def menu_label(self, roi):
""" Private method """
label = self.widgets.label[roi].get()
d_spacing = jcpds.lookup_jcpds_line(label)
if (d_spacing != None):
self.roi[roi].d_spacing = d_spacing
self.widgets.d_spacing[roi].setentry('%.3f' % d_spacing)
self.menu_do_fit()
self.roi[roi].label = label
def menu_label(self, roi):
""" Private method """
label = self.widgets.label[roi].get()
d_spacing = jcpds.lookup_jcpds_line(label)
if (d_spacing != None):
self.roi[roi].d_spacing = d_spacing
self.widgets.d_spacing[roi].setentry('%.3f' % d_spacing)
self.menu_do_fit()
self.roi[roi].label=label
def __init__(self, mca, command=None):
"""
Creates a new GUI window for calibrating 2-theta for an Mca object.
Inputs:
mca:
An Mca instance to be calibrated. The Mca must have at least 1
Regions of Interest (ROI) defined.
Keywords:
command:
A callback command that will be executed if the OK button on
the GUI window is pressed. The callback will be invoked as:
command(exit_status)
where exit_status is 1 if OK was pressed, and 0 if Cancel was
pressed or the window was closed with the window manager.
Procedure:
The calibration is done by determining the centroid position and
d-spacing of each ROI.
The centroids positions are computed by fitting the
ROI counts to a Gaussian, using CARSMath.fit_gaussian.
The d-spacing the ROI can be entered manually in the GUI window, or it
can be determined automatically if the label of the ROI can be
successfully used in jcpds.lookup_jcpds_line().
Each ROI can be selectively used or omitted when doing the calibration.
The errors in the 2-theta calibration, can be plotted using BltPlot.
"""
self.input_mca = mca
self.mca = copy.deepcopy(mca)
self.exit_command = command
self.roi = self.mca.get_rois()
self.nrois = len(self.roi)
if (self.nrois < 1):
tkMessageBox.showerror(
title='mcaCalibrate2theta Error',
message='Must have at least one ROI to perform calibration')
return
self.calibration = self.mca.get_calibration()
self.fwhm_chan = Numeric.zeros(self.nrois, Numeric.Float)
self.two_theta = Numeric.zeros(self.nrois, Numeric.Float)
self.widgets = mcaCalibrate2theta_widgets(self.nrois)
self.data = self.mca.get_data()
# Compute the centroid and FWHM of each ROI
for i in range(self.nrois):
left = self.roi[i].left
right = self.roi[i].right
total_counts = self.data[left:right + 1]
n_sel = right - left + 1
sel_chans = left + Numeric.arange(n_sel)
left_counts = self.data[left]
right_counts = self.data[right]
bgd_counts = (left_counts + Numeric.arange(float(n_sel)) /
(n_sel - 1) * (right_counts - left_counts))
net_counts = total_counts - bgd_counts
net = Numeric.sum(net_counts)
if ((net > 0.) and (n_sel >= 3)):
amplitude, centroid, fwhm = CARSMath.fit_gaussian(
sel_chans, net_counts)
self.roi[i].centroid = centroid
self.fwhm_chan[i] = fwhm
else:
self.roi[i].centroid = (left + right) / 2.
self.fwhm_chan[i] = right - left
self.roi[i].fwhm = (
self.mca.channel_to_energy(self.roi[i].centroid +
self.fwhm_chan[i] / 2.) -
self.mca.channel_to_energy(self.roi[i].centroid -
self.fwhm_chan[i] / 2.))
self.roi[i].energy = self.mca.channel_to_energy(
self.roi[i].centroid)
self.widgets.top = t = Pmw.Dialog(command=self.menu_ok_cancel,
buttons=('OK', 'Apply', 'Cancel'),
title='mcaCalibrate2theta')
top = t.component('dialogchildsite')
box = Frame(top, borderwidth=1, relief=SOLID)
box.pack(fill=X, pady=3)
t = Label(box, text='ROI')
t.grid(row=0, column=0)
t = Label(box, text='Use?')
t.grid(row=0, column=1)
t = Label(box, text='Energy')
t.grid(row=0, column=2)
t = Label(box, text='FWHM')
t.grid(row=0, column=3)
t = Label(box, text='D-spacing')
t.grid(row=0, column=4)
t = Label(box, text='HKL')
t.grid(row=0, column=5)
t = Label(box, text='Two-theta')
t.grid(row=0, column=6)
t = Label(box, text='Two-theta diff.')
t.grid(row=0, column=7)
text_width = 10
for i in range(self.nrois):
row = i + 1
t = Label(box, text=str(i))
t.grid(row=row, column=0)
self.widgets.use_flag[i] = t = Pmw.OptionMenu(
box,
items=('No', 'Yes'),
initialitem=self.roi[i].use,
command=lambda e, s=self, r=i: s.menu_use(e, r))
t.grid(row=row, column=1)
self.widgets.energy[i] = t = Pmw.EntryField(
box,
value=('%.3f' % self.roi[i].energy),
entry_width=text_width,
entry_justify=CENTER,
command=lambda s=self, r=i: s.menu_energy(r))
t.grid(row=row, column=2)
self.widgets.fwhm[i] = t = Label(box,
text=('%.3f' % self.roi[i].fwhm),
width=text_width,
justify=CENTER,
borderwidth=1,
relief=SOLID)
t.grid(row=row, column=3)
d = jcpds.lookup_jcpds_line(self.roi[i].label)
if (d != None): self.roi[i].d_spacing = d
self.widgets.d_spacing[i] = t = Pmw.EntryField(
box,
value=('%.3f' % self.roi[i].d_spacing),
entry_width=text_width,
entry_justify=CENTER,
command=lambda s=self, r=i: s.menu_d_spacing(r))
t.grid(row=row, column=4)
self.widgets.label[i] = t = Pmw.EntryField(
box,
value=str(self.roi[i].label),
entry_width=text_width,
entry_justify=CENTER,
command=lambda s=self, r=i: s.menu_label(r))
t.grid(row=row, column=5)
self.widgets.two_theta[i] = t = Label(box,
text=('%.3f' %
self.two_theta[i]),
width=text_width,
justify=CENTER,
borderwidth=1,
relief=SOLID)
t.grid(row=row, column=6)
self.widgets.two_theta_diff[i] = t = Label(box,
text=('%.3f' % 0.0),
width=text_width,
justify=CENTER,
borderwidth=1,
relief=SOLID)
t.grid(row=row, column=7)
row = Frame(top, borderwidth=1, relief=SOLID)
row.pack(fill=X, pady=3)
self.widgets.do_fit = t = Button(row,
text='Compute 2-theta',
command=self.menu_do_fit)
t.pack(side=LEFT, anchor=S)
self.widgets.plot_cal = t = Button(row,
text='Plot 2-theta error',
command=self.menu_plot_calibration)
t.pack(side=LEFT, anchor=S)
self.widgets.two_theta_fit = t = Pmw.EntryField(
row,
label_text='Two-theta',
labelpos=W,
value=self.calibration.two_theta,
entry_width=20,
entry_justify=CENTER,
command=self.menu_two_theta)
t.pack(side=LEFT)
self.menu_do_fit()
def __init__(self, mca, command=None):
"""
Creates a new GUI window for calibrating 2-theta for an Mca object.
Inputs:
mca:
An Mca instance to be calibrated. The Mca must have at least 1
Regions of Interest (ROI) defined.
Keywords:
command:
A callback command that will be executed if the OK button on
the GUI window is pressed. The callback will be invoked as:
command(exit_status)
where exit_status is 1 if OK was pressed, and 0 if Cancel was
pressed or the window was closed with the window manager.
Procedure:
The calibration is done by determining the centroid position and
d-spacing of each ROI.
The centroids positions are computed by fitting the
ROI counts to a Gaussian, using CARSMath.fit_gaussian.
The d-spacing the ROI can be entered manually in the GUI window, or it
can be determined automatically if the label of the ROI can be
successfully used in jcpds.lookup_jcpds_line().
Each ROI can be selectively used or omitted when doing the calibration.
The errors in the 2-theta calibration, can be plotted using BltPlot.
"""
self.input_mca = mca
self.mca = copy.deepcopy(mca)
self.exit_command = command
self.roi = self.mca.get_rois()
self.nrois = len(self.roi)
if (self.nrois < 1):
tkMessageBox.showerror(title='mcaCalibrate2theta Error',
message='Must have at least one ROI to perform calibration')
return
self.calibration = self.mca.get_calibration()
self.fwhm_chan = Numeric.zeros(self.nrois, Numeric.Float)
self.two_theta = Numeric.zeros(self.nrois, Numeric.Float)
self.widgets = mcaCalibrate2theta_widgets(self.nrois)
self.data = self.mca.get_data()
# Compute the centroid and FWHM of each ROI
for i in range(self.nrois):
left = self.roi[i].left
right = self.roi[i].right
total_counts = self.data[left:right+1]
n_sel = right - left + 1
sel_chans = left + Numeric.arange(n_sel)
left_counts = self.data[left]
right_counts = self.data[right]
bgd_counts = (left_counts + Numeric.arange(float(n_sel))/(n_sel-1) *
(right_counts - left_counts))
net_counts = total_counts - bgd_counts
net = Numeric.sum(net_counts)
if ((net > 0.) and (n_sel >= 3)):
amplitude, centroid, fwhm = CARSMath.fit_gaussian(sel_chans,
net_counts)
self.roi[i].centroid = centroid
self.fwhm_chan[i] = fwhm
else:
self.roi[i].centroid = (left + right)/2.
self.fwhm_chan[i] = right-left
self.roi[i].fwhm = (self.mca.channel_to_energy(self.roi[i].centroid +
self.fwhm_chan[i]/2.) -
self.mca.channel_to_energy(self.roi[i].centroid -
self.fwhm_chan[i]/2.))
self.roi[i].energy = self.mca.channel_to_energy(self.roi[i].centroid)
self.widgets.top = t = Pmw.Dialog(command=self.menu_ok_cancel,
buttons=('OK', 'Apply', 'Cancel'),
title='mcaCalibrate2theta')
top = t.component('dialogchildsite')
box = Frame(top, borderwidth=1, relief=SOLID); box.pack(fill=X, pady=3)
t = Label(box, text='ROI'); t.grid(row=0, column=0)
t = Label(box, text='Use?'); t.grid(row=0, column=1)
t = Label(box, text='Energy'); t.grid(row=0, column=2)
t = Label(box, text='FWHM'); t.grid(row=0, column=3)
t = Label(box, text='D-spacing'); t.grid(row=0, column=4)
t = Label(box, text='HKL'); t.grid(row=0, column=5)
t = Label(box, text='Two-theta'); t.grid(row=0, column=6)
t = Label(box, text='Two-theta diff.'); t.grid(row=0, column=7)
text_width=10
for i in range(self.nrois):
row=i+1
t = Label(box, text=str(i));
t.grid(row=row, column=0)
self.widgets.use_flag[i] = t = Pmw.OptionMenu(box,
items=('No','Yes'),
initialitem = self.roi[i].use,
command=lambda e, s=self, r=i: s.menu_use(e,r))
t.grid(row=row, column=1)
self.widgets.energy[i] = t = Pmw.EntryField(box,
value=('%.3f' % self.roi[i].energy),
entry_width=text_width, entry_justify=CENTER,
command=lambda s=self, r=i: s.menu_energy(r))
t.grid(row=row, column=2)
self.widgets.fwhm[i] = t = Label(box,
text=('%.3f' % self.roi[i].fwhm), width=text_width,
justify=CENTER, borderwidth=1, relief=SOLID)
t.grid(row=row, column=3)
d = jcpds.lookup_jcpds_line(self.roi[i].label)
if (d != None): self.roi[i].d_spacing = d
self.widgets.d_spacing[i] = t = Pmw.EntryField(box,
value=('%.3f' % self.roi[i].d_spacing),
entry_width=text_width, entry_justify=CENTER,
command=lambda s=self, r=i: s.menu_d_spacing(r))
t.grid(row=row, column=4)
self.widgets.label[i] = t = Pmw.EntryField(box,
value=str(self.roi[i].label),
entry_width=text_width, entry_justify=CENTER,
command=lambda s=self, r=i: s.menu_label(r))
t.grid(row=row, column=5)
self.widgets.two_theta[i] = t = Label(box,
text=('%.3f' % self.two_theta[i]), width=text_width,
justify=CENTER, borderwidth=1, relief=SOLID)
t.grid(row=row, column=6)
self.widgets.two_theta_diff[i] = t = Label(box,
text=('%.3f' % 0.0), width=text_width,
justify=CENTER, borderwidth=1, relief=SOLID)
t.grid(row=row, column=7)
row = Frame(top, borderwidth=1, relief=SOLID); row.pack(fill=X, pady=3)
self.widgets.do_fit = t = Button(row, text='Compute 2-theta',
command=self.menu_do_fit)
t.pack(side=LEFT, anchor=S)
self.widgets.plot_cal = t = Button(row, text='Plot 2-theta error',
command=self.menu_plot_calibration)
t.pack(side=LEFT, anchor=S)
self.widgets.two_theta_fit = t = Pmw.EntryField(row,
label_text='Two-theta', labelpos=W,
value=self.calibration.two_theta,
entry_width=20, entry_justify=CENTER,
command=self.menu_two_theta)
t.pack(side=LEFT)
self.menu_do_fit()
