class xaesa_viewer(QtGui.QWidget):
def __init__(self, parent=None):
super(xaesa_viewer, self).__init__()
self.x_data = [] #list with arrays
self.y_data = []
self.labels = [] #list with labels for each line
self.x_caption = ""
self.y_caption = ""
# mode = 0 - each line new color
# mode = 1 - combine 2 lines with the same color (for FT comparison)
self.mode = 0
self.plotXRange = [] #two element [min, max] (for XANES)
self.horizontalLine = []
self.lines = []
self.initUI()
def initUI(self):
#Figures
self.fig = plt.figure(1, figsize=(15, 6))
# self.ax_exafs = self.fig.add_subplot(111)
self.canv = FigureCanvas(self.fig)
self.tbar = NavigationToolbar(self.canv, self)
fnt = self.tbar.font()
fnt.setPointSize(20)
self.tbar.setFont(fnt)
# plt.tight_layout()
lfig = QtGui.QVBoxLayout()
lfig.addWidget(self.tbar)
lfig.addWidget(self.canv)
self.setLayout(lfig)
self.canv.draw()
def plot(self):
plt.clf()
self.ax_exafs = self.fig.add_subplot(111)
if self.mode == 0: #compare exafs
for i in range(len(self.x_data)):
l, = self.ax_exafs.plot(self.x_data[i],
self.y_data[i],
label=self.labels[i])
self.ax_exafs.set_xlabel(self.x_caption)
self.ax_exafs.set_ylabel(self.y_caption)
# self.ax_exafs.set_xlabel('Wavevector k, $\AA^{-1}$')
# self.ax_exafs.set_ylabel('EXAFS, $\AA^{-2}$')
if self.horizontalLine != []:
self.ax_exafs.axhline(
y=1,
linewidth=0.5,
color='k',
linestyle='--',
)
if self.plotXRange != []:
self.ax_exafs.set_xlim(self.plotXRange)
self.lines.append(l)
if self.mode == 1: #compare ft
for i in range(len(self.r) / 2):
line1, = self.ax_exafs.plot(self.x_data[2 * i],
self.y_data[2 * i],
label=self.labels[i])
line2, = self.ax_exafs.plot(self.x_data[2 * i + 1],
self.y_data[2 * i + 1])
line2.set_color(line1.get_color())
line2.set_linestyle('dotted')
self.ax_exafs.set_xlabel(self.x_caption)
self.ax_exafs.set_ylabel(self.y_caption)
# self.ax_exafs.set_xlabel('Distance R, $\AA$')
# self.ax_exafs.set_ylabel('Fourier transform, $\AA^{-3}$')
self.lines.append(line1)
self.lines1.append(line2)
self.fig.canvas.mpl_connect('pick_event', self.onpick)
self.fig.tight_layout()
box = self.ax_exafs.get_position()
self.ax_exafs.set_position(
[box.x0, box.y0, box.width * 0.7, box.height])
leg = self.ax_exafs.legend(loc='center left', bbox_to_anchor=(1, 0.5))
# we will set up a dict mapping legend line to orig line, and enable
# picking on the legend line
self.lined = dict()
for legline, origline in zip(leg.get_lines(), self.lines):
legline.set_picker(5) # 5 pts tolerance
self.lined[legline] = origline
if self.mode == 1:
self.lined1 = dict()
for legline, origline in zip(leg.get_lines(), self.lines1):
# legline.set_picker(5) # 5 pts tolerance
self.lined1[legline] = origline
self.canv.draw()
def onpick(self, event):
# on the pick event, find the orig line corresponding to the
# legend proxy line, and toggle the visibility
legline = event.artist
origline = self.lined[legline]
vis = not origline.get_visible()
origline.set_visible(vis)
if self.mode == 1:
origline = self.lined1[legline]
origline.set_visible(vis)
# Change the alpha on the line in the legend so we can see what lines
# have been toggled
if vis:
legline.set_alpha(1.0)
else:
legline.set_alpha(0.2)
self.fig.canvas.draw()
class xaesa_rxes(QtGui.QWidget):
def __init__(self, parent=None):
super(xaesa_rxes, self).__init__()
self.fluoEnergy = []
self.incidentEnergy = []
self.rxes = []
self.energyTransfer = False
self.initUI()
def initUI(self):
#Figures
self.fig = plt.figure(997, figsize=(15, 6))
self.ax_rxes = plt.subplot2grid((1, 2), (0, 0))
self.ax_cuts = plt.subplot2grid((1, 2), (0, 1))
if self.energyTransfer:
self.ax_rxes.set_xlabel('Incident energy, eV')
self.ax_rxes.set_ylabel('Energy transfer, eV')
self.ax_cuts.set_xlabel('Incident energy, eV')
self.ax_cuts.set_ylabel('Intensity, a.u.')
else:
self.ax_rxes.set_xlabel('Incident energy, eV')
self.ax_rxes.set_ylabel('Emission energy, eV')
self.ax_cuts.set_xlabel('Incident energy, eV')
self.ax_cuts.set_ylabel('HERFD XANES, a.u.')
self.fig.canvas.mpl_connect('button_press_event',
self.imageDoubleClick)
self.canv = FigureCanvas(self.fig)
self.tbar = NavigationToolbar(self.canv, self)
fnt = self.tbar.font()
fnt.setPointSize(20)
self.tbar.setFont(fnt)
# plt.tight_layout()
self.sl = QtGui.QSlider(QtCore.Qt.Horizontal)
self.sl.setMinimum(0)
self.sl.setMaximum(100)
self.sl.setValue(100)
self.sl.setTickPosition(QtGui.QSlider.TicksBelow)
self.sl.valueChanged.connect(self.valuechange)
# self.sl.setTickInterval(5)
glout = QtGui.QGridLayout()
glout.addWidget(self.sl, 0, 0, 1, 2)
glout.addWidget(QtGui.QLabel("Energy for HERFD-XANES"), 1, 0)
glout.addWidget(QtGui.QLabel("Delta energy for HERFD-XANES"), 2, 0)
self.edtEnergyHerfd = QtGui.QLineEdit()
glout.addWidget(self.edtEnergyHerfd, 1, 1)
self.edtDeltaHerfd = QtGui.QLineEdit()
glout.addWidget(self.edtDeltaHerfd, 2, 1)
self.btnCalculateHerfd = QtGui.QPushButton("Show HERFD XANES")
self.btnCalculateHerfd.clicked.connect(self.showHerfd)
glout.addWidget(self.btnCalculateHerfd, 3, 0, 1, 2)
self.btnCalculateHerfd = QtGui.QPushButton("save HERFD XANES")
self.btnCalculateHerfd.clicked.connect(self.saveHerfd)
glout.addWidget(self.btnCalculateHerfd, 4, 0, 1, 2)
glout.addWidget(QtGui.QLabel("Energy transfer min "), 1, 2)
glout.addWidget(QtGui.QLabel("Energy transfer max"), 2, 2)
self.edtEnergyTransMin = QtGui.QLineEdit()
glout.addWidget(self.edtEnergyTransMin, 1, 3)
self.edtEnergyTransMax = QtGui.QLineEdit()
glout.addWidget(self.edtEnergyTransMax, 2, 3)
self.btnCalculateHerfd = QtGui.QPushButton("Show energy transfer")
self.btnCalculateHerfd.clicked.connect(self.showEnergyTrans)
glout.addWidget(self.btnCalculateHerfd, 3, 2, 1, 2)
self.btnCalculateHerfd = QtGui.QPushButton("Save energy transfer")
self.btnCalculateHerfd.clicked.connect(self.saveEnergyTrans)
glout.addWidget(self.btnCalculateHerfd, 4, 2, 1, 2)
self.btnCancel = QtGui.QPushButton('Exit')
self.btnCancel.clicked.connect(self.cancel)
lfig = QtGui.QVBoxLayout()
lfig.addWidget(self.tbar)
lfig.addWidget(self.canv)
lfig.addLayout(glout)
lfig.addWidget(self.btnCancel)
self.setLayout(lfig)
self.canv.draw()
def plot(self):
savetxt("x.dat", self.incidentEnergy)
savetxt("y.dat", self.fluoEnergy)
savetxt("z.dat", self.rxes)
# self.image = self.ax_rxes.imshow(self.rxes, vmin = 0, vmax = self.zmax, aspect='auto', interpolation='none',cmap='gist_ncar')
self.image = self.ax_rxes.pcolormesh(self.incidentEnergy,
self.fluoEnergy, self.rxes)
# if amax(self.rxes) > 1:
# self.sl.setMaximum(amax(self.rxes))
self.fig.tight_layout()
self.canv.draw()
def cancel(self):
#do whatever you need with self.roiGroups
self.close()
def onpick(self, event):
# on the pick event, find the orig line corresponding to the
# legend proxy line, and toggle the visibility
legline = event.artist
origline = self.lined[legline]
vis = not origline.get_visible()
origline.set_visible(vis)
if self.mode == 1:
origline = self.lined1[legline]
origline.set_visible(vis)
# Change the alpha on the line in the legend so we can see what lines
# have been toggled
if vis:
legline.set_alpha(1.0)
else:
legline.set_alpha(0.2)
self.fig.canvas.draw()
def showHerfd(self):
emin = float(self.edtEnergyHerfd.text()) - float(
self.edtDeltaHerfd.text())
emax = float(self.edtEnergyHerfd.text()) + float(
self.edtDeltaHerfd.text())
if self.energyTransfer: #plot energy transfer intensity versus incident energy
indexes_where = where(
logical_and(self.fluoEnergy[:, 0] > emin,
self.fluoEnergy[:, 0] < emax))
tmp_array = []
for i in range(len(self.incidentEnergy[0])):
indexes_where = where(
logical_and(self.fluoEnergy[:, i] > emin,
self.fluoEnergy[:, i] < emax))
print(self.rxes[indexes_where, i][0])
number = sum(self.rxes[indexes_where, i][0]) / len(
self.rxes[indexes_where, i][0])
print(number)
tmp_array.append(number)
# hsum = sum(tmp_array, axis=0)
self.ax_cuts.clear()
self.ax_cuts.set_xlabel('Incident energy, eV')
self.ax_cuts.set_ylabel('Intensity, a.u.')
self.ax_cuts.plot(self.incidentEnergy[0], tmp_array)
else: # plot normal herfd
indexes_where = where(
logical_and(self.fluoEnergy[:, 0] > emin,
self.fluoEnergy[:, 0] < emax))
hsum = sum((self.rxes[indexes_where, :]), axis=1)
self.ax_cuts.clear()
self.ax_cuts.set_xlabel('Incident energy, eV')
self.ax_cuts.set_ylabel('HERFD XANES, a.u.')
self.ax_cuts.plot(self.incidentEnergy[0], hsum[0])
self.canv.draw()
def saveHerfd(self):
emin = float(self.edtEnergyHerfd.text()) - float(
self.edtDeltaHerfd.text())
emax = float(self.edtEnergyHerfd.text()) + float(
self.edtDeltaHerfd.text())
if self.energyTransfer: #plot energy transfer intensity versus incident energy
indexes_where = where(
logical_and(self.fluoEnergy[:, 0] > emin,
self.fluoEnergy[:, 0] < emax))
tmp_array = []
for i in range(len(self.incidentEnergy[0])):
indexes_where = where(
logical_and(self.fluoEnergy[:, i] > emin,
self.fluoEnergy[:, i] < emax))
print(self.rxes[indexes_where, i][0])
number = sum(self.rxes[indexes_where, i][0]) / len(
self.rxes[indexes_where, i][0])
print(number)
tmp_array.append(number)
# hsum = sum(tmp_array, axis=0)
forSave = concatenate(([self.incidentEnergy[0]], [tmp_array]))
else: # plot normal herfd
indexes_where = where(
logical_and(self.fluoEnergy[:, 0] > emin,
self.fluoEnergy[:, 0] < emax))
hsum = sum((self.rxes[indexes_where, :]), axis=1)
forSave = concatenate(([self.incidentEnergy[0]], [hsum[0]]))
fn = self.savefiledialog_qtgui()
if fn == "":
return
savetxt(fn, transpose(forSave))
def showEnergyTrans(self):
emin = float(self.edtEnergyTransMin.text())
emax = float(self.edtEnergyTransMax.text())
tmp_array = []
#vert sum Energy transfer
indexes_where = where(
logical_and(self.fluoEnergy[:, 0] > emin,
self.fluoEnergy[:, 0] < emax))
nr_points = len(indexes_where[0])
for i in range(len(self.incidentEnergy[0])):
indexes_where = where(
logical_and(self.fluoEnergy[:, i] > emin,
self.fluoEnergy[:, i] < emax))
first_i = indexes_where[0][0]
i_to_take = array(range(first_i, first_i + nr_points))
tmp_array.append(self.rxes[[i_to_take], i][0])
hsum = sum(tmp_array, axis=0)
indexes_where = where(
logical_and(self.fluoEnergy[:, 0] > emin,
self.fluoEnergy[:, 0] < emax))
self.ax_cuts.clear()
self.ax_cuts.set_xlabel('Incident energy, eV')
self.ax_cuts.set_ylabel('Intensity, a.u.')
self.ax_cuts.plot(self.fluoEnergy[:, 0][indexes_where], hsum)
self.canv.draw()
def saveEnergyTrans(self):
emin = float(self.edtEnergyTransMin.text())
emax = float(self.edtEnergyTransMax.text())
tmp_array = []
#vert sum Energy transfer
indexes_where = where(
logical_and(self.fluoEnergy[:, 0] > emin,
self.fluoEnergy[:, 0] < emax))
nr_points = len(indexes_where[0])
for i in range(len(self.incidentEnergy[0])):
indexes_where = where(
logical_and(self.fluoEnergy[:, i] > emin,
self.fluoEnergy[:, i] < emax))
first_i = indexes_where[0][0]
i_to_take = array(range(first_i, first_i + nr_points))
tmp_array.append(self.rxes[[i_to_take], i][0])
hsum = sum(tmp_array, axis=0)
indexes_where = where(
logical_and(self.fluoEnergy[:, 0] > emin,
self.fluoEnergy[:, 0] < emax))
forSave = concatenate(([self.fluoEnergy[:, 0][indexes_where]], [hsum]))
fn = self.savefiledialog_qtgui()
if fn == "":
return
savetxt(fn, transpose(forSave))
def valuechange(self):
# size = self.sl.value()
print(self.sl.value())
self.image.set_clim(vmin=0,
vmax=(self.sl.value() / 100) * amax(self.rxes))
self.canv.draw()
def imageDoubleClick(self, event):
print(event)
if event.dblclick == True:
#ask to change scale
num, ok = QtGui.QInputDialog.getDouble(self,
"Z scale",
"Z max",
value=self.zmax,
max=20000000,
min=0,
decimals=4)
if ok:
self.zmax = num
self.image.set_clim(vmax=self.zmax)
self.canv.draw()
else:
return
def savefiledialog_qtgui(self):
dlg = QtGui.QFileDialog()
dlg.setFileMode(QtGui.QFileDialog.AnyFile)
dlg.setAcceptMode(1) # save dialog
dlg.setNameFilters(["All files (*.*)"])
# dlg.setDirectory(self.currentdir)
if dlg.exec_():
flist = dlg.selectedFiles()
return flist[0]
else:
return ""
class CompareWindow(QtGui.QDialog):
def __init__(self):
super(CompareWindow, self).__init__()
self.exafs = []
self.k = []
self.r = []
self.fr = []
self.fi = []
self.bftk = []
self.bftexafs = []
self.labels = []
self.energy = []
self.mju = []
self.xes = []
self.E0 = 0
self.lines = []
self.lines1 = []
#mode
#0 - exafs
#1 - ft
#2 - bft
#3 - mju
#10 - Xes original
#11 - XES area Normalized
#12 - XES Max Normalized
self.mode = 0
self.initUI()
def initUI(self):
#Figures
self.fig = plt.figure(1, figsize=(15, 6))
# self.ax_exafs = self.fig.add_subplot(111)
self.canv = FigureCanvas(self.fig)
self.tbar = NavigationToolbar(self.canv, self)
fnt = self.tbar.font()
fnt.setPointSize(20)
self.tbar.setFont(fnt)
# plt.tight_layout()
self.btnCancel = QtGui.QPushButton('Exit')
self.btnCancel.clicked.connect(self.cancel)
lfig = QtGui.QVBoxLayout()
lfig.addWidget(self.tbar)
lfig.addWidget(self.canv)
lfig.addWidget(self.btnCancel)
self.setLayout(lfig)
self.canv.draw()
#wid.setLayout(lfig)
def plot(self):
# self.ax_exafs.clear()
plt.clf()
self.ax_exafs = self.fig.add_subplot(111)
if self.mode == 0: #compare exafs
for i in range(len(self.k)):
l, = self.ax_exafs.plot(self.k[i], self.exafs[i], label = self.labels[i], linewidth=1)
self.ax_exafs.set_xlabel('Wavevector k, $\AA^{-1}$')
self.ax_exafs.set_ylabel('EXAFS, $\AA^{-2}$')
self.lines.append(l)
if self.mode == 1: #compare ft
for i in range(len(self.r)):
line1, = self.ax_exafs.plot(self.r[i], self.fr[i], label = self.labels[i], linewidth=1)
line2, = self.ax_exafs.plot(self.r[i], self.fi[i], linewidth=1)
line2.set_color(line1.get_color())
line2.set_linestyle('dotted')
self.ax_exafs.set_xlabel('Distance R, $\AA$')
self.ax_exafs.set_ylabel('Fourier transform, $\AA^{-3}$')
self.lines.append(line1)
self.lines1.append(line2)
if self.mode == 2: #compare bft
for i in range(len(self.bftk)):
l, = self.ax_exafs.plot(self.bftk[i], self.bftexafs[i], label = self.labels[i], linewidth=1)
self.ax_exafs.set_xlabel('Wavevector k, $\AA^{-1}$')
self.ax_exafs.set_ylabel('EXAFS, $\AA^{-2}$')
self.lines.append(l)
if self.mode == 3: #compare mju
for i in range(len(self.energy)):
l, = self.ax_exafs.plot(self.energy[i], self.mju[i], label = self.labels[i], linewidth=1)
self.ax_exafs.set_xlabel('Energy, eV')
self.ax_exafs.set_ylabel('Absorption, a.u.')
self.lines.append(l)
if self.mode == 4: #compare xanes
for i in range(len(self.energy)):
l, = self.ax_exafs.plot(self.energy[i], self.mju[i], label = self.labels[i], linewidth=1)
self.ax_exafs.set_xlabel('Energy, eV')
self.ax_exafs.set_ylabel('Absorption, a.u.')
self.ax_exafs.axhline(y=1, linewidth=0.5, color = 'k', linestyle='--',)
self.ax_exafs.set_xlim([self.E0-75,self.E0+200])
self.lines.append(l)
if self.mode == 10: # XES original
for i in range(len(self.energy)):
l, = self.ax_exafs.plot(self.energy[i], self.xes[i], label = self.labels[i], linewidth=1)
self.ax_exafs.set_xlabel('Energy, eV')
self.ax_exafs.set_ylabel('Intensity, a.u.')
self.lines.append(l)
if self.mode == 11: # XES area normalized
for i in range(len(self.energy)):
l, = self.ax_exafs.plot(self.energy[i], self.xes[i], label = self.labels[i], linewidth=1)
self.ax_exafs.set_xlabel('Energy, eV')
self.ax_exafs.set_ylabel('Area normalized intensity')
self.lines.append(l)
self.fig.canvas.mpl_connect('pick_event', self.onpick)
self.fig.tight_layout()
box = self.ax_exafs.get_position()
self.ax_exafs.set_position([box.x0, box.y0, box.width * 0.7, box.height])
leg = self.ax_exafs.legend(loc='center left', bbox_to_anchor=(1, 0.5))
# we will set up a dict mapping legend line to orig line, and enable
# picking on the legend line
self.lined = dict()
for legline, origline in zip(leg.get_lines(), self.lines):
legline.set_picker(5) # 5 pts tolerance
self.lined[legline] = origline
if self.mode == 1:
self.lined1 = dict()
for legline, origline in zip(leg.get_lines(), self.lines1):
# legline.set_picker(5) # 5 pts tolerance
self.lined1[legline] = origline
self.canv.draw()
def cancel(self):
#do whatever you need with self.roiGroups
self.close()
def onpick(self, event):
# on the pick event, find the orig line corresponding to the
# legend proxy line, and toggle the visibility
legline = event.artist
origline = self.lined[legline]
vis = not origline.get_visible()
origline.set_visible(vis)
if self.mode == 1:
origline = self.lined1[legline]
origline.set_visible(vis)
# Change the alpha on the line in the legend so we can see what lines
# have been toggled
if vis:
legline.set_alpha(1.0)
else:
legline.set_alpha(0.2)
self.fig.canvas.draw()
