def make_contour_plot(self, **kwargs):
pi, bish, sp, ds, sm, de, du, sc = self.multiplot_ranges(**kwargs)
if "y_range" not in kwargs:
temp = numpy.where(self.s_axes[5] > 0)[0]
kwargs["y_range"] = [self.s_axes[5][temp[0]], self.s_axes[5][temp[-1]]]
for _sp in sp:
for _sm in sm:
for _du in du:
for _sc in sc:
if "ax" not in kwargs:
fig = plt.figure()
ax = fig.add_subplot(111)
else:
ax = kwargs["ax"]
del(kwargs["ax"])
if _sm == 0:
smx = "perpendicular"
else:
smx = "parallel"
kwargs["title"] = "{name}\n{smx}".format(name = self.objectname, smx = smx)
PL.contourplot(self.s[:, 0, 0, _sp, _sm, :, _du, _sc].T, self.s_axes[0], self.s_axes[5], x_label = "w3 (cm-1)", y_label = self.s_units[5], ax = ax, **kwargs)
if "ylog" in kwargs and kwargs["ylog"]:
ax.set_yscale('log')
def make_overview_plot(self, **kwargs):
"""
Make a single figure with all plots.
INPUT:
- kwargs:
- sp, sm, de, du, sc (lists, ndarray): lists that limit the range of spectra to be plotted. By default all spectra will be plotted.
- aspect (str, 'equal'): the aspect ratio of the axes.
- flip_spectrum (bool, False): by default (False) the x axis is w_3. If True, it will be w_1. Make sure the axes ranges are changed as well.
OUTPUT:
- -
DESCRIPTION:
- -
CHANGELOG:
2016014/RB: started function
"""
pi, bish, sp, ds, sm, de, du, sc = self.multiplot_ranges(**kwargs)
n_plots = len(sp) * len(sm) * len(de) * len(du) * len(sc)
x, y = FU.find_subplots(n_plots, flag_verbose = self.flag_verbose)
fig = plt.figure()
ax = [0] * n_plots
for ax_i in range(n_plots):
ax[ax_i] = fig.add_subplot(y, x, ax_i + 1)
if "aspect" in kwargs:
if kwargs["aspect"] != False:
ax[ax_i].set_aspect(kwargs["aspect"])
else:
ax[ax_i].set_aspect("equal")
ax_i = 0
for _sp in sp:
for _sm in sm:
for _de in de:
for _du in du:
for _sc in sc:
title = "{name}\nsp {spx}, sm {smx}, de {dex} fs".format(name = self._basename, spx = self.s_axes[3][_sp], smx = "x",#self.s_axes[4][:,_sm],
dex = self.s_axes[5][_de])
if "flip_spectrum" in kwargs and kwargs["flip_spectrum"]:
PL.contourplot(self.s[:, :, 0, _sp, _sm, _de, _du, _sc], self.s_axes[1], self.s_axes[0], x_label = "w1 (cm-1)", y_label = "w3 (cm-1)", ax = ax[ax_i], title = title, **kwargs)
else:
PL.contourplot(self.s[:, :, 0, _sp, _sm, _de, _du, _sc].T, self.s_axes[0], self.s_axes[1], x_label = "w3 (cm-1)", y_label = "w1 (cm-1)", ax = ax[ax_i], title = title, **kwargs)
ax_i += 1
return fig
def make_plots(self, **kwargs):
"""
Plot all 2D-IR spectra as separate plots.
INPUT:
- kwargs:
- sp, sm, de, du, sc (lists, ndarray): lists that limit the range of spectra to be plotted. By default all spectra will be plotted.
- aspect (str, 'equal'): the aspect ratio of the axes.
- flip_spectrum (bool, False): by default (False) the x axis is w_3. If True, it will be w_1. Make sure the axes ranges are changed as well.
DESCRIPTION:
- -
CHANGELOG:
201604-RB: started function
"""
pi, bish, sp, ds, sm, de, du, sc = self.multiplot_ranges(**kwargs)
flag_make_title = False
if "title" not in kwargs:
flag_make_title = True
if "ax" not in kwargs:
flag_create_fig = True
else:
flag_create_fig = False
ax = kwargs["ax"]
del(kwargs["ax"])
for _sp in sp:
for _sm in sm:
for _de in de:
for _du in du:
for _sc in sc:
if flag_create_fig:
fig = plt.figure()
ax = fig.add_subplot(111)
if "aspect" in kwargs:
if kwargs["aspect"] != False:
ax.set_aspect(kwargs["aspect"])
else:
ax.set_aspect("equal")
if flag_make_title:
kwargs["title"] = "%s %s fs" % (self._basename, self.s_axes[5][_de])
# kwargs["title"] = "{name}\nsp {spx}, sm {smx}, de {dex} fs".format(name = self._basename, spx = self.s_axes[3][_sp], smx = self.s_axes[4][:,_sm], dex = self.s_axes[5][_de])
if "flip_spectrum" in kwargs and kwargs["flip_spectrum"]:
PL.contourplot(self.s[:, :, 0, _sp, _sm, _de, _du, _sc], self.s_axes[1], self.s_axes[0], x_label = "w1 (cm-1)", y_label = "w3 (cm-1)", ax = ax, **kwargs)
else:
PL.contourplot(self.s[:, :, 0, _sp, _sm, _de, _du, _sc].T, self.s_axes[0], self.s_axes[1], x_label = "w3 (cm-1)", y_label = "w1 (cm-1)", ax = ax, **kwargs)
def make_contour_plot(self, **kwargs):
pi, bish, sp, ds, sm, de, du, sc = self.multiplot_ranges(**kwargs)
flag_make_title = False
if "title" not in kwargs:
flag_make_title = True
if "y_range" not in kwargs:
temp = numpy.where(self.s_axes[5] > 0)[0]
print(temp)
kwargs["y_range"] = [self.s_axes[5][temp[0]], self.s_axes[5][temp[-1]]]
print(kwargs["y_range"])
for _sp in sp:
for _sm in sm:
for _du in du:
for _sc in sc:
if "ax" not in kwargs:
fig = plt.figure()
ax = fig.add_subplot(111)
else:
ax = kwargs["ax"]
del(kwargs["ax"])
kwargs["aspect"] = False
if flag_make_title:
kwargs["title"] = "{name}\nsp {spx}, sm {smx}".format(name = self._basename, spx = self.s_axes[3][_sp], smx = self.s_axes[4][:,_sm])
PL.contourplot(self.s[:, 0, 0, _sp, _sm, :, _du, _sc].T, self.s_axes[0], self.s_axes[5], x_label = "w3 (cm-1)", y_label = self.s_units[5], ax = ax, **kwargs)
if "ylog" in kwargs and kwargs["ylog"]:
ax.set_yscale('log')
plt.show()
def plot(
self,
plot_type="S",
ax=False,
x_range=[0, 0],
y_range=[0, -1],
pixel=-1,
x_label="",
y_label="",
title="",
flipxy=False,
flag_verbose=False,
**kwargs
):
"""
Plot the data.
INPUT:
- plot_type ('S' (default), 'R', 'NR', 'T'): plot the spectrum, the rephasing, non-rephasing spectra or time domain. Note that R and NR only work if the Fourier transform has been done and saved.
- ax (False (default) or matplotlib axes instance): if False, it will make a new figure, otherwise it will use the axes instance, allowing subplots etc.
- x_label, y_label, title (string, default=''): the labels for the axes. If no label is set, it will use the default. Use 'no_label' or 'no_title' to show no label.
- pixel (int, -1): if pixel is an element of w_3, it will plot only this pixel, otherwise it will plot a 2D-plot
- flipxy (BOOL, False): will flip the data and the axes. Non-default labels will not be flipped.
- x_range, y_range (array with 2 elements, [0,0], [0,-1]): the range to be plotted.
Possible cases:
- [min, max]: plot range min to max
- [0, 0]: plot the whole range
- [0, -1]: use the range from the other axis. If both have this, it will plot both axes complete. (ie. it is identical to both having [0,0])
**kwargs (stuff for the plotting function)
- zlimit (number or list, -1): the z-range that will be used
Possible cases:
zlimit = 0, show all, not don't care about centering around zero
zlimit = -1, show all, centered around zero
zlimit = all else, use that, centered around zero
zlimit = [a,b], plot from a to b
- contours (number): number of contours to be used
- invert_colors (BOOL, False): data = -data
CHANGELOG:
20110910/RB: started as croc-function
20130131/RB: rewrote function for Crocodile. Integrated it with plot_T
20130213/RB: some arguments are now kwargs: they are not explicitly listed but are passed on to the plotting function.
"""
self.verbose("Plot", flag_verbose)
if plot_type == "S":
data = self.s
elif plot_type == "R":
data = numpy.real(numpy.exp(-1j * self.phase_rad) * self.f[0])
elif plot_type == "NR":
data = numpy.real(numpy.exp(1j * self.phase_rad) * self.f[1])
elif plot_type == "T":
data = numpy.concatenate((numpy.flipud(self.r[1][1:, :]), self.r[0])).T
if pixel < 0 or pixel > len(self.s_axis[2]):
self.verbose(" -> contourplot", flag_verbose)
# S, R and NR are freq-freq, T is time-freq
# flipxy will change the xy-axis
# the labels and range may be changed, if they are not at the defaults
if plot_type == "S" or plot_type == "R" or plot_type == "NR":
if flipxy:
# not the normal way
data = data.T
x_axis = self.s_axis[0]
y_axis = self.s_axis[2]
if x_label == "":
x_label = r"$\omega_1 (cm^{-1})$"
if y_label == "":
y_label = r"$\omega_3 (cm^{-1})$"
else:
x_axis = self.s_axis[2]
y_axis = self.s_axis[0]
if x_label == "":
x_label = r"$\omega_3 (cm^{-1})$"
if y_label == "":
y_label = r"$\omega_1 (cm^{-1})$"
else: # time domain
if flipxy:
# not the normal way
data = data.T
x_axis = self.r_axis[2]
y_axis = numpy.concatenate((-numpy.flipud(self.r_axis[0][1:]), self.r_axis[0]))
if x_label == "":
x_label = r"$\omega_3 (cm^{-1})$"
if y_label == "":
y_label = r"$t_1 (fs)$"
if y_range == [0, -1]:
y_range = [0, 0]
else:
x_axis = numpy.concatenate((-numpy.flipud(self.r_axis[0][1:]), self.r_axis[0]))
y_axis = self.r_axis[2]
if x_label == "":
x_label = r"$t_1 (fs)$"
if y_label == "":
y_label = r"$\omega_3 (cm^{-1})$"
if y_range == [0, -1]:
y_range = [0, 0]
PL.contourplot(
data,
x_axis,
y_axis,
ax=ax,
x_range=x_range,
y_range=y_range,
x_label=x_label,
y_label=y_label,
title=title,
flag_verbose=flag_verbose,
**kwargs
)
else:
self.verbose(" -> linear plot", flag_verbose)
if plot_type == "S" or plot_type == "R" or plot_type == "NR":
x_axis = self.s_axis[0]
x_label = r"$\omega_1 (cm^{-1})$"
else:
x_axis = self.r_axis[0]
x_label = r"$\t_1 (fs)$"
PL.linear(
data[pixel],
x_axis,
x_range=x_range,
y_range=y_range,
ax=ax,
x_label=x_label,
y_label=y_label,
title=title,
flag_verbose=flag_verbose,
**kwargs
)
if not ax:
plt.show()