def test_get_stacked_plot(self):
self.plotter = SpectrumPlotter(yshift=0.2, stack=True)
self.plotter.add_spectrum("Pd2O", self.xanes, "b")
xanes = self.xanes.copy()
xanes.y += np.random.randn(len(xanes.y)) * 0.005
self.plotter.add_spectrum("Pd2O + noise", xanes, "r")
plt = self.plotter.get_plot()
def test_get_plot(self):
self.plotter = SpectrumPlotter(yshift=0.2)
self.plotter.add_spectrum("Pd2O", self.xanes)
xanes = self.xanes.copy()
xanes.y += np.random.randn(len(xanes.y)) * 0.005
self.plotter.add_spectrum("Pd2O + noise", xanes)
self.plotter.add_spectrum("Pd2O - replot", xanes, "k")
plt = self.plotter.get_plot()
self.plotter.save_plot("spectrum_plotter_test.eps")
os.remove("spectrum_plotter_test.eps")
def test_get_stacked_plot(self):
self.plotter = SpectrumPlotter(yshift=0.2, stack=True)
self.plotter.add_spectrum("Pd2O", self.xanes, "b")
xanes = self.xanes.copy()
xanes.y += np.random.randn(len(xanes.y)) * 0.005
self.plotter.add_spectrum("Pd2O + noise", xanes, "r")
plt = self.plotter.get_plot()
def test_get_plot(self):
self.plotter = SpectrumPlotter(yshift=0.2)
self.plotter.add_spectrum("Pd2O", self.xanes)
xanes = self.xanes.copy()
xanes.y += np.random.randn(len(xanes.y)) * 0.005
self.plotter.add_spectrum("Pd2O + noise", xanes)
self.plotter.add_spectrum("Pd2O - replot", xanes, "k")
plt = self.plotter.get_plot()
self.plotter.save_plot("spectrum_plotter_test.eps")
os.remove("spectrum_plotter_test.eps")
def get_plotter(self,
components=("xx", ),
reim="reim",
broad=0.00005,
emin=0,
emax=None,
divs=500,
**kwargs):
"""
Return an instance of the Spectrum plotter containing the different requested components
Arguments:
components: A list with the components of the dielectric tensor to plot.
Can be either two indexes or a string like 'xx' to plot the (0,0) component
reim: If 're' (im) is present in the string plots the real (imaginary) part of the dielectric tensor
emin, emax: minimum and maximum energy in which to obtain the spectra
divs: number of frequency samples between emin and emax
"""
directions_map = {"x": 0, "y": 1, "z": 2, 0: 0, 1: 1, 2: 2}
reim_label = {"re": "Re", "im": "Im"}
plotter = SpectrumPlotter()
for component in components:
i, j = [directions_map[direction] for direction in component]
for fstr in ("re", "im"):
if fstr in reim:
label = r"%s{$\epsilon_{%s%s}$}" % (
reim_label[fstr],
"xyz"[i],
"xyz"[j],
)
spectrum = self.get_spectrum(component,
fstr,
broad=broad,
emin=emin,
emax=emax,
divs=divs)
spectrum.XLABEL = r"Frequency (meV)"
spectrum.YLABEL = r"$\epsilon(\omega)$"
plotter.add_spectrum(label, spectrum)
return plotter
class SpectrumPlotterTest(PymatgenTest):
def setUp(self):
self.xanes = XAS.from_dict(spect_data_dict)
def test_get_plot(self):
self.plotter = SpectrumPlotter(yshift=0.2)
self.plotter.add_spectrum("LiCoO2", self.xanes)
xanes = self.xanes.copy()
xanes.y += np.random.randn(len(xanes.y)) * 0.005
self.plotter.add_spectrum("LiCoO2 + noise", xanes)
self.plotter.add_spectrum("LiCoO2 - replot", xanes, "k")
plt = self.plotter.get_plot()
self.plotter.save_plot("spectrum_plotter_test.eps")
os.remove("spectrum_plotter_test.eps")
plt.close("all")
def test_get_stacked_plot(self):
self.plotter = SpectrumPlotter(yshift=0.2, stack=True)
self.plotter.add_spectrum("LiCoO2", self.xanes, "b")
xanes = self.xanes.copy()
xanes.y += np.random.randn(len(xanes.y)) * 0.005
self.plotter.add_spectrum("LiCoO2 + noise", xanes, "r")
plt = self.plotter.get_plot()
plt.close("all")
class SpectrumPlotterTest(PymatgenTest):
def setUp(self):
self.xanes = XANES.from_dict(spect_data_dict)
def test_get_plot(self):
self.plotter = SpectrumPlotter(yshift=0.2)
self.plotter.add_spectrum("Pd2O", self.xanes)
xanes = self.xanes.copy()
xanes.y += np.random.randn(len(xanes.y)) * 0.005
self.plotter.add_spectrum("Pd2O + noise", xanes)
self.plotter.add_spectrum("Pd2O - replot", xanes, "k")
plt = self.plotter.get_plot()
self.plotter.save_plot("spectrum_plotter_test.eps")
os.remove("spectrum_plotter_test.eps")
def test_get_stacked_plot(self):
self.plotter = SpectrumPlotter(yshift=0.2, stack=True)
self.plotter.add_spectrum("Pd2O", self.xanes, "b")
xanes = self.xanes.copy()
xanes.y += np.random.randn(len(xanes.y)) * 0.005
self.plotter.add_spectrum("Pd2O + noise", xanes, "r")
plt = self.plotter.get_plot()
