def klm_markers(self, in_z):
# Displays X-ray lines of element with atomic number Z.
# Check that Z is within bounds.
z = min(max(in_z, 1), 100)
self.display.klm = z
self.widgets.klm_element.selectitem(z-1, setentry=1)
lines = []
all_lines = self.display.k_lines + self.display.l_lines
graph = self.widgets.plot
for line in all_lines:
marker = 'KLM'+line
graph.marker_configure(marker, hide=1)
element = self.widgets.klm_element.getcurselection()[0]
show_lines = self.widgets.klm_line.getcurselection()
if (show_lines == 'K') or (show_lines == 'K & L'):
lines = lines + self.display.k_lines
if (show_lines == 'L') or (show_lines == 'K & L'):
lines = lines + self.display.l_lines
length = .25
# Convert marker sizes from fractions of display height to graph units
(ymin,ymax) = graph.yaxis_limits()
if (self.display.vlog):
l = math.exp(length*(math.log(ymax) - math.log(ymin)))
else:
l = length*(ymax-ymin)
for line in lines:
marker = 'KLM'+line
e = Xrf.lookup_xrf_line(element + ' ' + line)
if (e != 0.):
chan = self.foreground.scan.energy_to_channel(e, clip=1)
data = self.foreground.data[chan]
y = max(data, ymin+l)
graph.marker_configure(marker, coords=(chan, '-Inf', chan, y),
hide=0)
def menu_line(self, roi):
""" Private method """
line = self.widgets.line[roi].get()
energy = Xrf.lookup_xrf_line(line)
if (energy == None):
energy = Xrf.lookup_gamma_line(line)
if (energy != None):
self.roi[roi].energy = energy
self.widgets.energy[roi].setentry('%.3f' % energy)
def klm_mouse(self, event, marker):
g = self.widgets.plot
(x,y) = g.invtransform(event.x, event.y-25)
if (event.type == '7'): # Enter event - create a new text label
line = self.widgets.klm_element.getcurselection()[0] + ' ' + marker[3:]
energy = Xrf.lookup_xrf_line(line)
text = line + '\n' + ('%.3f' % energy) + ' keV'
g.marker_configure('klm_text', text=text, hide=0, coords=(x, y))
g.marker_configure(marker, outline=self.colors.highlight_klm)
elif (event.type == '8'): # Leave event - delete text label
g.marker_configure('klm_text', hide=1)
g.marker_configure(marker, outline=self.colors.klm)
def peak_label(self):
peaks=self.fit.peaks
label = self.widgets.label.get()
label = label.strip()
peaks[self.index].label = label
energy = Xrf.lookup_xrf_line(label)
if (energy == None): energy = Xrf.lookup_gamma_line(label)
if (energy != None):
peaks[self.index].initial_energy=energy
# Set the energy flag to 0, since energy is known
peaks[self.index].energy_flag=0
# Set FWHM flag to 0, since peak width will be defined by
# detector resolution
peaks[self.index].fwhm_flag=0
self.update_peaks()
def __init__(self, mca, command=None):
"""
Creates a new GUI window for calibrating energy for an Mca object.
Inputs:
mca:
An Mca instance to be calibrated. The Mca must have at least 2
Regions of Interest (ROIs) defined for a linear calibration and
2 ROIs defined for a quadratic calibration.
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
energy of each ROI.
The centroids positions are computed by fitting the
ROI counts to a Gaussian, using CARSMath.fit_gaussian.
The energy 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 Xrf.lookup_xrf_line() or Xrf.lookup_gamma_line().
Each ROI can be selectively used or omitted when doing the calibration.
The errors in the energy calibration and the FWHM of each ROI as a
function of energy, can be plotted using BltPlot.
"""
self.input_mca = mca
self.mca = copy.copy(mca)
self.exit_command = command
self.roi = self.mca.get_rois()
self.nrois = len(self.roi)
if (self.nrois < 2):
tkMessageBox.showerror(title='mcaCalibrateEnergy Error',
message='Must have at least two ROIs to perform calibration')
return
self.calibration = self.mca.get_calibration()
self.fwhm_chan = Numeric.zeros(self.nrois, Numeric.Float)
self.widgets = mcaCalibrateEnergy_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+1
total_counts = self.data[left:right]
n_sel = right - left
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.widgets.top = t = Pmw.Dialog(command=self.menu_ok_cancel,
buttons=('OK', 'Apply', 'Cancel'),
title='mcaCalibrateEnergy')
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='Centroid'); t.grid(row=0, column=2)
t = Label(box, text='FWHM'); t.grid(row=0, column=3)
t = Label(box, text='Energy'); t.grid(row=0, column=4)
t = Label(box, text='Fluor. line'); t.grid(row=0, column=5)
t = Label(box, text='Energy diff.'); t.grid(row=0, column=6)
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.centroid[i] = t = Pmw.EntryField(box,
value=('%.3f' % self.roi[i].centroid),
entry_width=text_width, entry_justify=CENTER,
command=lambda s=self, r=i: s.menu_centroid(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)
# If the ROI energy is zero, then try to use the label to lookup an
# XRF line energy
if (self.roi[i].energy == 0.0):
self.roi[i].energy = Xrf.lookup_xrf_line(self.roi[i].label)
if (self.roi[i].energy == None):
self.roi[i].energy = Xrf.lookup_gamma_line(self.roi[i].label)
if (self.roi[i].energy == None): self.roi[i].energy=0.0
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=4)
self.widgets.line[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_line(r))
t.grid(row=row, column=5)
self.widgets.energy_diff[i] = t = Label(box,
text=('%.3f' % 0.0), width=text_width,
justify=CENTER, borderwidth=1, relief=SOLID)
t.grid(row=row, column=6)
row = Frame(top, borderwidth=1, relief=SOLID); row.pack(fill=X, pady=3)
self.widgets.fit_type = t = Pmw.OptionMenu(row, labelpos=N,
label_text='Calibration type:',
items=('Linear','Quadratic'))
t.pack(side=LEFT, anchor=S)
self.widgets.do_fit = t = Button(row, text='Compute calibration',
command=self.menu_do_fit)
t.pack(side=LEFT, anchor=S)
self.widgets.plot_cal = t = Button(row, text='Plot calibration error',
command=self.menu_plot_calibration)
t.pack(side=LEFT, anchor=S)
self.widgets.plot_fwhm = t = Button(row, text='Plot FWHM',
command=self.menu_plot_fwhm)
t.pack(side=LEFT, anchor=S)
row = Frame(top, borderwidth=1, relief=SOLID); row.pack(fill=X, pady=3)
text_width=10
t = Label(row, text='Calibration coefficients'); t.pack()
self.widgets.cal_units = t = Pmw.EntryField(row,
label_text='Units:', labelpos=W,
value=self.calibration.units,
entry_width=text_width, entry_justify=CENTER)
t.pack(side=LEFT)
self.widgets.cal_offset = t = Pmw.EntryField(row,
label_text='Offset:', labelpos=W,
value=self.calibration.offset,
entry_width=text_width, entry_justify=CENTER)
t.pack(side=LEFT)
self.widgets.cal_slope = t = Pmw.EntryField(row,
label_text='Slope:', labelpos=W,
value=self.calibration.slope,
entry_width=text_width, entry_justify=CENTER)
t.pack(side=LEFT)
self.widgets.cal_quad = t = Pmw.EntryField(row,
label_text='Quadratic:', labelpos=W,
value=self.calibration.quad,
entry_width=text_width, entry_justify=CENTER)
t.pack(side=LEFT)
