def test_data_plot_no_errors_no_errorbar_warnings(caplog, statClass):
"""Should not see warnings when no error bars are drawn (See #621).
This is a copy of test_data_plot_see_errorbar_warnings except that
the 'yerrorbars' preference setting is set to False, so we should
not be generating any warnings.
Parameters
----------
statClass : sherpa.stats.Stat instance
"""
d = example_data()
plot = DataPlot()
prefs = plot.plot_prefs
prefname = 'yerrorbars'
prefs[prefname] = False
stat = statClass()
# Ensure that the logging is set to WARNING since there
# appears to be some test that changes it to ERROR.
#
with caplog.at_level(logging.INFO, logger='sherpa'):
plot.prepare(d, stat)
check_for_warning(caplog, 0, stat.name)
def test_fit_plot_see_errorbar_warnings(caplog, statClass, flag):
"""Do we see the warning when expected - fit plot?
This looks for the 'The displayed errorbars have been supplied with
the data or calculated using chi2xspecvar; the errors are not used in
fits with <>' message. These are messages displayed to the Sherpa
logger at the warning level, rather than using the warnings module,
so the Sherpa capture_all_warnings test fixture does not come into
play.
Parameters
----------
stat : sherpa.stats.Stat instance
flag : bool
True if the warning should be created, False otherwise
"""
d = example_data()
m = example_model()
dplot = DataPlot()
mplot = ModelPlot()
fplot = FitPlot()
# Internal check: this test requires that either yerrorbars is set
# to True, or not included, in the plot preferences. So check this
# assumption.
#
# I am skipping model plot here, since it is assumed that there
# are no errors on the model.
#
prefname = 'yerrorbars'
for plot in [dplot, fplot]:
prefs = plot.plot_prefs
assert (prefname not in prefs) or prefs[prefname]
stat = statClass()
# Ensure that the logging is set to WARNING since there
# appears to be some test that changes it to ERROR.
#
with caplog.at_level(logging.INFO, logger='sherpa'):
dplot.prepare(d, stat)
mplot.prepare(d, m, stat)
fplot.prepare(dplot, mplot)
if flag:
nwarn = 1
else:
nwarn = 0
check_for_warning(caplog, nwarn, stat.name)
def html_data1d(data):
"""HTML representation: Data1D
If have matplotlib then plot the data, otherwise summarize it.
"""
from sherpa.plot import DataPlot, backend
dtype = type(data).__name__
plotter = DataPlot()
plotter.prepare(data)
summary = '{} Plot'.format(dtype)
try:
out = backend.as_html_plot(plotter, summary)
except AttributeError:
out = None
if out is not None:
return formatting.html_from_sections(data, [out])
# Summary properties
#
meta = []
if data.name is not None and data.name != '':
meta.append(('Identifier', data.name))
meta.append(('Number of bins', len(data.x)))
# Should this only be displayed if a filter has been applied?
#
fexpr = data.get_filter_expr()
nbins = data.get_dep(filter=True).size
meta.append(('Using', '{} with {} bins'.format(fexpr, nbins)))
# Rely on the _fields ordering, ending at staterror
for f in data._fields[1:]:
if f == 'staterror':
break
meta.append((f.upper(), getattr(data, f)))
if data.staterror is not None:
meta.append(('Statistical error', data.staterror))
if data.syserror is not None:
meta.append(('Systematic error', data.syserror))
ls = [formatting.html_section(meta, summary=dtype + ' Summary',
open_block=True)]
return formatting.html_from_sections(data, ls)
def test_fit_residstyle_plot_no_errors_no_errorbar_warnings(
caplog, plotClass, statClass):
"""Should not see warnings when no error bars are drawn (See #621).
This is a copy of test_fit_residstyle_plot_see_errorbar_warnings
except that the 'yerrorbars' preference setting for all plots is
'False'.
Parameters
----------
plotClass : {sherpa.plot.ResidPlot, sherpa.plot.RatioPlot}
The plot to test.
statClass : sherpa.stats.Stat instance
Notes
-----
Is this an accurate example of how 'plot_fit_resid' is created?
"""
d = example_data()
m = example_model()
dplot = DataPlot()
mplot = ModelPlot()
fplot = FitPlot()
rplot = plotClass()
jplot = JointPlot()
prefname = 'yerrorbars'
for plot in [dplot, rplot]:
prefs = plot.plot_prefs
prefs[prefname] = False
stat = statClass()
# Ensure that the logging is set to WARNING since there
# appears to be some test that changes it to ERROR.
#
with caplog.at_level(logging.INFO, logger='sherpa'):
dplot.prepare(d, stat)
mplot.prepare(d, m, stat)
fplot.prepare(dplot, mplot)
rplot.prepare(d, m, stat)
jplot.plottop(fplot)
jplot.plotbot(rplot)
check_for_warning(caplog, 0, stat.name)
def test_warning_dataplot_linecolor(caplog):
"""We get a warning when using linecolor: DataPlot"""
data = Data1D('tst', np.asarray([1, 2, 3]), np.asarray([10, 12, 10.5]))
plot = DataPlot()
plot.prepare(data, stat=None)
with caplog.at_level(logging.INFO, logger='sherpa'):
plot.plot(linecolor='mousey')
assert len(caplog.records) == 1
lname, lvl, msg = caplog.record_tuples[0]
assert lname == 'sherpa.plot.pylab_backend'
assert lvl == logging.WARNING
assert msg == 'The linecolor attribute, set to mousey, is unused.'
def __init__(self):
DataPlot.__init__(self)
d.ignore(0, 5)
sinfo2 = f.calc_stat_info()
d.notice()
dump("sinfo1.numpoints")
dump("sinfo2.numpoints")
res = f.fit()
if res.succeeded: print("Fit succeeded")
if not res.succeeded: print("**** ERRRR, the fit failed folks")
report("res.format()")
report("res")
from sherpa.plot import DataPlot, ModelPlot
dplot = DataPlot()
dplot.prepare(f.data)
mplot = ModelPlot()
mplot.prepare(f.data, f.model)
dplot.plot()
mplot.overplot()
savefig("data_model_c0_c2.png")
dump("f.method.name")
original_method = f.method
from sherpa.optmethods import NelderMead
f.method = NelderMead()
resn = f.fit()
print("Change in statistic: {}".format(resn.dstatval))
#normalize spliced intensities & invert
y = -1.0 * (y_raw - min(y_raw)) / norm_factor + 1.0
#Set data and model for fits
icorr = 0
G1 = Gauss1D('G1')
d = Data1D('He 1083', x, y, staterror=sd)
#guess parameters, this is important or sherpa won't know where to start looking
G1.fwhm = .05
G1.pos = 1083.03 + ref_value * 5
mdl = G1
mplot = ModelPlot()
mplot.prepare(d, mdl)
dplot = DataPlot()
dplot.prepare(d)
mplot.overplot()
#set error methods, ChiSq() or LeastSq()
#Chi square is a way to compare which profile best describes data, ie: is it more gaussian or lorentzian
#Least Square says how good the data fits the particular model instance
#opt - optimizers improve the fit. Monte Carlo is what I used, it is slow but it is most robust. Many options on sherpas site
ustat = LeastSq()
opt = MonCar() #LevMar() #NelderMead() #
#apply actual Fit
f = Fit(d, mdl, stat=ustat, method=opt)
res = f.fit()
fplot = FitPlot()
mplot.prepare(d, mdl)
dump("pha")
dump("pha.get_background()")
dump("pha.get_arf()")
dump("pha.get_rmf()")
dump("pha.header['INSTRUME']")
dump("pha.header['DETNAM']")
dump("pha.channel.size")
pha.set_analysis('energy')
pha.notice(0.3, 7)
tabs = ~pha.mask
pha.group_counts(20, tabStops=tabs)
from sherpa.plot import DataPlot
dplot = DataPlot()
dplot.prepare(pha)
dplot.plot(xlog=True, ylog=True)
savefig('pha_data.png')
chans, = pha.get_indep(filter=True)
counts = pha.get_dep(filter=True)
dump("chans.size, counts.size")
gchans = pha.apply_filter(chans, pha._middle)
dump("gchans.size")
plt.clf()
plt.plot(gchans, counts, 'o')
plt.xlabel('Channel')
plt.ylabel('Counts')
def dump(name):
print("# dump")
print(name)
print(repr(eval(name)))
from sherpa.data import Data1D
x = [1, 1.5, 2, 4, 8, 17]
y = [1, 1.5, 1.75, 3.25, 6, 16]
d = Data1D('interpolation', x, y)
report("print(d)")
from sherpa.plot import DataPlot
dplot = DataPlot()
dplot.prepare(d)
dplot.plot()
savefig('data.png')
# Note: can not print(dplot) as there is a problem with the fact
# the input to the data object is a list, not ndarray
# Sherpa 4.10.0
from sherpa.models.basic import Polynom1D
mdl = Polynom1D()
report("print(mdl)")
mdl.c2.thaw()
from sherpa.plot import ModelPlot
def fit(star_name, data, model, silent=False, breakdown=False):
"""A function that will fit a given multi-part model to a given spectrum.
:param star_name: Name of the target star
:type star_name: str
:param data: Spectrum data in the form (wave, flux)
:type data: tuple
:param model: An unfit spectrum model
:type model: object
:param silent: If true, no plots will generate, defaults to False
:type silent: bool
:return: model that is fit to the data
:rtype: object
"""
wave, flux = data
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
d = Data1D(star_name, wave, flux)
# ==========================================
# Initial guesses
# Dataset 1
dplot = DataPlot()
dplot.prepare(d)
if silent is False:
dplot.plot()
mplot = ModelPlot()
mplot.prepare(d, model)
if silent is False:
dplot.plot()
mplot.overplot()
plt.show()
# =========================================
# Fitting happens here - don't break please
start = time.time()
stat = LeastSq()
opt = LevMar()
opt.verbose = 0
opt.ftol = 1e-15
opt.xtol = 1e-15
opt.gtol = 1e-15
opt.epsfcn = 1e-15
if silent is False:
print(opt)
vfit = Fit(d, model, stat=stat, method=opt)
if silent is False:
print(vfit)
vres = vfit.fit()
if silent is False:
print()
print()
print(vres.format())
# =========================================
# Plotting after fit
# Dataset 1
if silent is False:
fplot = FitPlot()
mplot.prepare(d, model)
fplot.prepare(dplot, mplot)
fplot.plot()
# residual
plt.title(star_name)
plt.plot(wave, flux - model(wave))
# plt.xaxis(fontsize = )
plt.xlabel("Wavelength (AA)", fontsize=12)
plt.ylabel("Flux", fontsize=12)
plt.tick_params(axis="both", labelsize=12)
if silent is False:
duration = time.time() - start
print()
print("Time taken: " + str(duration))
print()
plt.show()
if breakdown is True:
params = []
cont = model[0]
if silent is False:
plt.scatter(wave, flux, marker=".", c="black")
plt.plot(wave, model(wave), c="C1")
for line in model:
if line.name[0] != "(":
if line.name == "Cont_flux":
if silent is False:
print(line)
plt.plot(wave, line(wave), linestyle="--")
else:
params.append(line)
if silent is False:
print()
print(line)
plt.plot(wave, line(wave) * cont(wave), linestyle="--")
plt.show()
return model, params
return model
def multifit(star_name, data_list, model_list, silent=False):
"""A function that will fit 2 models to 2 spectra simultaneously.
This was created to fit the NaI doublets at ~3300 and ~5890 Angstroms.
:param star_name: Name of the target star
:type star_name: str
:param data_list: List of spectrum data in the form [(wave, flux), (wave, flux),...]
:type data_list: tuple
:param model_list: A list of unfit spectrum models
:type model_list: list
:param silent: If true, no plots will generate, defaults to False
:type silent: bool
:return: models that are fit to the data
:rtype: list
"""
wave1, flux1 = data_list[0]
wave2, flux2 = data_list[1]
model1 = model_list[0]
model2 = model_list[1]
name_1 = star_name + " 1"
name_2 = star_name + " 2"
d1 = Data1D(name_1, wave1, flux1)
d2 = Data1D(name_2, wave2, flux2)
dall = DataSimulFit("combined", (d1, d2))
mall = SimulFitModel("combined", (model1, model2))
# # ==========================================
# # Initial guesses
# Dataset 1
dplot1 = DataPlot()
dplot1.prepare(d1)
if silent is False:
dplot1.plot()
mplot1 = ModelPlot()
mplot1.prepare(d1, model1)
if silent is False:
dplot1.plot()
mplot1.overplot()
plt.show()
# Dataset 2
dplot2 = DataPlot()
dplot2.prepare(d2)
if silent is False:
dplot2.plot()
mplot2 = ModelPlot()
mplot2.prepare(d2, model2)
if silent is False:
dplot2.plot()
mplot2.overplot()
plt.show()
# # =========================================
# # Fitting happens here - don't break please
stat = LeastSq()
opt = LevMar()
opt.verbose = 0
opt.ftol = 1e-15
opt.xtol = 1e-15
opt.gtol = 1e-15
opt.epsfcn = 1e-15
print(opt)
vfit = Fit(dall, mall, stat=stat, method=opt)
print(vfit)
vres = vfit.fit()
print()
print()
print("Did the fit succeed? [bool]")
print(vres.succeeded)
print()
print()
print(vres.format())
# # =========================================
# # Plotting after fit
if silent is False:
# Dataset 1
fplot1 = FitPlot()
mplot1.prepare(d1, model1)
fplot1.prepare(dplot1, mplot1)
fplot1.plot()
# residual
title = "Data 1"
plt.title(title)
plt.plot(wave1, flux1 - model1(wave1))
plt.show()
# Dataset 2
fplot2 = FitPlot()
mplot2.prepare(d2, model2)
fplot2.prepare(dplot2, mplot2)
fplot2.plot()
# residual
title = "Data 2"
plt.title(title)
plt.plot(wave2, flux2 - model2(wave2))
plt.show()
# both datasets - no residuals
splot = SplitPlot()
splot.addplot(fplot1)
splot.addplot(fplot2)
plt.tight_layout()
plt.show()
return model_list
#normalize spliced intensities & invert
y = -1.0 * (y_raw - min(y_raw)) / norm_factor + 1.0
#Set data and model for fits
icorr = 0
G1 = Gauss1D('G1')
d = Data1D('He 1083', x, y, staterror=sd)
#guess parameters, this is important or sherpa won't know where to start looking
G1.fwhm = 2
G1.pos = 1082.74 + ref_value * 5
mdl = G1
mplot = ModelPlot()
mplot.prepare(d, mdl)
dplot = DataPlot()
dplot.prepare(d)
mplot.overplot()
#set error methods, ChiSq() or LeastSq()
#Chi square is a way to compare which profile best describes data, ie: is it more gaussian or lorentzian
#Least Square says how good the data fits the particular model instance
#opt - optimizers improve the fit. Monte Carlo is what I used, it is slow but it is most robust. Many options on sherpas site
ustat = LeastSq()
opt = MonCar() #LevMar() #NelderMead() #
#apply actual Fit
f = Fit(d, mdl, stat=ustat, method=opt)
res = f.fit()
fplot = FitPlot()
mplot.prepare(d, mdl)
def dump(name):
print("# dump")
print("{}".format(name))
print(repr(eval(name)))
print("----------------------------------------")
edges = np.asarray([-10, -5, 5, 12, 17, 20, 30, 56, 60])
y = np.asarray([28, 62, 17, 4, 2, 4, 125, 55])
from sherpa.data import Data1DInt
d = Data1DInt('example histogram', edges[:-1], edges[1:], y)
from sherpa.plot import DataPlot
dplot = DataPlot()
dplot.prepare(d)
dplot.plot()
savefig('dataplot_histogram.png')
from sherpa.plot import Histogram
hplot = Histogram()
hplot.overplot(d.xlo, d.xhi, d.y)
savefig('dataplot_histogram_overplot.png')
from sherpa.models.basic import Const1D, Gauss1D
mdl = Const1D('base') - Gauss1D('line')
mdl.pars[0].val = 10
mdl.pars[1].val = 25
def dump(name):
print("# dump")
print(name)
print(repr(eval(name)))
from sherpa.data import Data1D
x = [1, 1.5, 2, 4, 8, 17]
y = [1, 1.5, 1.75, 3.25, 6, 16]
d = Data1D('interpolation', x, y)
report("print(d)")
from sherpa.plot import DataPlot
dplot = DataPlot()
dplot.prepare(d)
dplot.plot()
savefig('data.png')
# Note: can not print(dplot) as there is a problem with the fact
# the input to the data object is a list, not ndarray
# Sherpa 4.10.0
from sherpa.models.basic import Polynom1D
mdl = Polynom1D()
report("print(mdl)")
mdl.c2.thaw()
from sherpa.plot import ModelPlot
from openpyxl import load_workbook
wb = load_workbook('pone.0171996.s001.xlsx')
fig4 = wb['Fig4data']
t = []; y = []; dy = []
for r in list(fig4.values)[2:]:
t.append(r[0])
y.append(r[3])
dy.append(r[4])
from sherpa.data import Data1D
d = Data1D('NaNO_3', t, y, dy)
from sherpa.plot import DataPlot
dplot = DataPlot()
dplot.prepare(d)
dplot.plot()
savefig("data.png")
report("d")
dump("d.get_filter()")
d.ignore(None, 1)
dump("d.get_filter()")
dump("d.get_filter(format='%d')")
dplot.prepare(d)
from sherpa.models.basic import Const1D, Exp