
dummy = Quantity()
rep_y = y.subs(x, dummy)
if rep_y.has(dummy):
# get titles
if isinstance(x, Quantity):
x_title = ((x.longname + " ") if x.longname else "") + str(x)
else:
x_title = str(x)
y_title = str(y)
# check if x not only quantity but more complicated expression
if not isinstance(x, Quantity):
# replace by Dummy
y = rep_y
x = dummy
if not ignore_dim:
# get factors
x_factor, xunit = convert_to_unit(x_dim, outputUnit=xunit)
y_factor, yunit = convert_to_unit(y_dim, outputUnit=yunit)
# scale function to units
y = y.subs(x, x * x_factor) / y_factor
# if only one thing on plot, write labels to x-axis and y-axis
if single_plot:
title = None
x_label = x_title + ("" if xunit == S.One else " [" +
str(xunit) + "]")
y_label = y_title + ("" if yunit == S.One else " [" +
str(yunit) + "]")
# if more than one thing, use legend for title
else:
title = y_title
functions.append({"x": x, "term": y, "title": title})
# if y doesn't contain x, it must be a data set
else:
# calculate expressions first if necessary
if isinstance(expr_pair[0], Quantity):
x = expr_pair[0]
x_title = ((x.longname + " ") if x.longname else "") + str(x)
else:
# dummy quantity for calculation
x = Quantity()
x.value = get_value(expr_pair[0])
x.error = get_error(expr_pair[0])[0]
x.dim = x_dim
x_title = str(expr_pair[0])
if isinstance(expr_pair[1], Quantity):
y = expr_pair[1]
y_title = ((y.longname + " ") if y.longname else "") + str(y)
else:
# dummy quantity for calculation
y = Quantity()
y.value = get_value(expr_pair[1])
y.error = get_error(expr_pair[1])[0]
y.dim = y_dim
y_title = str(expr_pair[1])
if ignore_dim:
x_values = x.value
x_errors = x.error
y_values = y.value
y_errors = y.error
else:
# get values and errors all in one unit
x_values, x_errors, xunit = adjust_to_unit(x, unit=xunit)
y_values, y_errors, yunit = adjust_to_unit(y, unit=yunit)
# if only one thing on plot, write labels to x-axis and y-axis
if single_plot:
title = None
x_label = x_title + ("" if xunit == S.One else " [" +
str(xunit) + "]")
y_label = y_title + ("" if yunit == S.One else " [" +
str(yunit) + "]")
# if more than one thing, use legend for title
else:
title = y_title
data_sets.append({
"x_values": x_values,
"y_values": y_values,
"x_errors": x_errors,
"y_errors": y_errors,
"title": title
})
# if more than one thing on plot, write only units to axes
if not single_plot:
x_label = ("" if xunit == S.One else "[" + str(xunit) + "]")
y_label = ("" if yunit == S.One else "[" + str(yunit) + "]")
# plot
if config["plot_module"] == "matplotlib":
from errorpro import plot_mat
return plot_mat.plot(data_sets,
functions,
save=save,
xrange=xrange,
yrange=yrange,
x_label=x_label,
y_label=y_label)
elif config["plot_module"] == "gnuplot":
from errorpro import plot_gnu
return plot_gnu.plot(data_sets,
functions,
save=save,
xrange=xrange,
yrange=yrange,
x_label=x_label,
y_label=y_label)
else:
raise ValueError("There is not plot module called '%s'" %
config["plot_module"])
def assign(self,
name,
value=None,
error=None,
unit=None,
longname=None,
value_unit=None,
error_unit=None,
replace=False,
ignore_dim=False):
""" Assigns value and/or error to quantity
Args:
name: quantity name
longname: description of quantity
value: value to assign, can be expression, string, list or number
error: error to assign, can be expression, string, list or number, but mustn't depend on other quantities
unit: unit of both value and error, replaces 'value_unit' and 'error_unit' if given
value_unit: value unit expression or string
error_unit: error unit expression or string
replace: if True, will replace quantity instead of trying to keep data
ignore_dim: if True, will ignore calculated dimension and use given unit instead
"""
if not unit is None:
value_unit = unit
error_unit = unit
if value is None and error is None:
raise ValueError(
"At least either value or error must be specified.")
value_len = None
value_dim = None
value_formula = None
error_len = None
error_dim = None
error_formula = None
# if value is given
if not value is None:
# parse unit if given
if not value_unit is None:
factor, value_dim, value_unit = units.parse_unit(value_unit)
# parse value
if isinstance(value, list) or isinstance(value, tuple):
# if it's a list, parse each element
parsed_list = []
for v in value:
parsed_list.append(quantities.parse_expr(v, self.data))
elif isinstance(value, str) or isinstance(value, Expr):
# if it's not a list, parse once
value = quantities.parse_expr(value, self.data)
# if it's a calculation
if isinstance(value, Expr) and not value.is_number:
# calculate value from dependency
value_formula = value
value = quantities.get_value(value_formula)
# calculate dimension from dependency
if not ignore_dim:
calculated_dim = quantities.get_dimension(value_formula)
if not value_dim is None and not calculated_dim == value_dim:
raise RuntimeError(
"dimension mismatch for '%s'\n%s != %s" %
(name, value_dim, calculated_dim))
elif value_dim is None:
value_dim = calculated_dim
else:
# if ignore_dim is True and there's no unit given -> dimensionless
if value_dim is None:
factor = 1
value_dim = Dimension()
value_unit = S.One
# calculated value must be converted to given unit (ignore_dim=True)
value = np.float_(factor) * value
# if it's a number
else:
# if no unit given, set dimensionless
if value_unit is None:
factor = 1
value_dim = Dimension()
value_unit = S.One
value = np.float_(factor) * np.float_(value)
# calculate value length
if isinstance(value, np.ndarray):
value_len = len(value)
else:
value_len = 1
# if error is given
if not error is None:
# parse unit if given
if not error_unit is None:
factor, error_dim, error_unit = units.parse_unit(error_unit)
# parse value
if isinstance(error, list) or isinstance(error, tuple):
# if it's a list, parse each element
parsed_list = []
for u in error:
parsed_list.append(quantities.parse_expr(u, self.data))
elif isinstance(error, str) or isinstance(error, Expr):
# if it's not a list, parse once
error = quantities.parse_expr(error, self.data)
# make sure error is a number
if isinstance(error, Expr) and not error.is_number:
raise RuntimeError("error '%s' is not a number" % error)
# if no unit given, set dimensionless
if error_unit is None:
factor = 1
error_dim = Dimension()
error_unit = S.One
error = np.float_(factor) * np.float_(error)
# calculate error length, ignore len(error)==1 because it can be duplicated to fit any value length
if isinstance(error, np.ndarray):
error_len = len(error)
# if error can be calculated
elif not value_formula is None:
error, error_formula = quantities.get_error(value_formula)
# merge dimensions
dim = value_dim
if not dim is None and not error_dim is None and not dim == error_dim:
raise RuntimeError(
"value dimension and error dimension are not the same\n%s != %s"
% (dim, error_dim))
if not error_dim is None:
dim = error_dim
# merge lengths
new_len = value_len
if not new_len is None and not error_len is None and not new_len == error_len:
raise RuntimeError(
"value length doesn't fit error length for '%s':\n%s != %s" %
(name, new_len, error_len))
if not error_len is None:
new_len = error_len
# if quantity didn't exist
if not name in self.data or replace:
self.data[name] = quantities.Quantity(name)
# if it did exist
else:
# get old length, len(error)=1 is not a length, because it can be duplicated to fit any value length
old_len = None
if not self.data[name].value is None:
if isinstance(self.data[name].value, np.ndarray):
old_len = len(self.data[name].value)
else:
old_len = 1
if not self.data[name].error is None and isinstance(
self.data[name].error, np.ndarray):
old_len = len(self.data[name].error)
# if new dimension or new length, create new quantity
if (not self.data[name].dim == dim
or (not old_len is None and not new_len is None
and not old_len == new_len)):
self.data[name] = quantities.Quantity(name)
# save stuff
if not longname is None:
self.data[name].longname = longname
if not value is None:
self.data[name].value = value
self.data[name].value_formula = value_formula
if not value_unit is None:
self.data[name].prefer_unit = value_unit
elif not error_unit is None:
self.data[name].prefer_unit = error_unit
if not error is None:
self.data[name].error = error
self.data[name].error_formula = error_formula
self.data[name].dim = dim
# check if error must be duplicated to adjust to value length
if isinstance(self.data[name].value, np.ndarray) and isinstance(
self.data[name].error, np.float_):
error_arr = np.full(len(self.data[name].value),
self.data[name].error)
self.data[name].error = error_arr
def fit(self,
fit_function,
xydata,
parameters,
weighted=None,
plot=False,
ignore_dim=False):
""" fits function to data
Args:
fit_function: function to fit, e.g. "n*t**2 + m*t + b"
xydata: pair of x-quantity and y-quantity of data to fit to, e.g. ["t","U"]
parameters: list of parameters in fit function, e.g. ["n","m","b"]
weighted: if True, will weight fit by errors (returns error if not possible)
if False, will not weight fit by errors
if None, will try to weight fit, but if at least one error is not given, will not weight it
plot: Bool, if data and fit function should be plotted
ignore_dim: if True, will ignore dimensions and just calculate in base units instead
"""
if self.config["fit_module"] == "scipy":
import errorpro.fit_scipy as fit_module
else:
raise ValueError("no fit module called '%s'." %
self.config["fit_module"])
# get parameter quantities
parameters_obj = []
for p in parameters:
if isinstance(p, str):
if not p in self.data:
self.data[p] = quantities.Quantity(p)
self.data[p].dim = Dimension()
parameters_obj.append(self.data[p])
elif isinstance(p, quantities.Quantity):
parameters_obj.append(p)
else:
raise TypeError(
"parameters can only be strings or Quantity objects")
# parse fit function
fit_function = quantities.parse_expr(fit_function, self.data)
# get data quantities
x_data = quantities.parse_expr(xydata[0], self.data)
# if x-data is an expression
if not isinstance(x_data, quantities.Quantity):
dummy = quantities.Quantity()
fit_function = fit_function.subs(x_data, dummy)
dummy.value = quantities.get_value(x_data)
dummy.error = quantities.get_error(x_data)[0]
dummy.dim = quantities.get_dimension(x_data)
x_data = dummy
y_data = quantities.parse_expr(xydata[1], self.data)
# if y-data is an expression
if not isinstance(y_data, quantities.Quantity):
dummy = quantities.Quantity()
dummy.value = quantities.get_value(y_data)
dummy.error = quantities.get_error(y_data)[0]
dummy.dim = quantities.get_dimension(y_data)
y_data = dummy
# check if dimension fits
if not ignore_dim:
try:
dim_func = quantities.get_dimension(fit_function)
except ValueError:
dim_func = None
if not dim_func == y_data.dim:
# try to solve for dimensionless parameters
known_dimensions = {x_data.name: x_data.dim}
known_dimensions = dim_solve(fit_function, y_data.dim,
known_dimensions)
for q_name in known_dimensions:
if q_name in self.data:
if not self.data[q_name].dim == known_dimensions[
q_name]:
self.data[q_name].dim = known_dimensions[q_name]
self.data[q_name].prefer_unit = None
dim_func = quantities.get_dimension(fit_function)
# if it still doesn't work, raise error
if not dim_func == y_data.dim:
raise RuntimeError("Finding dimensions of fit parameters was not sucessful.\n"\
"Check fit function or specify parameter units manually.\n"\
"This error will occur until dimensions are right.")
# fit
values, errors = fit_module.fit(x_data, y_data, fit_function,
parameters_obj, weighted)
# save results
i = 0
for p in parameters_obj:
p.value = values[i]
p.value_formula = "fit"
p.error = errors[i]
p.error_formula = "fit"
i += 1
# plot
if plot:
return plotting.plot([(x_data, y_data), (x_data, fit_function)],
self.config,
ignore_dim=ignore_dim)
else:
return self.table(*parameters_obj)