def eem(multi_xas, name):
start_time = time.time()
# matplotlib.rcParams['figure.figsize'] = (14, 10)
name = name.upper()
if name == "SDD1":
intensity = multi_xas.sdd1
# intensity = np.array(intensity)
elif name == "SDD2":
intensity = multi_xas.sdd2
# intensity = np.array(intensity)
elif name == "SDD3":
intensity = multi_xas.sdd3
# intensity = np.array(intensity)
elif name == "SDD4":
intensity = multi_xas.sdd4
# intensity = np.array(intensity)
else:
return "Invalid name for the intensity of EEM"
energy_array = np.array(multi_xas.energy)
num_of_points = len(energy_array)
num_of_emission_bins = len(intensity[0])
bin_num_for_x = np.zeros(shape=(num_of_points, num_of_emission_bins))
for i in range(num_of_points):
bin_num_for_x[i].fill(energy_array[i])
bin_num_for_y = np.zeros(shape=(num_of_points, num_of_emission_bins))
bin_num_for_y[0:] = np.arange(10, (num_of_emission_bins + 1) * 10, 10)
v_max = max(intensity[0])
for i in range(1, num_of_points):
temp_max = max(intensity[i])
if temp_max > v_max:
v_max = temp_max
# print ("v_max: ", v_max)
intensity = np.array(intensity)
plotview = NXPlotView()
plotview.figure.clf()
ax = plotview.figure.gca()
ax.axes.get_xaxis().set_visible(True)
ax.axes.get_yaxis().set_visible(True)
# print("--- %s seconds ---" % (time.time() - start_time))
ax.scatter(bin_num_for_x,
bin_num_for_y,
c=intensity,
s=7,
linewidths=0,
vmax=v_max,
vmin=0)
print("--- %s seconds ---" % (time.time() - start_time))
ax.set_xlabel('Incident Energy (eV)')
ax.set_ylabel('Emission Energy (eV)')
ax.set_title("Excitation Emission Matrix")
plotview.grid()
plotview.draw()
print("--- %s seconds ---" % (time.time() - start_time))
def summary_plot(self, name):
start_time = time.time()
# matplotlib.rcParams['figure.figsize'] = (13, 10)
# select intensity
name = name.upper()
if name == "TEY":
intensity = self.tey
elif name == "I0" or name == "IO":
intensity = self.i0
elif name == "DIODE" or name == "PD1":
intensity = self.diode
elif name == "PFY_SDD1":
intensity = self.pfy_sdd1
elif name == "PFY_SDD2":
intensity = self.pfy_sdd2
elif name == "PFY_SDD3":
intensity = self.pfy_sdd3
elif name == "PFY_SDD4":
intensity = self.pfy_sdd4
else:
return "Invalid name for the intensity of summary plot"
total_cscan_num = len(self.energy)
# print (total_cscan_num)
# show the plot in Nexpy, similar to figure.show()
plotview = NXPlotView()
# setup the size of figure and pop-up window
plotview.setMinimumHeight(200)
if total_cscan_num > 10:
ratio = total_cscan_num / 10
else:
ratio = 1
plotview.resize(700, 280 * ratio)
plotview.figure.clf()
# setup axis
ax = plotview.figure.gca()
ax.axes.get_xaxis().set_visible(True)
ax.axes.get_yaxis().set_visible(True)
print("--- %s seconds ---" % (time.time() - start_time))
energy_tuple = np.array(self.energy[0][:])
intensity_tuple = np.array(intensity[0][:])
scan_num_tuple = np.zeros(len(self.energy[0]))
scan_num_tuple.fill(1)
# prepare data as tuples for x, y, and color of scatter plot
for i in range(1, total_cscan_num):
scan_num_list = np.zeros(len(self.energy[i]))
scan_num_list.fill(i + 1)
scan_num_tuple = np.concatenate([scan_num_tuple, scan_num_list])
energy_tuple = np.concatenate(
[energy_tuple, np.array(self.energy[i][:])])
intensity_tuple = np.concatenate(
[intensity_tuple, np.array(intensity[i][:])])
# comment out the old way to generate scatter plot
#plt.scatter(self.energy[i][:], scan_num_list, c=intensity[i][:], s=140, linewidths=0, marker='s')
# print("--- %s seconds ---" % (time.time() - start_time))
# main function call to generate color scatter plot
ax.scatter(energy_tuple,
scan_num_tuple,
c=intensity_tuple,
s=140,
linewidths=0,
marker='s')
# this locator puts ticks at regular intervals
loc = plticker.MultipleLocator(base=1.0)
# set regular ticks interval
ax.yaxis.set_major_locator(loc)
# set the limitation of y axis
ax.set_ylim(ymin=0, ymax=total_cscan_num + 1)
# manipulate the ytick labels
t = np.arange(len(self.selected_scan_entry)) + 1.0
ax.set_yticks(t)
ax.set_yticklabels(self.selected_scan_entry)
# add title of the figure
ax.set_title("Summary Plot (Intensity: %s)" % (name))
# add labels for x and y axis
ax.set_xlabel('Incident Energy(eV)')
ax.set_ylabel('Scan Entry')
# set limit of y axis
print("selected_scan_entry: ", self.selected_scan_entry)
plotview.grid(True)
plotview.draw()
print("--- %s seconds ---" % (time.time() - start_time))
