def plot_avg_xas_single(bin_xas, detector):
plotview = NXPlotView()
if detector == "I0":
y_array = bin_xas.i0
elif detector == "TEY":
y_array = bin_xas.tey
elif detector == "DIODE" or detector == "PD1":
y_array = bin_xas.diode
elif detector == "PFY_SDD1":
y_array = bin_xas.pfy_sdd1
elif detector == "PFY_SDD2":
y_array = bin_xas.pfy_sdd2
elif detector == "PFY_SDD3":
y_array = bin_xas.pfy_sdd3
elif detector == "PFY_SDD4":
y_array = bin_xas.pfy_sdd4
else:
return "Invalid dividend name"
plotview.figure.clf()
ax = plotview.figure.gca()
ax.axes.get_xaxis().set_visible(True)
ax.axes.get_yaxis().set_visible(True)
ax.plot(bin_xas.energy, y_array)
ax.set_xlabel('Energy (eV)')
ax.set_ylabel(detector)
plotview.draw()
def plot_data(self):
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect = 'equal'
self.plotview.ytab.flipped = True
self.clear_peaks()
def load_file(self):
self.data = load_image(self.get_filename())
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect = 'equal'
self.plotview.ytab.flipped = True
def plot_data(self):
if self.plotview is None:
if 'Mask Editor' in plotviews:
self.plotview = plotviews['Mask Editor']
else:
self.plotview = NXPlotView('Mask Editor')
self.plotview.plot(self.data, log=True)
self.plotview.aspect='equal'
self.plotview.ytab.flipped = True
self.plotview.draw()
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
x, y, z = [
self.table_view.model().peak_list[row][i] for i in range(1, 4)
]
xmin, xmax = max(0, x - 200), min(x + 200, data.nxsignal.shape[2])
ymin, ymax = max(0, y - 200), min(y + 200, data.nxsignal.shape[1])
zmin, zmax = max(0, z - 200), min(z + 200, data.nxsignal.shape[0])
zslab = np.s_[z, ymin:ymax, xmin:xmax]
if self.plotview is None:
self.plotview = NXPlotView('X-Y Projection')
self.plotview.plot(data[zslab], log=True)
self.plotview.crosshairs(x, y)
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
i, x, y, z = [
self.table_view.model().peak_list[row][i] for i in range(4)
]
signal = data.nxsignal
xmin, xmax = max(0, x - 200), min(x + 200, signal.shape[2])
ymin, ymax = max(0, y - 200), min(y + 200, signal.shape[1])
zmin, zmax = max(0, z - 20), min(z + 20, signal.shape[0])
zslab = np.s_[zmin:zmax, ymin:ymax, xmin:xmax]
if self.plotview is None:
self.plotview = NXPlotView('Peak Plot')
self.plotview.plot(data[zslab], log=True)
self.plotview.ax.set_title('%s: Peak %s' % (data.nxtitle, i))
self.plotview.ztab.maxbox.setValue(z)
self.plotview.aspect = 'equal'
self.plotview.crosshairs(x, y, color='r', linewidth=0.5)
def load_file(self):
self.data = load_image(self.get_filename())
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect='equal'
self.plotview.ytab.flipped = True
def plot_data(self):
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect='equal'
self.plotview.ytab.flipped = True
self.clear_peaks()
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
x, y, z = [self.table_view.model().peak_list[row][i] for i in range(1, 4)]
xmin, xmax = max(0,x-200), min(x+200,data.nxsignal.shape[2])
ymin, ymax = max(0,y-200), min(y+200,data.nxsignal.shape[1])
zmin, zmax = max(0,z-200), min(z+200,data.nxsignal.shape[0])
zslab=np.s_[z,ymin:ymax,xmin:xmax]
if self.plotview is None:
self.plotview = NXPlotView('X-Y Projection')
self.plotview.plot(data[zslab], log=True)
self.plotview.crosshairs(x, y)
def plot_cake(self):
if 'Cake Plot' in plotviews:
plotview = plotviews['Cake Plot']
else:
plotview = NXPlotView('Cake Plot')
if not self.is_calibrated:
raise NeXusError('No refinement performed')
res = self.cake_geometry.integrate2d(self.counts,
1024,
1024,
method='csr',
unit='2th_deg',
correctSolidAngle=True)
self.cake_data = NXdata(res[0],
(NXfield(res[2], name='azimumthal_angle'),
NXfield(res[1], name='polar_angle')))
self.cake_data['title'] = self.entry['instrument/calibration/title']
plotview.plot(self.cake_data, log=True)
wavelength = self.parameters['wavelength'].value
polar_angles = [
2 * np.degrees(np.arcsin(wavelength / (2 * d)))
for d in self.calibrant.dSpacing
]
plotview.vlines([
polar_angle
for polar_angle in polar_angles if polar_angle < plotview.xaxis.max
],
linestyle=':',
color='r')
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 plot_cake(self):
if 'Cake Plot' in plotviews:
plotview = plotviews['Cake Plot']
else:
plotview = NXPlotView('Cake Plot')
if not self.is_calibrated:
raise NeXusError('No refinement performed')
res = self.cake_geometry.integrate2d(self.counts,
1024, 1024,
method='csr',
unit='2th_deg',
correctSolidAngle=True)
self.cake_data = NXdata(res[0], (NXfield(res[2], name='azimumthal_angle'),
NXfield(res[1], name='polar_angle')))
self.cake_data['title'] = self.entry['instrument/calibration/title']
plotview.plot(self.cake_data, log=True)
wavelength = self.parameters['wavelength'].value
polar_angles = [2 * np.degrees(np.arcsin(wavelength/(2*d)))
for d in self.calibrant.dSpacing]
plotview.vlines([polar_angle for polar_angle in polar_angles
if polar_angle < plotview.xaxis.max],
linestyle=':', color='r')
class LoadDialog(BaseDialog):
def __init__(self, parent=None):
super(LoadDialog, self).__init__(parent)
self.plotview = None
self.data = None
self.set_layout(self.filebox('Choose Powder Calibration File'),
self.action_buttons(('Load File', self.load_file)),
self.select_entry(), self.close_buttons(save=True))
self.set_title('Loading Calibration')
def load_file(self):
self.data = load_image(self.get_filename())
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect = 'equal'
self.plotview.ytab.flipped = True
def accept(self):
if self.data is None:
self.reject()
else:
if 'calibration' in self.entry['instrument']:
if confirm_action(
"Do you want to overwrite existing calibration data?"):
del self.entry['instrument/calibration']
else:
self.reject()
return
self.entry['instrument/calibration'] = self.data
super(LoadDialog, self).accept()
if 'Powder Calibration' in plotviews and self.plotview == plotviews[
'Powder Calibration']:
self.plotview.close_view()
def reject(self):
super(LoadDialog, self).reject()
if 'Powder Calibration' in plotviews and self.plotview == plotviews[
'Powder Calibration']:
self.plotview.close_view()
class LoadDialog(BaseDialog):
def __init__(self, parent=None):
super(LoadDialog, self).__init__(parent)
self.plotview = None
self.data = None
self.set_layout(self.filebox('Choose Powder Calibration File'),
self.action_buttons(('Load File', self.load_file)),
self.select_entry(),
self.close_buttons(save=True))
self.set_title('Loading Calibration')
def load_file(self):
self.data = load_image(self.get_filename())
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect='equal'
self.plotview.ytab.flipped = True
def accept(self):
if self.data is None:
self.reject()
else:
if 'calibration' in self.entry['instrument']:
if confirm_action(
"Do you want to overwrite existing calibration data?"):
del self.entry['instrument/calibration']
else:
self.reject()
return
self.entry['instrument/calibration'] = self.data
super(LoadDialog, self).accept()
if 'Powder Calibration' in plotviews and self.plotview == plotviews['Powder Calibration']:
self.plotview.close_view()
def reject(self):
super(LoadDialog, self).reject()
if 'Powder Calibration' in plotviews and self.plotview == plotviews['Powder Calibration']:
self.plotview.close_view()
def plot_normalized(xas, dividend, divisor):
plotview = NXPlotView()
# convert the string to uppercase
dividend = dividend.upper()
divisor = divisor.upper()
if dividend == "I0":
dividend_array = xas.i0
elif dividend == "TEY":
dividend_array = xas.tey
elif dividend == "DIODE" or dividend == "PD1":
dividend_array = xas.diode
elif dividend == "PFY_SDD1":
dividend_array = xas.pfy_sdd1
elif dividend == "PFY_SDD2":
dividend_array = xas.pfy_sdd2
elif dividend == "PFY_SDD3":
dividend_array = xas.pfy_sdd3
elif dividend == "PFY_SDD4":
dividend_array = xas.pfy_sdd4
else:
return "Invalid dividend name"
if divisor == "I0":
divisor_array = xas.i0
elif divisor == "TEY":
divisor_array = xas.tey
elif divisor == "DIODE" or divisor == "PD1":
divisor_array = xas.diode
elif divisor == "PFY_SDD1":
divisor_array = xas.pfy_sdd1
elif divisor == "PFY_SDD2":
divisor_array = xas.pfy_sdd2
elif divisor == "PFY_SDD3":
divisor_array = xas.pfy_sdd3
elif divisor == "PFY_SDD4":
divisor_array = xas.pfy_sdd4
else:
return "Invalid divisor name"
normalized_array = np.array(dividend_array) / np.array(divisor_array)
# the old code using Matplotlib to plot diagrams
# plt.figure()
# plt.plot(xas.energy, normalized_array)
# str_y_axis = StringIO()
# str_y_axis.write(dividend + ' / ' + divisor)
# plt.ylabel(str_y_axis.getvalue())
# plt.title("Averaged %s / Averaged %s" % (dividend, divisor))
plotview.figure.clf()
ax = plotview.figure.gca()
ax.axes.get_xaxis().set_visible(True)
ax.axes.get_yaxis().set_visible(True)
ax.plot(xas.energy, normalized_array)
ax.set_xlabel('Energy (eV)')
str_y_axis = StringIO()
str_y_axis.write(dividend + ' / ' + divisor)
ax.set_ylabel(str_y_axis.getvalue())
ax.set_title("Averaged %s / Averaged %s" % (dividend, divisor))
plotview.draw()
return xas.energy, normalized_array
def plot_avg_xas_all(bin_xas):
"""
Generate all plots (matplotlib figures) for averaged data at once
:return: None
"""
print("Plotting average XAS.")
# matplotlib.rcParams['figure.figsize'] = (14, 22)
plotview = NXPlotView()
plotview.setMinimumHeight(200)
plotview.resize(1400, 800)
plotview.figure.clf()
en = bin_xas.energy
i0 = bin_xas.i0
tey = bin_xas.tey
diode = bin_xas.diode
pfy_sdd1 = bin_xas.pfy_sdd1
pfy_sdd2 = bin_xas.pfy_sdd2
pfy_sdd3 = bin_xas.pfy_sdd3
pfy_sdd4 = bin_xas.pfy_sdd4
plt.subplot(2, 4, 1)
plt.plot(en, tey)
# add lable for x and y axis
plt.xlabel('Energy (eV)')
plt.ylabel('TEY')
# add title of the figure
plt.title('Binned(Averaged) TEY')
plt.subplot(2, 4, 2)
plt.plot(en, i0)
plt.xlabel('Energy (eV)')
plt.ylabel('I0')
plt.title('Binned(Averaged) I0')
plt.subplot(2, 4, 3)
plt.plot(en, diode)
plt.xlabel('Energy (eV)')
plt.ylabel('Diode')
plt.title('Binned(Averaged) Diode')
plt.subplot(2, 4, 5)
plt.plot(en, pfy_sdd1)
plt.xlabel('Energy (eV)')
plt.ylabel('PFY_SDD1')
plt.title('Binned(Averaged) PFY_SDD1')
plt.subplot(2, 4, 6)
plt.plot(en, pfy_sdd2)
plt.xlabel('Energy (eV)')
plt.ylabel('PFY_SDD2')
plt.title('Binned(Averaged) PFY_SDD2')
plt.subplot(2, 4, 7)
plt.plot(en, pfy_sdd3)
plt.xlabel('Energy (eV)')
plt.ylabel('PFY_SDD3')
plt.title('Binned(Averaged) PFY_SDD3')
plt.subplot(2, 4, 8)
plt.plot(en, pfy_sdd4)
plt.xlabel('Energy (eV)')
plt.ylabel('PFY_SDD4')
plt.title('Binned(Averaged) PFY_SDD4')
plt.tight_layout()
# use plotview from Nexpy to generate plots
plotview.figure = plt
plotview.tab_widget.removeTab(0)
plotview.tab_widget.removeTab(0)
plotview.draw()
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))
class MaskDialog(BaseDialog):
def __init__(self, parent=None):
super(MaskDialog, self).__init__(parent)
self.plotview = None
self.shapes = []
self.select_entry(self.choose_entry)
self.shape_box = self.select_box(['Rectangle', 'Circle'])
self.set_layout(self.entry_layout,
self.make_layout(
self.action_buttons(('Add Shape', self.add_shape)),
self.shape_box),
self.close_buttons(save=True))
self.set_title('Mask Data')
def choose_entry(self):
if 'calibration' not in self.entry['instrument']:
raise NeXusError('Please load calibration data to this entry')
self.data = self.entry['instrument/calibration']
self.counts = self.data.nxsignal.nxvalue
self.mask = self.entry['instrument/detector/pixel_mask'].nxvalue
self.plot_data()
shape = self.data.nxsignal.shape
def plot_data(self):
if self.plotview is None:
if 'Mask Editor' in plotviews:
self.plotview = plotviews['Mask Editor']
else:
self.plotview = NXPlotView('Mask Editor')
self.plotview.plot(self.data, log=True)
self.plotview.aspect='equal'
self.plotview.ytab.flipped = True
self.plotview.draw()
def add_shape(self):
self.plotview.deactivate()
xlo, xhi = self.plotview.xaxis.lo, self.plotview.xaxis.hi
ylo, yhi = self.plotview.yaxis.lo, self.plotview.yaxis.hi
xc, yc = xlo + 0.5 * (xhi - xlo), ylo + 0.5 * (yhi - ylo)
r = (xhi - xlo) / 4
if self.shape_box.currentText() == 'Rectangle':
self.shapes.append(NXrectangle(xc-r, yc-r, 2*r, 2*r,
border_tol=0.1, plotview=self.plotview,
facecolor='r', edgecolor='k',
linewidth=1, alpha=0.3))
else:
self.shapes.append(NXcircle(xc, yc, r, border_tol=0.1,
plotview=self.plotview,
facecolor='r', edgecolor='k',
linewidth=1, alpha=0.3))
self.plotview.draw()
self.shapes[-1].connect()
def accept(self):
x, y = np.arange(self.mask.shape[1]), np.arange(self.mask.shape[0])
for shape in self.shapes:
if isinstance(shape, NXrectangle):
rect = shape.rectangle
x0, y0 = int(rect.get_x()), int(rect.get_y())
x1, y1 = int(x0+rect.get_width()), int(y0+rect.get_height())
self.mask[y0:y1,x0:x1] = 1
else:
circle = shape.circle
xc, yc = circle.center
r = circle.radius
inside = (x[None,:]-int(xc))**2+(y[:,None]-int(yc))**2 < r**2
self.mask = self.mask | inside
self.mask[np.where(self.counts<0)] = 1
self.entry['instrument/detector/pixel_mask'] = self.mask
super(MaskDialog, self).accept()
if 'Mask Editor' in plotviews:
plotviews['Mask Editor'].close_view()
def reject(self):
super(MaskDialog, self).reject()
if 'Mask Editor' in plotviews:
plotviews['Mask Editor'].close_view()
class RefineLatticeDialog(BaseDialog):
def __init__(self, parent=None):
super(RefineLatticeDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine(self.entry)
self.refine.read_parameters()
self.parameters = GridParameters()
self.parameters.add('symmetry', self.refine.symmetries, 'Symmetry',
None, self.set_symmetry)
self.parameters.add('a', self.refine.a, 'Unit Cell - a (Ang)', True)
self.parameters.add('b', self.refine.b, 'Unit Cell - b (Ang)', True)
self.parameters.add('c', self.refine.c, 'Unit Cell - c (Ang)', True)
self.parameters.add('alpha', self.refine.alpha, 'Unit Cell - alpha (deg)', False)
self.parameters.add('beta', self.refine.beta, 'Unit Cell - beta (deg)', False)
self.parameters.add('gamma', self.refine.gamma, 'Unit Cell - gamma (deg)', False)
self.parameters.add('wavelength', self.refine.wavelength, 'Wavelength (Ang)', False)
self.parameters.add('distance', self.refine.distance, 'Distance (mm)', False)
self.parameters.add('yaw', self.refine.yaw, 'Yaw (deg)', False)
self.parameters.add('pitch', self.refine.pitch, 'Pitch (deg)', False)
self.parameters.add('roll', self.refine.roll, 'Roll (deg)')
self.parameters.add('xc', self.refine.xc, 'Beam Center - x', False)
self.parameters.add('yc', self.refine.yc, 'Beam Center - y', False)
self.parameters.add('phi_start', self.refine.phi_start, 'Phi Start (deg)', False)
self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)')
self.parameters.add('chi_start', self.refine.chi_start, 'Chi Start (deg)', False)
self.parameters.add('chi_step', self.refine.chi_step, 'Chi Step (deg)')
self.parameters.add('omega_start', self.refine.omega_start, 'Omega Start (deg)', False)
self.parameters.add('omega_step', self.refine.omega_step, 'Omega Step (deg)')
self.parameters.add('polar', self.refine.polar_max,
'Max. Polar Angle (deg)', None, self.set_polar_max)
self.parameters.add('polar_tolerance', self.refine.polar_tolerance, 'Polar Angle Tolerance')
self.parameters.add('peak_tolerance', self.refine.peak_tolerance, 'Peak Angle Tolerance')
self.parameters.add('orientation_matrix', False, 'Orientation Matrix', False)
self.refine_buttons = self.action_buttons(
('Refine Angles', self.refine_angles),
('Refine HKLs', self.refine_hkls),
('Restore', self.restore_parameters),
('Reset', self.reset_parameters))
self.lattice_buttons = self.action_buttons(
('Plot', self.plot_lattice),
('List', self.list_peaks),
('Save', self.write_parameters))
self.set_layout(self.entry_layout, self.parameters.grid(),
self.refine_buttons, self.lattice_buttons,
self.close_buttons())
self.parameters.grid_layout.setVerticalSpacing(1)
self.set_title('Refining Lattice')
self.parameters['symmetry'].value = self.refine.symmetry
self.set_symmetry()
self.peaks_box = None
def choose_entry(self):
self.refine = NXRefine(self.entry)
self.update_parameters()
def update_parameters(self):
self.parameters['a'].value = self.refine.a
self.parameters['b'].value = self.refine.b
self.parameters['c'].value = self.refine.c
self.parameters['alpha'].value = self.refine.alpha
self.parameters['beta'].value = self.refine.beta
self.parameters['gamma'].value = self.refine.gamma
self.parameters['wavelength'].value = self.refine.wavelength
self.parameters['distance'].value = self.refine.distance
self.parameters['yaw'].value = self.refine.yaw
self.parameters['pitch'].value = self.refine.pitch
self.parameters['roll'].value = self.refine.roll
self.parameters['xc'].value = self.refine.xc
self.parameters['yc'].value = self.refine.yc
self.parameters['phi_start'].value = self.refine.phi_start
self.parameters['phi_step'].value = self.refine.phi_step
self.parameters['chi_start'].value = self.refine.chi_start
self.parameters['chi_step'].value = self.refine.chi_step
self.parameters['omega_start'].value = self.refine.omega_start
self.parameters['omega_step'].value = self.refine.omega_step
self.parameters['polar'].value = self.refine.polar_max
self.parameters['polar_tolerance'].value = self.refine.polar_tolerance
try:
self.refine.polar_angles, self.refine.azimuthal_angles = \
self.refine.calculate_angles(self.refine.xp, self.refine.yp)
except Exception:
pass
def transfer_parameters(self):
self.refine.a, self.refine.b, self.refine.c, \
self.refine.alpha, self.refine.beta, self.refine.gamma = \
self.get_lattice_parameters()
self.refine.set_symmetry()
self.refine.wavelength = self.get_wavelength()
self.refine.distance = self.get_distance()
self.refine.yaw, self.refine.pitch, self.refine.roll = self.get_tilts()
self.refine.xc, self.refine.yc = self.get_centers()
self.refine.phi_start, self.refine.phi_step = self.get_phi()
self.refine.chi_start, self.refine.chi_step = self.get_chi()
self.refine.omega_start, self.refine.omega_step = self.get_omega()
self.refine.polar_max = self.get_polar_max()
self.refine.polar_tol = self.get_tolerance()
self.refine.polar_angles
def write_parameters(self):
self.transfer_parameters()
polar_angles, azimuthal_angles = self.refine.calculate_angles(
self.refine.xp, self.refine.yp)
self.refine.write_angles(polar_angles, azimuthal_angles)
self.refine.write_parameters()
def get_symmetry(self):
return self.parameters['symmetry'].value
def set_symmetry(self):
self.refine.symmetry = self.get_symmetry()
self.refine.set_symmetry()
self.update_parameters()
if self.refine.symmetry == 'cubic':
self.parameters['b'].vary = False
self.parameters['c'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'tetragonal':
self.parameters['b'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'orthorhombic':
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'hexagonal':
self.parameters['b'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'monoclinic':
self.parameters['alpha'].vary = False
self.parameters['gamma'].vary = False
def get_lattice_parameters(self):
return (self.parameters['a'].value,
self.parameters['b'].value,
self.parameters['c'].value,
self.parameters['alpha'].value,
self.parameters['beta'].value,
self.parameters['gamma'].value)
def get_wavelength(self):
return self.parameters['wavelength'].value
def get_distance(self):
return self.parameters['distance'].value
def get_tilts(self):
return (self.parameters['yaw'].value,
self.parameters['pitch'].value,
self.parameters['roll'].value)
def get_centers(self):
return self.parameters['xc'].value, self.parameters['yc'].value
def get_polar_max(self):
return self.parameters['polar'].value
def set_polar_max(self):
self.refine.polar_max = self.get_polar_max()
def get_tolerance(self):
return self.parameters['polar_tolerance'].value
def get_phi(self):
return (self.parameters['phi_start'].value,
self.parameters['phi_step'].value)
def get_chi(self):
return (self.parameters['chi_start'].value,
self.parameters['chi_step'].value)
def get_omega(self):
return (self.parameters['omega_start'].value,
self.parameters['omega_step'].value)
def get_hkl_tolerance(self):
try:
return np.float32(self.tolerance_box.text())
except Exception:
return self.refine.hkl_tolerance
def plot_lattice(self):
self.transfer_parameters()
self.set_polar_max()
self.plot_peaks()
self.plot_rings()
def plot_peaks(self):
try:
x, y = self.refine.xp[self.refine.idx], self.refine.yp[self.refine.idx]
polar_angles, azimuthal_angles = self.refine.calculate_angles(x, y)
if polar_angles[0] > polar_angles[-1]:
polar_angles = polar_angles[::-1]
azimuthal_angles = azimuthal_angles[::-1]
azimuthal_field = NXfield(azimuthal_angles, name='azimuthal_angle')
azimuthal_field.long_name = 'Azimuthal Angle'
polar_field = NXfield(polar_angles, name='polar_angle')
polar_field.long_name = 'Polar Angle'
plotview = get_plotview()
plotview.plot(NXdata(azimuthal_field, polar_field, title='Peak Angles'))
except NeXusError as error:
report_error('Plotting Lattice', error)
def plot_rings(self, polar_max=None):
if polar_max is None:
polar_max = self.refine.polar_max
peaks = self.refine.calculate_rings(polar_max)
plotview = get_plotview()
plotview.vlines(peaks, colors='r', linestyles='dotted')
plotview.draw()
def plot_peak(self, i):
x, y, z = self.refine.xp[i], self.refine.yp[i], self.refine.zp[i]/10.0
xmin, xmax = max(0,int(x)-200), min(int(x)+200,data.v.shape[2])
ymin, ymax = max(0,int(y)-200), min(int(y)+200,data.v.shape[1])
zmin, zmax = max(0.0,z-20.0), min(z+20.0, 360.0)
xslab=np.s_[zmin:zmax,ymin:ymax,x]
yslab=np.s_[zmin:zmax,y,xmin:xmax]
zslab=np.s_[z,ymin:ymax,xmin:xmax]
pvz.plot(data[zslab], log=True)
pvz.crosshairs(x, y)
pvy.plot(data[yslab], log=True)
pvy.crosshairs(x, z)
pvx.plot(data[xslab], log=True)
pvx.crosshairs(y, z)
def refine_angles(self):
self.parameters['orientation_matrix'].vary = False
self.parameters['phi_start'].vary = False
self.parameters['chi_start'].vary = False
self.parameters['omega_start'].vary = False
self.parameters.refine_parameters(self.angle_residuals)
self.update_parameters()
def angle_residuals(self, p):
self.parameters.get_parameters(p)
self.transfer_parameters()
polar_angles, _ = self.refine.calculate_angles(self.refine.x, self.refine.y)
rings = self.refine.calculate_rings()
residuals = np.array([find_nearest(rings, polar_angle) - polar_angle
for polar_angle in polar_angles])
return np.sum(residuals**2)
def refine_hkls(self):
self.parameters.refine_parameters(self.hkl_residuals)
self.update_parameters()
if self.peaks_box is None:
self.list_peaks()
else:
self.update_table()
def hkl_residuals(self, p):
self.parameters.get_parameters(p)
self.transfer_parameters()
return self.refine.score(self.refine.idx)
def restore_parameters(self):
self.parameters.restore_parameters()
self.transfer_parameters()
def reset_parameters(self):
self.refine.read_parameters()
self.update_parameters()
def list_peaks(self):
if self.peaks_box is not None:
self.update_table()
return
self.peaks_box = BaseDialog(self)
self.peaks_box.setMinimumWidth(600)
self.peaks_box.setMinimumHeight(600)
header = ['i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity',
'H', 'K', 'L', 'Diff']
peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
orient_layout = QtGui.QHBoxLayout()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = QtGui.QLineEdit(str(self.refine.primary))
self.primary_box.setAlignment(QtCore.Qt.AlignRight)
self.primary_box.setFixedWidth(80)
self.secondary_box = QtGui.QLineEdit(str(self.refine.secondary))
self.secondary_box.setAlignment(QtCore.Qt.AlignRight)
self.secondary_box.setFixedWidth(80)
orient_button = QtGui.QPushButton('Orient')
orient_button.clicked.connect(self.orient)
orient_layout.addStretch()
orient_layout.addWidget(QtGui.QLabel('Primary'))
orient_layout.addWidget(self.primary_box)
orient_layout.addWidget(QtGui.QLabel('Secondary'))
orient_layout.addWidget(self.secondary_box)
orient_layout.addStretch()
orient_layout.addWidget(orient_button)
self.table_view = QtGui.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
layout = QtGui.QVBoxLayout()
layout.addLayout(orient_layout)
layout.addWidget(self.table_view)
close_layout = QtGui.QHBoxLayout()
self.status_text = QtGui.QLabel('Score: %.4f' % self.refine.score())
self.tolerance_box = QtGui.QLineEdit(str(self.refine.hkl_tolerance))
self.tolerance_box.setAlignment(QtCore.Qt.AlignRight)
self.tolerance_box.setMaxLength(5)
self.tolerance_box.editingFinished.connect(self.update_table)
self.tolerance_box.setFixedWidth(80)
save_button = QtGui.QPushButton('Save Orientation')
save_button.clicked.connect(self.save_orientation)
close_button = QtGui.QPushButton('Close Window')
close_button.clicked.connect(self.close_peaks_box)
close_layout.addWidget(self.status_text)
close_layout.addStretch()
close_layout.addWidget(QtGui.QLabel('Threshold'))
close_layout.addWidget(self.tolerance_box)
close_layout.addStretch()
close_layout.addWidget(save_button)
close_layout.addStretch()
close_layout.addWidget(close_button)
layout.addLayout(close_layout)
self.peaks_box.setLayout(layout)
self.peaks_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
def update_table(self):
self.transfer_parameters()
self.refine.hkl_tolerance = self.get_hkl_tolerance()
self.table_model.peak_list = self.refine.get_peaks()
rows, columns = len(self.table_model.peak_list), 11
self.table_model.dataChanged.emit(self.table_model.createIndex(0, 0),
self.table_model.createIndex(rows-1, columns-1))
self.status_text.setText('Score: %.4f' % self.refine.score())
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
x, y, z = [self.table_view.model().peak_list[row][i] for i in range(1, 4)]
xmin, xmax = max(0,x-200), min(x+200,data.nxsignal.shape[2])
ymin, ymax = max(0,y-200), min(y+200,data.nxsignal.shape[1])
zmin, zmax = max(0,z-200), min(z+200,data.nxsignal.shape[0])
zslab=np.s_[z,ymin:ymax,xmin:xmax]
if self.plotview is None:
self.plotview = NXPlotView('X-Y Projection')
self.plotview.plot(data[zslab], log=True)
self.plotview.crosshairs(x, y)
def orient(self):
self.refine.primary = int(self.primary_box.text())
self.refine.secondary = int(self.secondary_box.text())
self.refine.Umat = self.refine.get_UBmat(self.refine.primary,
self.refine.secondary) \
* self.refine.Bimat
self.update_table()
def save_orientation(self):
self.write_parameters()
def close_peaks_box(self):
self.peaks_box.close()
self.peaks_box = None
class CalibrateDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.plotview = None
self.data = None
self.counts = None
self.points = []
self.pattern_geometry = None
self.cake_geometry = None
self.polarization = None
self.is_calibrated = False
self.phi_max = -np.pi
cstr = str(ALL_CALIBRANTS)
calibrants = sorted(cstr[cstr.index(':')+2:].split(', '))
self.parameters = GridParameters()
self.parameters.add('calibrant', calibrants, 'Calibrant')
self.parameters['calibrant'].value = 'CeO2'
self.parameters.add('wavelength', 0.5, 'Wavelength (Ang)', False)
self.parameters.add('distance', 100.0, 'Detector Distance (mm)', True)
self.parameters.add('xc', 512, 'Beam Center - x', True)
self.parameters.add('yc', 512, 'Beam Center - y', True)
self.parameters.add('yaw', 0.0, 'Yaw (degrees)', True)
self.parameters.add('pitch', 0.0, 'Pitch (degrees)', True)
self.parameters.add('roll', 0.0, 'Roll (degrees)', True)
self.parameters.add('search_size', 10, 'Search Size (pixels)')
self.rings_box = self.select_box([f'Ring{i}' for i in range(1, 21)])
self.set_layout(self.select_entry(self.choose_entry),
self.progress_layout(close=True))
self.set_title('Calibrating Powder')
def choose_file(self):
super().choose_file()
powder_file = self.get_filename()
if powder_file:
self.data = load_image(powder_file)
self.counts = self.data.nxsignal.nxvalue
self.plot_data()
def choose_entry(self):
if self.layout.count() == 2:
self.insert_layout(
1, self.filebox('Choose Powder Calibration File'))
self.insert_layout(2, self.parameters.grid(header=False))
self.insert_layout(
3, self.action_buttons(('Select Points', self.select),
('Autogenerate Rings', self.auto),
('Clear Points', self.clear_points)))
self.insert_layout(4, self.make_layout(self.rings_box))
self.insert_layout(
5, self.action_buttons(('Calibrate', self.calibrate),
('Plot Cake', self.plot_cake),
('Restore', self.restore_parameters),
('Save', self.save_parameters)))
self.parameters['wavelength'].value = (
self.entry['instrument/monochromator/wavelength'])
detector = self.entry['instrument/detector']
self.parameters['distance'].value = detector['distance']
self.parameters['yaw'].value = detector['yaw']
self.parameters['pitch'].value = detector['pitch']
self.parameters['roll'].value = detector['roll']
if 'beam_center_x' in detector:
self.parameters['xc'].value = detector['beam_center_x']
if 'beam_center_y' in detector:
self.parameters['yc'].value = detector['beam_center_y']
self.pixel_size = (
self.entry['instrument/detector/pixel_size'].nxvalue * 1e-3)
self.pixel_mask = self.entry['instrument/detector/pixel_mask'].nxvalue
self.ring = self.selected_ring
if 'calibration' in self.entry['instrument']:
self.data = self.entry['instrument/calibration']
self.counts = self.data.nxsignal.nxvalue
self.plot_data()
else:
self.close_plots()
@property
def search_size(self):
return int(self.parameters['search_size'].value)
@property
def selected_ring(self):
return int(self.rings_box.currentText()[4:]) - 1
@property
def ring_color(self):
colors = ['r', 'b', 'g', 'c', 'm'] * 4
return colors[self.ring]
def plot_data(self):
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect = 'equal'
self.plotview.ytab.flipped = True
self.clear_points()
def on_button_press(self, event):
self.plotview.make_active()
if event.inaxes:
self.xp, self.yp = event.x, event.y
else:
self.xp, self.yp = 0, 0
def on_button_release(self, event):
self.ring = self.selected_ring
if event.inaxes:
if abs(event.x - self.xp) > 5 or abs(event.y - self.yp) > 5:
return
x, y = self.plotview.inverse_transform(event.xdata, event.ydata)
for i, point in enumerate(self.points):
circle = point[0]
if circle.shape.contains_point(
self.plotview.ax.transData.transform((x, y))):
circle.remove()
for circle in point[2]:
circle.remove()
del self.points[i]
return
self.add_points(x, y)
def circle(self, idx, idy, alpha=1.0):
return self.plotview.circle(idx, idy, self.search_size,
facecolor=self.ring_color, edgecolor='k',
alpha=alpha)
def select(self):
self.plotview.cidpress = self.plotview.mpl_connect(
'button_press_event', self.on_button_press)
self.plotview.cidrelease = self.plotview.mpl_connect(
'button_release_event', self.on_button_release)
def auto(self):
xc, yc = self.parameters['xc'].value, self.parameters['yc'].value
wavelength = self.parameters['wavelength'].value
distance = self.parameters['distance'].value * 1e-3
self.start_progress((0, self.selected_ring+1))
for ring in range(self.selected_ring+1):
self.update_progress(ring)
if len([p for p in self.points if p[3] == ring]) > 0:
continue
self.ring = ring
theta = 2 * np.arcsin(wavelength /
(2*self.calibrant.dSpacing[ring]))
r = distance * np.tan(theta) / self.pixel_size
phi = self.phi_max = -np.pi
while phi < np.pi:
x, y = np.int(xc + r*np.cos(phi)), np.int(yc + r*np.sin(phi))
if ((x > 0 and x < self.data.x.max()) and
(y > 0 and y < self.data.y.max()) and
not self.pixel_mask[y, x]):
self.add_points(x, y, phi)
phi = self.phi_max + 0.2
else:
phi = phi + 0.2
self.stop_progress()
def add_points(self, x, y, phi=0.0):
xc, yc = self.parameters['xc'].value, self.parameters['yc'].value
idx, idy = self.find_peak(x, y)
points = [(idy, idx)]
circles = []
massif = Massif(self.counts)
extra_points = massif.find_peaks((idy, idx))
for point in extra_points:
points.append(point)
circles.append(self.circle(point[1], point[0], alpha=0.3))
phis = np.array([np.arctan2(p[0]-yc, p[1]-xc) for p in points])
if phi < -0.5*np.pi:
phis[np.where(phis > 0.0)] -= 2 * np.pi
self.phi_max = max(*phis, self.phi_max)
self.points.append([self.circle(idx, idy), points, circles, self.ring])
def find_peak(self, x, y):
s = self.search_size
left = int(np.round(x - s * 0.5))
if left < 0:
left = 0
top = int(np.round(y - s * 0.5))
if top < 0:
top = 0
region = self.counts[top:(top+s), left:(left+s)]
idy, idx = np.where(region == region.max())
idx = left + idx[0]
idy = top + idy[0]
return idx, idy
def clear_points(self):
for i, point in enumerate(self.points):
circle = point[0]
circle.remove()
for circle in point[2]:
circle.remove()
self.points = []
@property
def calibrant(self):
return ALL_CALIBRANTS[self.parameters['calibrant'].value]
@property
def point_array(self):
points = []
for point in self.points:
for p in point[1]:
points.append((p[0], p[1], point[3]))
return np.array(points)
def prepare_parameters(self):
self.parameters.set_parameters()
self.wavelength = self.parameters['wavelength'].value * 1e-10
self.distance = self.parameters['distance'].value * 1e-3
self.yaw = np.radians(self.parameters['yaw'].value)
self.pitch = np.radians(self.parameters['pitch'].value)
self.roll = np.radians(self.parameters['roll'].value)
self.xc = self.parameters['xc'].value
self.yc = self.parameters['yc'].value
def calibrate(self):
self.prepare_parameters()
self.orig_pixel1 = self.pixel_size
self.orig_pixel2 = self.pixel_size
self.pattern_geometry = GeometryRefinement(self.point_array,
dist=self.distance,
wavelength=self.wavelength,
pixel1=self.pixel_size,
pixel2=self.pixel_size,
calibrant=self.calibrant)
self.refine()
self.create_cake_geometry()
self.pattern_geometry.reset()
def refine(self):
self.pattern_geometry.data = self.point_array
if self.parameters['wavelength'].vary:
self.pattern_geometry.refine2()
fix = []
else:
fix = ['wavelength']
if not self.parameters['distance'].vary:
fix.append('dist')
self.pattern_geometry.refine2_wavelength(fix=fix)
self.read_parameters()
self.is_calibrated = True
self.create_cake_geometry()
self.pattern_geometry.reset()
def create_cake_geometry(self):
self.cake_geometry = AzimuthalIntegrator()
pyFAI_parameter = self.pattern_geometry.getPyFAI()
pyFAI_parameter['wavelength'] = self.pattern_geometry.wavelength
self.cake_geometry.setPyFAI(dist=pyFAI_parameter['dist'],
poni1=pyFAI_parameter['poni1'],
poni2=pyFAI_parameter['poni2'],
rot1=pyFAI_parameter['rot1'],
rot2=pyFAI_parameter['rot2'],
rot3=pyFAI_parameter['rot3'],
pixel1=pyFAI_parameter['pixel1'],
pixel2=pyFAI_parameter['pixel2'])
self.cake_geometry.wavelength = pyFAI_parameter['wavelength']
def plot_cake(self):
if 'Cake Plot' in plotviews:
plotview = plotviews['Cake Plot']
else:
plotview = NXPlotView('Cake Plot')
if not self.is_calibrated:
raise NeXusError('No refinement performed')
res = self.cake_geometry.integrate2d(self.counts,
1024, 1024,
method='csr',
unit='2th_deg',
correctSolidAngle=True)
self.cake_data = NXdata(res[0],
(NXfield(res[2], name='azimumthal_angle'),
NXfield(res[1], name='polar_angle')))
self.cake_data['title'] = 'Cake Plot'
plotview.plot(self.cake_data, log=True)
wavelength = self.parameters['wavelength'].value
polar_angles = [2 * np.degrees(np.arcsin(wavelength/(2*d)))
for d in self.calibrant.dSpacing]
plotview.vlines([polar_angle for polar_angle in polar_angles
if polar_angle < plotview.xaxis.max],
linestyle=':', color='r')
def read_parameters(self):
pyFAI = self.pattern_geometry.getPyFAI()
fit2d = self.pattern_geometry.getFit2D()
self.parameters['wavelength'].value = (
self.pattern_geometry.wavelength * 1e10)
self.parameters['distance'].value = pyFAI['dist'] * 1e3
self.parameters['yaw'].value = np.degrees(pyFAI['rot1'])
self.parameters['pitch'].value = np.degrees(pyFAI['rot2'])
self.parameters['roll'].value = np.degrees(pyFAI['rot3'])
self.parameters['xc'].value = fit2d['centerX']
self.parameters['yc'].value = fit2d['centerY']
def restore_parameters(self):
self.parameters.restore_parameters()
def save_parameters(self):
if not self.is_calibrated:
raise NeXusError('No refinement performed')
elif 'calibration' in self.entry['instrument']:
if confirm_action(
"Do you want to overwrite existing calibration data?"):
del self.entry['instrument/calibration']
else:
return
self.entry['instrument/calibration'] = self.data
if 'refinement' in self.entry['instrument/calibration']:
if confirm_action('Overwrite previous refinement?'):
del self.entry['instrument/calibration/refinement']
else:
return
self.entry['instrument/calibration/calibrant'] = (
self.parameters['calibrant'].value)
process = NXprocess()
process.program = 'pyFAI'
process.version = pyFAI.version
process.parameters = NXcollection()
process.parameters['Detector'] = (
self.entry['instrument/detector/description'])
pyFAI_parameter = self.pattern_geometry.getPyFAI()
process.parameters['PixelSize1'] = pyFAI_parameter['pixel1']
process.parameters['PixelSize2'] = pyFAI_parameter['pixel2']
process.parameters['Distance'] = pyFAI_parameter['dist']
process.parameters['Poni1'] = pyFAI_parameter['poni1']
process.parameters['Poni2'] = pyFAI_parameter['poni2']
process.parameters['Rot1'] = pyFAI_parameter['rot1']
process.parameters['Rot2'] = pyFAI_parameter['rot2']
process.parameters['Rot3'] = pyFAI_parameter['rot3']
process.parameters['Wavelength'] = pyFAI_parameter['wavelength']
self.entry['instrument/calibration/refinement'] = process
self.entry['instrument/monochromator/wavelength'] = (
self.parameters['wavelength'].value)
self.entry['instrument/monochromator/energy'] = (
12.398419739640717 / self.parameters['wavelength'].value)
detector = self.entry['instrument/detector']
detector['distance'] = self.parameters['distance'].value
detector['yaw'] = self.parameters['yaw'].value
detector['pitch'] = self.parameters['pitch'].value
detector['roll'] = self.parameters['roll'].value
detector['beam_center_x'] = self.parameters['xc'].value
detector['beam_center_y'] = self.parameters['yc'].value
try:
detector['polarization'] = self.pattern_geometry.polarization(
factor=0.99, shape=detector['mask'].shape)
except Exception:
pass
def close_plots(self):
if 'Powder Calibration' in plotviews:
plotviews['Powder Calibration'].close()
if 'Cake Plot' in plotviews:
plotviews['Cake Plot'].close()
def closeEvent(self, event):
self.close_plots()
event.accept()
def accept(self):
super().accept()
self.close_plots()
def reject(self):
super().reject()
self.close_plots()
class OrientationDialog(BaseDialog):
def __init__(self, parent=None):
super(OrientationDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine(self.entry)
self.refine.read_parameters()
self.parameters = GridParameters()
self.parameters.add('phi_start', self.refine.phi, 'Phi Start (deg)')
self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)')
self.parameters.add('chi', self.refine.chi, 'Chi (deg)')
self.parameters.add('omega', self.refine.omega, 'Omega (deg)')
self.parameters.add('polar', self.refine.polar_max,
'Max. Polar Angle (deg)')
self.parameters.add('polar_tolerance', self.refine.polar_tolerance,
'Polar Angle Tolerance')
self.parameters.add('peak_tolerance', self.refine.peak_tolerance,
'Peak Angle Tolerance')
action_buttons = self.action_buttons(
('Generate Grains', self.generate_grains),
('List Peaks', self.list_peaks))
self.grain_layout = QtWidgets.QHBoxLayout()
self.grain_combo = QtWidgets.QComboBox()
self.grain_combo.setSizeAdjustPolicy(
QtWidgets.QComboBox.AdjustToContents)
self.grain_combo.currentIndexChanged.connect(self.set_grain)
self.grain_textbox = QtWidgets.QLabel()
self.grain_layout.addWidget(self.grain_combo)
self.grain_layout.addStretch()
self.grain_layout.addWidget(self.grain_textbox)
bottom_layout = QtWidgets.QHBoxLayout()
self.result_textbox = QtWidgets.QLabel()
bottom_layout.addWidget(self.result_textbox)
bottom_layout.addStretch()
bottom_layout.addWidget(self.close_buttons())
self.set_layout(self.entry_layout, self.parameters.grid(),
action_buttons, bottom_layout)
self.set_title('Defining Orientation')
def choose_entry(self):
self.refine = NXRefine(self.entry)
self.update_parameters()
def update_parameters(self):
self.parameters['phi_start'].value = self.refine.phi
self.parameters['phi_step'].value = self.refine.phi_step
self.parameters['chi'].value = self.refine.chi
self.parameters['omega'].value = self.refine.omega
self.parameters['polar'].value = self.refine.polar_max
self.parameters['polar_tolerance'].value = self.refine.polar_tolerance
self.parameters['peak_tolerance'].value = self.refine.peak_tolerance
def get_phi(self):
return (self.parameters['phi_start'].value,
self.parameters['phi_step'].value)
def set_phi(self):
self.refine.phi_start, self.refine.phi_step = self.get_phi()
def get_chi(self):
return self.parameters['chi'].value
def set_chi(self):
self.refine.chi = self.get_chi()
def get_omega(self):
return self.parameters['omega'].value
def set_omega(self):
self.refine.omega = self.get_omega()
@property
def polar_max(self):
return self.parameters['polar'].value
def set_polar_max(self):
self.refine.polar_max = self.polar_max
def get_polar_tolerance(self):
return self.parameters['polar_tolerance'].value
def set_polar_tolerance(self):
self.refine.polar_tolerance = self.get_polar_tolerance()
def get_peak_tolerance(self):
return self.parameters['peak_tolerance'].value
def set_peak_tolerance(self):
self.refine.peak_tolerance = self.get_peak_tolerance()
def generate_grains(self):
self.set_polar_max()
self.refine.generate_grains()
if self.refine.grains is not None:
self.layout.insertLayout(2, self.grain_layout)
self.grain_combo.clear()
for i in range(len(self.refine.grains)):
self.grain_combo.addItem('Grain %s' % i)
self.grain_combo.setCurrentIndex(0)
self.set_grain()
def set_grain(self):
try:
grain = self.refine.grains[self.get_grain()]
self.grain_textbox.setText('%s peaks; Score: %.4f' %
(len(grain), grain.score))
self.refine.Umat = grain.Umat
self.refine.primary = grain.primary
self.refine.secondary = grain.secondary
self.get_score()
except:
self.grain_textbox.setText('')
def get_grain(self):
return int(self.grain_combo.currentText().split()[-1])
def list_peaks(self):
self.refine.phi = self.get_phi()
self.refine.chi = self.get_chi()
self.refine.omega = self.get_omega()
if self.refine.grains is not None:
grain = self.refine.grains[self.get_grain()]
self.refine.Umat = grain.Umat
self.list_orientations()
else:
self.list_orientations()
def get_score(self):
if self.refine.Umat is not None:
self.score = self.refine.score()
self.result_textbox.setText('%s peaks; Score: %.4f' %
(len(self.refine.idx), self.score))
def list_orientations(self):
message_box = BaseDialog(self)
message_box.setMinimumWidth(600)
message_box.setMinimumHeight(600)
header = [
'i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity', 'H', 'K', 'L',
'Diff'
]
peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
orient_layout = QtWidgets.QHBoxLayout()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = QtWidgets.QLineEdit(str(self.refine.primary))
self.primary_box.setAlignment(QtCore.Qt.AlignRight)
self.primary_box.setFixedWidth(80)
self.secondary_box = QtWidgets.QLineEdit(str(self.refine.secondary))
self.secondary_box.setAlignment(QtCore.Qt.AlignRight)
self.secondary_box.setFixedWidth(80)
orient_button = QtWidgets.QPushButton('Orient')
orient_button.clicked.connect(self.orient)
refine_button = QtWidgets.QPushButton('Refine')
refine_button.clicked.connect(self.refine_orientation)
restore_button = QtWidgets.QPushButton('Restore')
restore_button.clicked.connect(self.restore_orientation)
orient_layout.addStretch()
orient_layout.addWidget(QtWidgets.QLabel('Primary'))
orient_layout.addWidget(self.primary_box)
orient_layout.addWidget(QtWidgets.QLabel('Secondary'))
orient_layout.addWidget(self.secondary_box)
orient_layout.addStretch()
orient_layout.addWidget(orient_button)
orient_layout.addWidget(refine_button)
orient_layout.addWidget(restore_button)
grid = QtWidgets.QGridLayout()
grid.setSpacing(10)
self.lattice = GridParameters()
self.lattice.add('a', self.refine.a, 'a', False)
self.lattice.add('b', self.refine.b, 'b', False)
self.lattice.add('c', self.refine.c, 'c', False)
self.lattice.add('alpha', self.refine.alpha, 'alpha', False)
self.lattice.add('beta', self.refine.beta, 'beta', False)
self.lattice.add('gamma', self.refine.gamma, 'gamma', False)
p = self.lattice['a']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 0, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 1, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 2, QtCore.Qt.AlignHCenter)
p = self.lattice['b']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 3, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 4, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 5, QtCore.Qt.AlignHCenter)
p = self.lattice['c']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 6, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 7, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 8, QtCore.Qt.AlignHCenter)
p = self.lattice['alpha']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 0, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 1, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 2, QtCore.Qt.AlignHCenter)
p = self.lattice['beta']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 3, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 4, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 5, QtCore.Qt.AlignHCenter)
p = self.lattice['gamma']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 6, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 7, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 8, QtCore.Qt.AlignHCenter)
self.table_view = QtWidgets.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(
QtWidgets.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
layout = QtWidgets.QVBoxLayout()
layout.addLayout(orient_layout)
layout.addLayout(grid)
layout.addWidget(self.table_view)
close_layout = QtWidgets.QHBoxLayout()
self.status_text = QtWidgets.QLabel('Score: %.4f' %
self.refine.score())
self.tolerance_box = QtWidgets.QLineEdit(str(
self.refine.hkl_tolerance))
self.tolerance_box.setAlignment(QtCore.Qt.AlignRight)
self.tolerance_box.setMaxLength(5)
self.tolerance_box.editingFinished.connect(self.update_table)
self.tolerance_box.setFixedWidth(80)
save_button = QtWidgets.QPushButton('Save Orientation')
save_button.clicked.connect(self.save_orientation)
close_button = QtWidgets.QPushButton('Close Window')
close_button.clicked.connect(message_box.close)
close_layout.addWidget(self.status_text)
close_layout.addStretch()
close_layout.addWidget(QtWidgets.QLabel('Threshold'))
close_layout.addWidget(self.tolerance_box)
close_layout.addStretch()
close_layout.addWidget(save_button)
close_layout.addStretch()
close_layout.addWidget(close_button)
layout.addLayout(close_layout)
message_box.setLayout(layout)
message_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
message_box.adjustSize()
message_box.show()
self.plotview = None
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
x, y, z = [
self.table_view.model().peak_list[row][i] for i in range(1, 4)
]
xmin, xmax = max(0, x - 200), min(x + 200, data.nxsignal.shape[2])
ymin, ymax = max(0, y - 200), min(y + 200, data.nxsignal.shape[1])
zmin, zmax = max(0, z - 200), min(z + 200, data.nxsignal.shape[0])
zslab = np.s_[z, ymin:ymax, xmin:xmax]
if self.plotview is None:
self.plotview = NXPlotView('X-Y Projection')
self.plotview.plot(data[zslab], log=True)
self.plotview.crosshairs(x, y)
def orient(self):
self.refine.primary = int(self.primary_box.text())
self.refine.secondary = int(self.secondary_box.text())
self.refine.Umat = self.refine.get_UBmat(self.refine.primary,
self.refine.secondary) \
* self.refine.Bimat
self.update_table()
def refine_orientation(self):
idx = self.refine.idx
intensities = self.refine.intensity[idx]
sigma = np.average(intensities) / intensities
p0 = self.set_parameters(idx)
def diffs(p):
self.get_parameters(p)
UBimat = np.linalg.inv(self.refine.UBmat)
Q = [UBimat * self.Gvec[i] for i in idx]
dQ = Q - np.rint(Q)
return np.array([
np.linalg.norm(self.refine.Bmat * np.matrix(dQ[i]))
for i in idx
]) / sigma
popt, C, info, msg, success = leastsq(diffs, p0, full_output=1)
self.get_parameters(popt)
self.update_lattice()
self.update_table()
self.status_text.setText('Score: %.4f' % self.refine.score())
def restore_orientation(self):
self.refine.Umat = self.Umat
for par in self.lattice.values():
par.value = par.init_value
self.update_table()
def update_table(self):
self.refine.hkl_tolerance = np.float32(self.tolerance_box.text())
self.table_model.peak_list = self.refine.get_peaks()
rows, columns = len(self.table_model.peak_list), 11
self.table_model.dataChanged.emit(
self.table_model.createIndex(0, 0),
self.table_model.createIndex(rows - 1, columns - 1))
self.status_text.setText('Score: %.4f' % self.refine.score())
def update_lattice(self):
self.lattice['a'].value = self.refine.a
self.lattice['b'].value = self.refine.b
self.lattice['c'].value = self.refine.c
self.lattice['alpha'].value = self.refine.alpha
self.lattice['beta'].value = self.refine.beta
self.lattice['gamma'].value = self.refine.gamma
def set_parameters(self, idx):
x, y, z = self.refine.xp[idx], self.refine.yp[idx], self.refine.zp[idx]
self.Gvec = [
self.refine.Gvec(xx, yy, zz) for xx, yy, zz in zip(x, y, z)
]
self.Umat = self.refine.Umat
pars = []
for par in self.lattice.values():
par.init_value = par.value
if par.vary:
pars.append(par.value)
p0 = np.zeros(shape=(len(pars) + 9), dtype=np.float32)
p0[:len(pars)] = pars
p0[len(pars):] = np.ravel(self.refine.Umat)
return p0
def get_parameters(self, p):
i = 0
for par in self.lattice.values():
if par.vary:
par.value = p[i]
i += 1
self.refine.a, self.refine.b, self.refine.c, \
self.refine.alpha, self.refine.beta, self.refine.gamma = \
[par.value for par in self.lattice.values()]
self.refine.set_symmetry()
self.refine.Umat = np.matrix(p[i:]).reshape(3, 3)
def save_orientation(self):
self.write_parameters()
def write_parameters(self):
try:
self.refine.write_parameters()
except NeXusError as error:
report_error('Defining Orientation', error)
class MaskDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.plotview = None
self.shapes = []
self.parameters = {}
self.select_entry(self.choose_entry)
self.shape_box = self.select_box(['Rectangle', 'Circle'])
self.shape_choice = self.select_box([], slot=self.choose_shape)
self.set_layout(
self.entry_layout,
self.make_layout(
self.action_buttons(('Add Shape', self.add_shape)),
self.shape_box), self.shape_choice,
self.close_buttons(save=True))
self.shape_choice.setVisible(False)
self.set_title('Mask Data')
def choose_entry(self):
if 'calibration' not in self.entry['instrument']:
raise NeXusError('Please load calibration data to this entry')
self.data = self.entry['instrument/calibration']
self.counts = self.data.nxsignal.nxvalue
self.mask = self.entry['instrument/detector/pixel_mask'].nxvalue
self.xc = self.entry['instrument/detector/beam_center_x'].nxvalue
self.yc = self.entry['instrument/detector/beam_center_y'].nxvalue
self.plot_data()
shape = self.data.nxsignal.shape
def plot_data(self):
if self.plotview is None:
if 'Mask Editor' in plotviews:
self.plotview = plotviews['Mask Editor']
else:
self.plotview = NXPlotView('Mask Editor')
self.plotview.plot(self.data, log=True)
self.plotview.aspect = 'equal'
self.plotview.ytab.flipped = True
self.plotview.draw()
def add_shape(self):
if self.shape_box.currentText() == 'Rectangle':
self.shapes.append(
NXrectangle(self.xc - 50,
self.yc - 50,
100,
100,
border_tol=0.1,
plotview=self.plotview,
resize=True,
facecolor='r',
edgecolor='k',
linewidth=1,
alpha=0.3))
else:
self.shapes.append(
NXcircle(self.xc,
self.yc,
50,
border_tol=0.1,
plotview=self.plotview,
resize=True,
facecolor='r',
edgecolor='k',
linewidth=1,
alpha=0.3))
self.plotview.draw()
self.shapes[-1].connect()
self.shape_choice.addItem(repr(self.shapes[-1]))
self.shape_choice.setVisible(True)
self.insert_layout(self.shape_options(self.shapes[-1]))
def shape_options(self, shape):
p = self.parameters[shape] = GridParameters()
if isinstance(shape, NXrectangle):
x, y = shape.xy
w, h = shape.width, shape.height
p.add('x', x, 'Left Pixel')
p.add('y', y, 'Bottom Pixel')
p.add('w', w, 'Width')
p.add('h', h, 'Height')
else:
x, y = shape.center
r = abs(shape.width) / 2
p.add('x', x, 'X-Center')
p.add('y', y, 'Y-Center')
p.add('r', r, 'Radius')
return p.grid(header=False)
def choose_shape(self):
pass
def accept(self):
x, y = np.arange(self.mask.shape[1]), np.arange(self.mask.shape[0])
for shape in self.shapes:
if isinstance(shape, NXrectangle):
x0, y0 = shape.xy
x1, y1 = x0 + shape.width, y0 + shape.height
self.mask[int(y0):int(y1), int(x0):int(x1)] = 1
else:
xc, yc = shape.center
r = shape.radius
inside = (x[None, :] - int(xc))**2 + (y[:, None] -
int(yc))**2 < r**2
self.mask = self.mask | inside
self.mask[np.where(self.counts < 0)] = 1
try:
self.entry['instrument/detector/pixel_mask'] = self.mask
except NeXusError as error:
report_error("Creating Mask", error)
return
super().accept()
if 'Mask Editor' in plotviews:
plotviews['Mask Editor'].close_view()
def reject(self):
super().reject()
if 'Mask Editor' in plotviews:
plotviews['Mask Editor'].close_view()
class CalibrateDialog(BaseDialog):
def __init__(self, parent=None):
super(CalibrateDialog, self).__init__(parent)
self.plotview = None
self.data = None
self.counts = None
self.points = []
self.pattern_geometry = None
self.cake_geometry = None
self.is_calibrated = False
cstr = str(ALL_CALIBRANTS)
calibrants = sorted(cstr[cstr.index(':') + 2:].split(', '))
self.parameters = GridParameters()
self.parameters.add('calibrant', calibrants, 'Calibrant')
self.parameters['calibrant'].value = 'CeO2'
self.parameters.add('wavelength', 0.5, 'Wavelength (Ang)', False)
self.parameters.add('distance', 100.0, 'Detector Distance (mm)', True)
self.parameters.add('xc', 512, 'Beam Center - x', True)
self.parameters.add('yc', 512, 'Beam Center - y', True)
self.parameters.add('yaw', 0.0, 'Yaw (degrees)', True)
self.parameters.add('pitch', 0.0, 'Pitch (degrees)', True)
self.parameters.add('roll', 0.0, 'Roll (degrees)', True)
self.parameters.add('search_size', 10, 'Search Size (pixels)')
rings = ['Ring1', 'Ring2', 'Ring3', 'Ring4', 'Ring5']
self.rings_box = self.select_box(rings)
self.set_layout(
self.select_entry(self.choose_entry),
self.action_buttons(('Plot Calibration', self.plot_data)),
self.parameters.grid(header=False),
self.make_layout(
self.action_buttons(('Select Points', self.select)),
self.rings_box),
self.action_buttons(('Calibrate', self.calibrate),
('Plot Cake', self.plot_cake),
('Restore', self.restore_parameters),
('Save', self.save_parameters)),
self.close_buttons(close=True))
self.set_title('Calibrating Powder')
def choose_entry(self):
if 'calibration' not in self.entry['instrument']:
raise NeXusError('Please load calibration data to this entry')
self.update_parameters()
self.plot_data()
def update_parameters(self):
self.parameters['wavelength'].value = self.entry[
'instrument/monochromator/wavelength']
detector = self.entry['instrument/detector']
self.parameters['distance'].value = detector['distance']
self.parameters['yaw'].value = detector['yaw']
self.parameters['pitch'].value = detector['pitch']
self.parameters['roll'].value = detector['roll']
if 'beam_center_x' in detector:
self.parameters['xc'].value = detector['beam_center_x']
if 'beam_center_y' in detector:
self.parameters['yc'].value = detector['beam_center_y']
self.data = self.entry['instrument/calibration']
self.counts = self.data.nxsignal.nxvalue
@property
def search_size(self):
return int(self.parameters['search_size'].value)
@property
def ring(self):
return int(self.rings_box.currentText()[-1]) - 1
@property
def ring_color(self):
colors = ['r', 'b', 'g', 'c', 'm']
return colors[self.ring]
def plot_data(self):
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect = 'equal'
self.plotview.ytab.flipped = True
self.clear_peaks()
def on_button_press(self, event):
self.plotview.make_active()
if event.inaxes:
self.xp, self.yp = event.x, event.y
else:
self.xp, self.yp = 0, 0
def on_button_release(self, event):
if event.inaxes:
if abs(event.x - self.xp) > 5 or abs(event.y - self.yp) > 5:
return
x, y = self.plotview.inverse_transform(event.xdata, event.ydata)
for i, point in enumerate(self.points):
circle = point[0]
if circle.contains_point(
self.plotview.ax.transData.transform((x, y))):
circle.remove()
for circle in point[2]:
circle.remove()
del self.points[i]
return
idx, idy = self.find_peak(x, y)
points = [(idy, idx)]
circles = []
massif = Massif(self.counts)
extra_points = massif.find_peaks((idy, idx))
for point in extra_points:
points.append(point)
circles.append(self.circle(point[1], point[0], alpha=0.3))
self.points.append(
[self.circle(idx, idy), points, circles, self.ring])
def circle(self, idx, idy, alpha=1.0):
return self.plotview.circle(idx,
idy,
self.search_size,
facecolor=self.ring_color,
edgecolor='k',
alpha=alpha)
def select(self):
self.plotview.cidpress = self.plotview.mpl_connect(
'button_press_event', self.on_button_press)
self.plotview.cidrelease = self.plotview.mpl_connect(
'button_release_event', self.on_button_release)
def find_peak(self, x, y):
s = self.search_size
left = int(np.round(x - s * 0.5))
if left < 0:
left = 0
top = int(np.round(y - s * 0.5))
if top < 0:
top = 0
region = self.counts[top:(top + s), left:(left + s)]
idy, idx = np.where(region == region.max())
idx = left + idx[0]
idy = top + idy[0]
return idx, idy
def clear_peaks(self):
self.points = []
@property
def calibrant(self):
return ALL_CALIBRANTS[self.parameters['calibrant'].value]
@property
def point_array(self):
points = []
for point in self.points:
for p in point[1]:
points.append((p[0], p[1], point[3]))
return np.array(points)
def prepare_parameters(self):
self.parameters.set_parameters()
self.wavelength = self.parameters['wavelength'].value * 1e-10
self.distance = self.parameters['distance'].value * 1e-3
self.yaw = np.radians(self.parameters['yaw'].value)
self.pitch = np.radians(self.parameters['pitch'].value)
self.roll = np.radians(self.parameters['roll'].value)
self.pixel_size = self.entry[
'instrument/detector/pixel_size'].nxvalue * 1e-3
self.xc = self.parameters['xc'].value
self.yc = self.parameters['yc'].value
def calibrate(self):
self.prepare_parameters()
self.orig_pixel1 = self.pixel_size
self.orig_pixel2 = self.pixel_size
self.pattern_geometry = GeometryRefinement(self.point_array,
dist=self.distance,
wavelength=self.wavelength,
pixel1=self.pixel_size,
pixel2=self.pixel_size,
calibrant=self.calibrant)
self.refine()
self.create_cake_geometry()
self.pattern_geometry.reset()
def refine(self):
self.pattern_geometry.data = self.point_array
if self.parameters['wavelength'].vary:
self.pattern_geometry.refine2()
fix = []
else:
fix = ['wavelength']
if not self.parameters['distance'].vary:
fix.append('dist')
self.pattern_geometry.refine2_wavelength(fix=fix)
self.read_parameters()
self.is_calibrated = True
self.create_cake_geometry()
self.pattern_geometry.reset()
def create_cake_geometry(self):
self.cake_geometry = AzimuthalIntegrator()
pyFAI_parameter = self.pattern_geometry.getPyFAI()
pyFAI_parameter['wavelength'] = self.pattern_geometry.wavelength
self.cake_geometry.setPyFAI(dist=pyFAI_parameter['dist'],
poni1=pyFAI_parameter['poni1'],
poni2=pyFAI_parameter['poni2'],
rot1=pyFAI_parameter['rot1'],
rot2=pyFAI_parameter['rot2'],
rot3=pyFAI_parameter['rot3'],
pixel1=pyFAI_parameter['pixel1'],
pixel2=pyFAI_parameter['pixel2'])
self.cake_geometry.wavelength = pyFAI_parameter['wavelength']
def plot_cake(self):
if 'Cake Plot' in plotviews:
plotview = plotviews['Cake Plot']
else:
plotview = NXPlotView('Cake Plot')
if not self.is_calibrated:
raise NeXusError('No refinement performed')
res = self.cake_geometry.integrate2d(self.counts,
1024,
1024,
method='csr',
unit='2th_deg',
correctSolidAngle=True)
self.cake_data = NXdata(res[0],
(NXfield(res[2], name='azimumthal_angle'),
NXfield(res[1], name='polar_angle')))
self.cake_data['title'] = self.entry['instrument/calibration/title']
plotview.plot(self.cake_data, log=True)
wavelength = self.parameters['wavelength'].value
polar_angles = [
2 * np.degrees(np.arcsin(wavelength / (2 * d)))
for d in self.calibrant.dSpacing
]
plotview.vlines([
polar_angle
for polar_angle in polar_angles if polar_angle < plotview.xaxis.max
],
linestyle=':',
color='r')
def read_parameters(self):
pyFAI = self.pattern_geometry.getPyFAI()
fit2d = self.pattern_geometry.getFit2D()
self.parameters[
'wavelength'].value = self.pattern_geometry.wavelength * 1e10
self.parameters['distance'].value = pyFAI['dist'] * 1e3
self.parameters['yaw'].value = np.degrees(pyFAI['rot1'])
self.parameters['pitch'].value = np.degrees(pyFAI['rot2'])
self.parameters['roll'].value = np.degrees(pyFAI['rot3'])
self.parameters['xc'].value = fit2d['centerX']
self.parameters['yc'].value = fit2d['centerY']
def restore_parameters(self):
self.parameters.restore_parameters()
def save_parameters(self):
if not self.is_calibrated:
raise NeXusError('No refinement performed')
elif 'refinement' in self.entry['instrument/calibration']:
if confirm_action('Overwrite previous refinement?'):
del self.entry['instrument/calibration/refinement']
else:
return
self.entry['instrument/calibration/calibrant'] = self.parameters[
'calibrant'].value
process = NXprocess()
process.program = 'pyFAI'
process.version = pyFAI.version
process.parameters = NXcollection()
process.parameters['Detector'] = self.entry[
'instrument/detector/description']
pyFAI_parameter = self.pattern_geometry.getPyFAI()
process.parameters['PixelSize1'] = pyFAI_parameter['pixel1']
process.parameters['PixelSize2'] = pyFAI_parameter['pixel2']
process.parameters['Distance'] = pyFAI_parameter['dist']
process.parameters['Poni1'] = pyFAI_parameter['poni1']
process.parameters['Poni2'] = pyFAI_parameter['poni2']
process.parameters['Rot1'] = pyFAI_parameter['rot1']
process.parameters['Rot2'] = pyFAI_parameter['rot2']
process.parameters['Rot3'] = pyFAI_parameter['rot3']
process.parameters['Wavelength'] = pyFAI_parameter['wavelength']
self.entry['instrument/calibration/refinement'] = process
self.entry['instrument/monochromator/wavelength'] = self.parameters[
'wavelength'].value
self.entry[
'instrument/monochromator/energy'] = 12.398419739640717 / self.parameters[
'wavelength'].value
detector = self.entry['instrument/detector']
detector['distance'] = self.parameters['distance'].value
detector['yaw'] = self.parameters['yaw'].value
detector['pitch'] = self.parameters['pitch'].value
detector['roll'] = self.parameters['roll'].value
detector['beam_center_x'] = self.parameters['xc'].value
detector['beam_center_y'] = self.parameters['yc'].value
def reject(self):
super(CalibrateDialog, self).reject()
if 'Powder Calibration' in plotviews:
plotviews['Powder Calibration'].close_view()
if 'Cake Plot' in plotviews:
plotviews['Cake Plot'].close_view()
class PrepareDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
default = NXSettings().settings['nxreduce']
self.parameters = GridParameters()
self.parameters.add('first', default['first'], 'First Frame')
self.parameters.add('last', default['last'], 'Last Frame')
self.parameters.add('threshold1', '2', 'Threshold 1')
self.parameters.add('horizontal1', '11', 'Horizontal Size 1')
self.parameters.add('threshold2', '0.8', 'Threshold 2')
self.parameters.add('horizontal2', '51', 'Horizontal Size 2')
self.parameters.grid()
self.prepare_button = NXPushButton('Prepare Mask', self.prepare_mask)
self.plot_button = NXPushButton('Plot Mask', self.plot_mask)
self.prepare_layout = self.make_layout(self.prepare_button,
self.plot_button,
align='center')
self.plot_button.setVisible(False)
self.set_layout(self.entry_layout,
self.close_layout(save=True, progress=True))
self.set_title('Prepare 3D Mask')
self.reduce = None
self.mask = None
self.plotview = None
def choose_entry(self):
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid_layout)
self.insert_layout(2, self.prepare_layout)
self.reduce = NXReduce(self.entry)
self.parameters['first'].value = self.reduce.first
self.parameters['last'].value = self.reduce.last
@property
def first(self):
try:
return int(self.parameters['first'].value)
except Exception as error:
report_error("Preparing Mask", error)
@property
def last(self):
try:
return int(self.parameters['last'].value)
except Exception as error:
report_error("Preparing Mask", error)
@property
def threshold1(self):
try:
return float(self.parameters['threshold1'].value)
except Exception as error:
report_error("Preparing Mask", error)
@property
def horizontal1(self):
try:
return int(self.parameters['horizontal1'].value)
except Exception as error:
report_error("Preparing Mask", error)
@property
def threshold2(self):
try:
return float(self.parameters['threshold2'].value)
except Exception as error:
report_error("Preparing Mask", error)
@property
def horizontal2(self):
try:
return int(self.parameters['horizontal2'].value)
except Exception as error:
report_error("Preparing Mask", error)
def prepare_mask(self):
if is_file_locked(self.reduce.data_file):
return
self.start_thread()
self.reduce = NXReduce(self.entry,
prepare=True,
first=self.first,
last=self.last,
overwrite=True,
gui=True)
self.reduce.mask_parameters['threshold_1'] = self.threshold1
self.reduce.mask_parameters['threshold_1'] = self.threshold1
self.reduce.mask_parameters['horizontal_size_1'] = self.horizontal1
self.reduce.mask_parameters['threshold_2'] = self.threshold2
self.reduce.mask_parameters['horizontal_size_2'] = self.horizontal2
self.reduce.moveToThread(self.thread)
self.reduce.start.connect(self.start_progress)
self.reduce.update.connect(self.update_progress)
self.reduce.result.connect(self.get_mask)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxprepare)
self.thread.start()
def get_mask(self, mask):
self.mask = mask
self.status_message.setText("Mask complete")
self.status_message.setVisible(True)
self.plot_button.setVisible(True)
def plot_mask(self):
self.plotview = NXPlotView('3D Mask')
self.plotview.plot(
NXdata(self.mask,
self.reduce.data.nxaxes,
title=f"3D Mask: {self.reduce.name}"))
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.stop_thread()
def accept(self):
try:
if self.mask is None:
raise NeXusError("No mask has been created")
elif self.entry.nxfilemode == 'r':
raise NeXusError("NeXus file opened as readonly")
self.reduce.write_mask(self.mask)
self.reduce.record('nxprepare',
masked_file=self.reduce.mask_file,
threshold1=self.threshold1,
horizontal1=self.horizontal1,
threshold2=self.threshold2,
horizontal2=self.horizontal2,
process='nxprepare_mask')
self.reduce.record_end('nxprepare')
super().accept()
except Exception as error:
report_error("Preparing Mask", error)
def reject(self):
self.stop()
super().reject()
def plot_mask(self):
self.plotview = NXPlotView('3D Mask')
self.plotview.plot(
NXdata(self.mask,
self.reduce.data.nxaxes,
title=f"3D Mask: {self.reduce.name}"))
class OrientationDialog(BaseDialog):
def __init__(self, parent=None):
super(OrientationDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine(self.entry)
self.refine.read_parameters()
self.parameters = GridParameters()
self.parameters.add('phi_start', self.refine.phi, 'Phi Start (deg)')
self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)')
self.parameters.add('chi', self.refine.chi, 'Chi (deg)')
self.parameters.add('omega', self.refine.omega, 'Omega (deg)')
self.parameters.add('polar', self.refine.polar_max,
'Max. Polar Angle (deg)')
self.parameters.add('polar_tolerance', self.refine.polar_tolerance,
'Polar Angle Tolerance')
self.parameters.add('peak_tolerance', self.refine.peak_tolerance,
'Peak Angle Tolerance')
action_buttons = self.action_buttons(
('Generate Grains', self.generate_grains),
('List Peaks', self.list_peaks))
self.grain_layout = QtWidgets.QHBoxLayout()
self.grain_combo = QtWidgets.QComboBox()
self.grain_combo.setSizeAdjustPolicy(QtWidgets.QComboBox.AdjustToContents)
self.grain_combo.currentIndexChanged.connect(self.set_grain)
self.grain_textbox = QtWidgets.QLabel()
self.grain_layout.addWidget(self.grain_combo)
self.grain_layout.addStretch()
self.grain_layout.addWidget(self.grain_textbox)
bottom_layout = QtWidgets.QHBoxLayout()
self.result_textbox = QtWidgets.QLabel()
bottom_layout.addWidget(self.result_textbox)
bottom_layout.addStretch()
bottom_layout.addWidget(self.close_buttons())
self.set_layout(self.entry_layout, self.parameters.grid(),
action_buttons, bottom_layout)
self.set_title('Defining Orientation')
def choose_entry(self):
self.refine = NXRefine(self.entry)
self.update_parameters()
def update_parameters(self):
self.parameters['phi_start'].value = self.refine.phi
self.parameters['phi_step'].value = self.refine.phi_step
self.parameters['chi'].value = self.refine.chi
self.parameters['omega'].value = self.refine.omega
self.parameters['polar'].value = self.refine.polar_max
self.parameters['polar_tolerance'].value = self.refine.polar_tolerance
self.parameters['peak_tolerance'].value = self.refine.peak_tolerance
def get_phi(self):
return (self.parameters['phi_start'].value,
self.parameters['phi_step'].value)
def set_phi(self):
self.refine.phi_start, self.refine.phi_step = self.get_phi()
def get_chi(self):
return self.parameters['chi'].value
def set_chi(self):
self.refine.chi = self.get_chi()
def get_omega(self):
return self.parameters['omega'].value
def set_omega(self):
self.refine.omega = self.get_omega()
@property
def polar_max(self):
return self.parameters['polar'].value
def set_polar_max(self):
self.refine.polar_max = self.polar_max
def get_polar_tolerance(self):
return self.parameters['polar_tolerance'].value
def set_polar_tolerance(self):
self.refine.polar_tolerance = self.get_polar_tolerance()
def get_peak_tolerance(self):
return self.parameters['peak_tolerance'].value
def set_peak_tolerance(self):
self.refine.peak_tolerance = self.get_peak_tolerance()
def generate_grains(self):
self.set_polar_max()
self.refine.generate_grains()
if self.refine.grains is not None:
self.layout.insertLayout(2, self.grain_layout)
self.grain_combo.clear()
for i in range(len(self.refine.grains)):
self.grain_combo.addItem('Grain %s' % i)
self.grain_combo.setCurrentIndex(0)
self.set_grain()
def set_grain(self):
try:
grain = self.refine.grains[self.get_grain()]
self.grain_textbox.setText('%s peaks; Score: %.4f'
% (len(grain), grain.score))
self.refine.Umat = grain.Umat
self.refine.primary = grain.primary
self.refine.secondary = grain.secondary
self.get_score()
except:
self.grain_textbox.setText('')
def get_grain(self):
return int(self.grain_combo.currentText().split()[-1])
def list_peaks(self):
self.refine.phi = self.get_phi()
self.refine.chi = self.get_chi()
self.refine.omega = self.get_omega()
if self.refine.grains is not None:
grain = self.refine.grains[self.get_grain()]
self.refine.Umat = grain.Umat
self.list_orientations()
else:
self.list_orientations()
def get_score(self):
if self.refine.Umat is not None:
self.score = self.refine.score()
self.result_textbox.setText('%s peaks; Score: %.4f'
% (len(self.refine.idx), self.score))
def list_orientations(self):
message_box = BaseDialog(self)
message_box.setMinimumWidth(600)
message_box.setMinimumHeight(600)
header = ['i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity',
'H', 'K', 'L', 'Diff']
peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
orient_layout = QtWidgets.QHBoxLayout()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = QtWidgets.QLineEdit(str(self.refine.primary))
self.primary_box.setAlignment(QtCore.Qt.AlignRight)
self.primary_box.setFixedWidth(80)
self.secondary_box = QtWidgets.QLineEdit(str(self.refine.secondary))
self.secondary_box.setAlignment(QtCore.Qt.AlignRight)
self.secondary_box.setFixedWidth(80)
orient_button = QtWidgets.QPushButton('Orient')
orient_button.clicked.connect(self.orient)
refine_button = QtWidgets.QPushButton('Refine')
refine_button.clicked.connect(self.refine_orientation)
restore_button = QtWidgets.QPushButton('Restore')
restore_button.clicked.connect(self.restore_orientation)
orient_layout.addStretch()
orient_layout.addWidget(QtWidgets.QLabel('Primary'))
orient_layout.addWidget(self.primary_box)
orient_layout.addWidget(QtWidgets.QLabel('Secondary'))
orient_layout.addWidget(self.secondary_box)
orient_layout.addStretch()
orient_layout.addWidget(orient_button)
orient_layout.addWidget(refine_button)
orient_layout.addWidget(restore_button)
grid = QtWidgets.QGridLayout()
grid.setSpacing(10)
self.lattice = GridParameters()
self.lattice.add('a', self.refine.a, 'a', False)
self.lattice.add('b', self.refine.b, 'b', False)
self.lattice.add('c', self.refine.c, 'c', False)
self.lattice.add('alpha', self.refine.alpha, 'alpha', False)
self.lattice.add('beta', self.refine.beta, 'beta', False)
self.lattice.add('gamma', self.refine.gamma, 'gamma', False)
p = self.lattice['a']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 0, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 1, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 2, QtCore.Qt.AlignHCenter)
p = self.lattice['b']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 3, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 4, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 5, QtCore.Qt.AlignHCenter)
p = self.lattice['c']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 6, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 7, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 8, QtCore.Qt.AlignHCenter)
p = self.lattice['alpha']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 0, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 1, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 2, QtCore.Qt.AlignHCenter)
p = self.lattice['beta']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 3, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 4, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 5, QtCore.Qt.AlignHCenter)
p = self.lattice['gamma']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 6, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 7, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 8, QtCore.Qt.AlignHCenter)
self.table_view = QtWidgets.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
layout = QtWidgets.QVBoxLayout()
layout.addLayout(orient_layout)
layout.addLayout(grid)
layout.addWidget(self.table_view)
close_layout = QtWidgets.QHBoxLayout()
self.status_text = QtWidgets.QLabel('Score: %.4f' % self.refine.score())
self.tolerance_box = QtWidgets.QLineEdit(str(self.refine.hkl_tolerance))
self.tolerance_box.setAlignment(QtCore.Qt.AlignRight)
self.tolerance_box.setMaxLength(5)
self.tolerance_box.editingFinished.connect(self.update_table)
self.tolerance_box.setFixedWidth(80)
save_button = QtWidgets.QPushButton('Save Orientation')
save_button.clicked.connect(self.save_orientation)
close_button = QtWidgets.QPushButton('Close Window')
close_button.clicked.connect(message_box.close)
close_layout.addWidget(self.status_text)
close_layout.addStretch()
close_layout.addWidget(QtWidgets.QLabel('Threshold'))
close_layout.addWidget(self.tolerance_box)
close_layout.addStretch()
close_layout.addWidget(save_button)
close_layout.addStretch()
close_layout.addWidget(close_button)
layout.addLayout(close_layout)
message_box.setLayout(layout)
message_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
message_box.adjustSize()
message_box.show()
self.plotview = None
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
x, y, z = [self.table_view.model().peak_list[row][i] for i in range(1, 4)]
xmin, xmax = max(0,x-200), min(x+200,data.nxsignal.shape[2])
ymin, ymax = max(0,y-200), min(y+200,data.nxsignal.shape[1])
zmin, zmax = max(0,z-200), min(z+200,data.nxsignal.shape[0])
zslab=np.s_[z,ymin:ymax,xmin:xmax]
if self.plotview is None:
self.plotview = NXPlotView('X-Y Projection')
self.plotview.plot(data[zslab], log=True)
self.plotview.crosshairs(x, y)
def orient(self):
self.refine.primary = int(self.primary_box.text())
self.refine.secondary = int(self.secondary_box.text())
self.refine.Umat = self.refine.get_UBmat(self.refine.primary,
self.refine.secondary) \
* self.refine.Bimat
self.update_table()
def refine_orientation(self):
idx = self.refine.idx
intensities = self.refine.intensity[idx]
sigma = np.average(intensities) / intensities
p0 = self.set_parameters(idx)
def diffs(p):
self.get_parameters(p)
UBimat = np.linalg.inv(self.refine.UBmat)
Q = [UBimat * self.Gvec[i] for i in idx]
dQ = Q - np.rint(Q)
return np.array([np.linalg.norm(self.refine.Bmat*np.matrix(dQ[i]))
for i in idx]) / sigma
popt, C, info, msg, success = leastsq(diffs, p0, full_output=1)
self.get_parameters(popt)
self.update_lattice()
self.update_table()
self.status_text.setText('Score: %.4f' % self.refine.score())
def restore_orientation(self):
self.refine.Umat = self.Umat
for par in self.lattice.values():
par.value = par.init_value
self.update_table()
def update_table(self):
self.refine.hkl_tolerance = np.float32(self.tolerance_box.text())
self.table_model.peak_list = self.refine.get_peaks()
rows, columns = len(self.table_model.peak_list), 11
self.table_model.dataChanged.emit(self.table_model.createIndex(0, 0),
self.table_model.createIndex(rows-1, columns-1))
self.status_text.setText('Score: %.4f' % self.refine.score())
def update_lattice(self):
self.lattice['a'].value = self.refine.a
self.lattice['b'].value = self.refine.b
self.lattice['c'].value = self.refine.c
self.lattice['alpha'].value = self.refine.alpha
self.lattice['beta'].value = self.refine.beta
self.lattice['gamma'].value = self.refine.gamma
def set_parameters(self, idx):
x, y, z = self.refine.xp[idx], self.refine.yp[idx], self.refine.zp[idx]
self.Gvec = [self.refine.Gvec(xx,yy,zz) for xx,yy,zz in zip(x,y,z)]
self.Umat = self.refine.Umat
pars = []
for par in self.lattice.values():
par.init_value = par.value
if par.vary:
pars.append(par.value)
p0 = np.zeros(shape=(len(pars)+9), dtype=np.float32)
p0[:len(pars)] = pars
p0[len(pars):] = np.ravel(self.refine.Umat)
return p0
def get_parameters(self, p):
i = 0
for par in self.lattice.values():
if par.vary:
par.value = p[i]
i += 1
self.refine.a, self.refine.b, self.refine.c, \
self.refine.alpha, self.refine.beta, self.refine.gamma = \
[par.value for par in self.lattice.values()]
self.refine.set_symmetry()
self.refine.Umat = np.matrix(p[i:]).reshape(3,3)
def save_orientation(self):
self.write_parameters()
def write_parameters(self):
try:
self.refine.write_parameters()
except NeXusError as error:
report_error('Defining Orientation', error)
class FindDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
default = NXSettings().settings['nxreduce']
self.parameters = GridParameters()
self.parameters.add('threshold', default['threshold'], 'Threshold')
self.parameters.add('first', default['first'], 'First Frame')
self.parameters.add('last', default['last'], 'Last Frame')
self.parameters.add('min_pixels', default['min_pixels'],
'Minimum Pixels in Peak')
self.parameters.grid()
self.find_button = NXPushButton('Find Peaks', self.find_peaks)
self.find_layout = self.make_layout(self.action_buttons(
('Find Peaks', self.find_peaks), ('List Peaks', self.list_peaks)),
align='center')
self.set_layout(self.entry_layout,
self.close_layout(save=True, progress=True))
self.set_title('Find Peaks')
self.reduce = None
self.refine = None
self.peaks_box = None
def choose_entry(self):
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid_layout)
self.insert_layout(2, self.find_layout)
self.reduce = NXReduce(self.entry)
self.refine = NXRefine(self.entry)
self.refine.polar_max = self.refine.two_theta_max()
if self.reduce.first is not None:
self.parameters['first'].value = self.reduce.first
if self.reduce.last:
self.parameters['last'].value = self.reduce.last
else:
try:
self.parameters['last'].value = self.reduce.shape[0]
except Exception:
pass
self.parameters['threshold'].value = self.reduce.threshold
@property
def threshold(self):
try:
return int(self.parameters['threshold'].value)
except Exception as error:
report_error("Finding Peaks", error)
@property
def first(self):
try:
return int(self.parameters['first'].value)
except Exception as error:
report_error("Finding Peaks", error)
@property
def last(self):
try:
return int(self.parameters['last'].value)
except Exception as error:
report_error("Finding Peaks", error)
@property
def min_pixels(self):
try:
return int(self.parameters['min_pixels'].value)
except Exception as error:
report_error("Finding Peaks", error)
def find_peaks(self):
if is_file_locked(self.reduce.data_file):
return
self.start_thread()
self.reduce = NXReduce(self.entry,
threshold=self.threshold,
first=self.first,
last=self.last,
min_pixels=self.min_pixels,
find=True,
overwrite=True,
gui=True)
self.reduce.moveToThread(self.thread)
self.reduce.start.connect(self.start_progress)
self.reduce.update.connect(self.update_progress)
self.reduce.result.connect(self.get_peaks)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxfind)
self.thread.start()
def get_peaks(self, peaks):
self.peaks = peaks
self.status_message.setText(f'{len(self.peaks)} peaks found')
self.status_message.setVisible(True)
self.refine.xp = np.array([peak.x for peak in peaks])
self.refine.yp = np.array([peak.y for peak in peaks])
self.refine.zp = np.array([peak.z for peak in peaks])
self.refine.intensity = np.array([peak.intensity for peak in peaks])
self.refine.polar_angle, self.refine.azimuthal_angle = (
self.refine.calculate_angles(self.refine.xp, self.refine.yp))
self.update_table()
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.stop_thread()
def list_peaks(self):
if self.peaks_box in self.mainwindow.dialogs:
self.update_table()
return
self.peaks_box = NXDialog(self)
self.peaks_box.setMinimumWidth(600)
self.peaks_box.setMinimumHeight(600)
header = [
'i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity', 'H', 'K', 'L',
'Diff'
]
peak_list = self.refine.get_peaks()
self.table_view = QtWidgets.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(
QtWidgets.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
self.peaks_box.set_layout(self.table_view,
self.close_buttons(close=True))
self.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
def update_table(self):
if self.peaks_box not in self.mainwindow.dialogs:
return
elif self.table_model is None:
self.close_peaks_box()
self.list_peaks()
self.table_model.peak_list = self.refine.get_peaks()
rows, columns = len(self.table_model.peak_list), 11
self.table_model.dataChanged.emit(
self.table_model.createIndex(0, 0),
self.table_model.createIndex(rows - 1, columns - 1))
self.table_view.resizeColumnsToContents()
self.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
self.peaks_box.setVisible(True)
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
i, x, y, z = [
self.table_view.model().peak_list[row][i] for i in range(4)
]
signal = data.nxsignal
xmin, xmax = max(0, x - 200), min(x + 200, signal.shape[2])
ymin, ymax = max(0, y - 200), min(y + 200, signal.shape[1])
zmin, zmax = max(0, z - 20), min(z + 20, signal.shape[0])
zslab = np.s_[zmin:zmax, ymin:ymax, xmin:xmax]
if 'Peak Plot' in self.plotviews:
self.plotview = self.plotviews['Peak Plot']
else:
self.plotview = NXPlotView('Peak Plot')
self.plotview.plot(data[zslab], log=True)
self.plotview.ax.set_title(f'{data.nxtitle}: Peak {i}')
self.plotview.ztab.maxbox.setValue(z)
self.plotview.aspect = 'equal'
self.plotview.crosshairs(x, y, color='r', linewidth=0.5)
def close_peaks_box(self):
try:
self.peaks_box.close()
except Exception:
pass
self.peaks_box = None
def accept(self):
try:
self.reduce.write_peaks(self.peaks)
self.reduce.record('nxfind',
threshold=self.threshold,
first_frame=self.first,
last_frame=self.last,
min_pixels=self.min_pixels,
peak_number=len(self.peaks))
self.reduce.record_end('nxfind')
super().accept()
except Exception as error:
report_error("Finding Peaks", error)
def reject(self):
self.stop()
super().reject()
class RefineLatticeDialog(BaseDialog):
def __init__(self, parent=None):
super(RefineLatticeDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine()
self.parameters = GridParameters()
self.parameters.add('symmetry', self.refine.symmetries, 'Symmetry',
None, self.set_lattice_parameters)
self.parameters.add('a',
self.refine.a,
'Unit Cell - a (Ang)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('b',
self.refine.b,
'Unit Cell - b (Ang)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('c',
self.refine.c,
'Unit Cell - c (Ang)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('alpha',
self.refine.alpha,
'Unit Cell - alpha (deg)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('beta',
self.refine.beta,
'Unit Cell - beta (deg)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('gamma',
self.refine.gamma,
'Unit Cell - gamma (deg)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('wavelength', self.refine.wavelength,
'Wavelength (Ang)', False)
self.parameters.add('distance', self.refine.distance, 'Distance (mm)',
False)
self.parameters.add('yaw', self.refine.yaw, 'Yaw (deg)', False)
self.parameters.add('pitch', self.refine.pitch, 'Pitch (deg)', False)
self.parameters.add('roll', self.refine.roll, 'Roll (deg)')
self.parameters.add('xc', self.refine.xc, 'Beam Center - x', False)
self.parameters.add('yc', self.refine.yc, 'Beam Center - y', False)
self.parameters.add('phi', self.refine.phi, 'Phi Start (deg)', False)
self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)')
self.parameters.add('chi', self.refine.chi, 'Chi (deg)', False)
self.parameters.add('omega', self.refine.omega, 'Omega (deg)', False)
self.parameters.add('twotheta', self.refine.twotheta,
'Two Theta (deg)')
self.parameters.add('gonpitch', self.refine.gonpitch,
'Goniometer Pitch (deg)', False)
self.parameters.add('polar', self.refine.polar_max,
'Max. Polar Angle (deg)', None, self.set_polar_max)
self.parameters.add('polar_tolerance', self.refine.polar_tolerance,
'Polar Angle Tolerance')
self.parameters.add('peak_tolerance', self.refine.peak_tolerance,
'Peak Angle Tolerance')
self.set_symmetry()
self.refine_buttons = self.action_buttons(
('Refine Angles', self.refine_angles),
('Refine HKLs', self.refine_hkls),
('Restore', self.restore_parameters),
('Reset', self.reset_parameters))
self.orientation_button = self.action_buttons(
('Refine Orientation Matrix', self.refine_orientation))
self.lattice_buttons = self.action_buttons(
('Plot', self.plot_lattice), ('List', self.list_peaks),
('Save', self.write_parameters))
self.set_layout(self.entry_layout, self.parameters.grid(),
self.refine_buttons, self.orientation_button,
self.parameters.report_layout(), self.lattice_buttons,
self.close_layout())
self.parameters.grid_layout.setVerticalSpacing(1)
self.layout.setSpacing(2)
self.set_title('Refining Lattice')
self.peaks_box = None
self.table_model = None
self.fit_report = []
def choose_entry(self):
self.refine = NXRefine(self.entry)
self.update_parameters()
if self.peaks_box:
self.update_table()
def report_score(self):
try:
self.status_message.setText('Score: %.4f' % self.refine.score())
except Exception as error:
pass
def update_parameters(self):
self.parameters['a'].value = self.refine.a
self.parameters['b'].value = self.refine.b
self.parameters['c'].value = self.refine.c
self.parameters['alpha'].value = self.refine.alpha
self.parameters['beta'].value = self.refine.beta
self.parameters['gamma'].value = self.refine.gamma
self.parameters['wavelength'].value = self.refine.wavelength
self.parameters['distance'].value = self.refine.distance
self.parameters['yaw'].value = self.refine.yaw
self.parameters['pitch'].value = self.refine.pitch
self.parameters['roll'].value = self.refine.roll
self.parameters['xc'].value = self.refine.xc
self.parameters['yc'].value = self.refine.yc
self.parameters['phi'].value = self.refine.phi
self.parameters['phi_step'].value = self.refine.phi_step
self.parameters['chi'].value = self.refine.chi
self.parameters['omega'].value = self.refine.omega
self.parameters['twotheta'].value = self.refine.twotheta
self.parameters['gonpitch'].value = self.refine.gonpitch
self.parameters['polar'].value = self.refine.polar_max
self.parameters['polar_tolerance'].value = self.refine.polar_tolerance
self.parameters['symmetry'].value = self.refine.symmetry
try:
self.refine.polar_angles, self.refine.azimuthal_angles = \
self.refine.calculate_angles(self.refine.xp, self.refine.yp)
except Exception:
pass
self.report_score()
def transfer_parameters(self):
self.refine.a, self.refine.b, self.refine.c, \
self.refine.alpha, self.refine.beta, self.refine.gamma = \
self.get_lattice_parameters()
self.refine.set_symmetry()
self.refine.wavelength = self.get_wavelength()
self.refine.distance = self.get_distance()
self.refine.yaw, self.refine.pitch, self.refine.roll = self.get_tilts()
self.refine.xc, self.refine.yc = self.get_centers()
self.refine.phi, self.refine.phi_step = self.get_phi()
self.refine.chi, self.refine.omega, self.refine.twotheta, \
self.refine.gonpitch = self.get_angles()
self.refine.polar_max = self.get_polar_max()
self.refine.polar_tol = self.get_tolerance()
def write_parameters(self):
self.transfer_parameters()
polar_angles, azimuthal_angles = self.refine.calculate_angles(
self.refine.xp, self.refine.yp)
self.refine.write_angles(polar_angles, azimuthal_angles)
self.refine.write_parameters()
reduce = NXReduce(self.entry)
reduce.record('nxrefine', fit_report='\n'.join(self.fit_report))
root = self.entry.nxroot
entries = [entry for entry in root.entries if entry != 'entry']
if entries and self.confirm_action(
'Copy orientation to other entries? (%s)' %
(', '.join(entries))):
om = self.entry['instrument/detector/orientation_matrix']
for entry in entries:
root[entry]['instrument/detector/orientation_matrix'] = om
def get_symmetry(self):
return self.parameters['symmetry'].value
def set_symmetry(self):
self.refine.symmetry = self.get_symmetry()
self.refine.set_symmetry()
self.update_parameters()
if self.refine.symmetry == 'cubic':
self.parameters['b'].vary = False
self.parameters['c'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'tetragonal':
self.parameters['b'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'orthorhombic':
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'hexagonal':
self.parameters['b'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'monoclinic':
self.parameters['alpha'].vary = False
self.parameters['gamma'].vary = False
def get_lattice_parameters(self):
return (self.parameters['a'].value, self.parameters['b'].value,
self.parameters['c'].value, self.parameters['alpha'].value,
self.parameters['beta'].value, self.parameters['gamma'].value)
def set_lattice_parameters(self):
symmetry = self.get_symmetry()
if symmetry == 'cubic':
self.parameters['b'].value = self.parameters['a'].value
self.parameters['c'].value = self.parameters['a'].value
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].disable(vary=False)
self.parameters['c'].disable(vary=False)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'tetragonal':
self.parameters['b'].value = self.parameters['a'].value
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].disable(vary=False)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'orthorhombic':
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].enable(vary=True)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'hexagonal':
self.parameters['b'].value = self.parameters['a'].value
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 120.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].disable(vary=False)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'monoclinic':
self.parameters['alpha'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].enable(vary=True)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].enable(vary=True)
self.parameters['gamma'].disable(vary=False)
else:
self.parameters['a'].enable(vary=True)
self.parameters['b'].enable(vary=True)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].enable(vary=True)
self.parameters['beta'].enable(vary=True)
self.parameters['gamma'].enable(vary=True)
def get_wavelength(self):
return self.parameters['wavelength'].value
def get_distance(self):
return self.parameters['distance'].value
def get_tilts(self):
return (self.parameters['yaw'].value, self.parameters['pitch'].value,
self.parameters['roll'].value)
def get_centers(self):
return self.parameters['xc'].value, self.parameters['yc'].value
def get_phi(self):
return (self.parameters['phi'].value,
self.parameters['phi_step'].value)
def get_angles(self):
return (self.parameters['chi'].value, self.parameters['omega'].value,
self.parameters['twotheta'].value,
self.parameters['gonpitch'].value)
def get_polar_max(self):
return self.parameters['polar'].value
def set_polar_max(self):
self.refine.polar_max = self.get_polar_max()
def get_tolerance(self):
return self.parameters['polar_tolerance'].value
def get_hkl_tolerance(self):
try:
return np.float32(self.tolerance_box.text())
except Exception:
return self.refine.hkl_tolerance
def plot_lattice(self):
self.transfer_parameters()
self.set_polar_max()
self.plot_peaks()
self.plot_rings()
def plot_peaks(self):
try:
x, y = (self.refine.xp[self.refine.idx],
self.refine.yp[self.refine.idx])
polar_angles, azimuthal_angles = self.refine.calculate_angles(x, y)
if polar_angles[0] > polar_angles[-1]:
polar_angles = polar_angles[::-1]
azimuthal_angles = azimuthal_angles[::-1]
azimuthal_field = NXfield(azimuthal_angles, name='azimuthal_angle')
azimuthal_field.long_name = 'Azimuthal Angle'
polar_field = NXfield(polar_angles, name='polar_angle')
polar_field.long_name = 'Polar Angle'
plotview = get_plotview()
plotview.plot(
NXdata(azimuthal_field, polar_field, title='Peak Angles'))
except NeXusError as error:
report_error('Plotting Lattice', error)
def plot_rings(self, polar_max=None):
if polar_max is None:
polar_max = self.refine.polar_max
peaks = self.refine.calculate_rings(polar_max)
plotview = get_plotview()
plotview.vlines(peaks, colors='r', linestyles='dotted')
plotview.draw()
@property
def refined(self):
refined = {}
for p in self.parameters:
if self.parameters[p].vary:
refined[p] = True
return refined
def refine_angles(self):
self.parameters.status_message.setText('Fitting...')
self.parameters.status_message.repaint()
self.mainwindow.app.app.processEvents()
self.parameters['phi'].vary = False
self.transfer_parameters()
self.set_symmetry()
self.refine.refine_angles(**self.refined)
self.parameters.result = self.refine.result
self.parameters.fit_report = self.refine.fit_report
self.fit_report.append(self.refine.fit_report)
self.update_parameters()
self.parameters.status_message.setText(self.parameters.result.message)
if self.peaks_box and self.peaks_box.isVisible():
self.update_table()
def refine_hkls(self):
self.parameters.status_message.setText('Fitting...')
self.parameters.status_message.repaint()
self.mainwindow.app.app.processEvents()
self.set_symmetry()
self.transfer_parameters()
self.refine.refine_hkls(**self.refined)
self.parameters.result = self.refine.result
self.parameters.fit_report = self.refine.fit_report
self.fit_report.append(self.refine.fit_report)
self.update_parameters()
self.parameters.status_message.setText(self.parameters.result.message)
if self.peaks_box and self.peaks_box.isVisible():
self.update_table()
def refine_orientation(self):
self.parameters.status_message.setText('Fitting...')
self.parameters.status_message.repaint()
self.mainwindow.app.app.processEvents()
self.transfer_parameters()
self.refine.refine_orientation_matrix()
self.parameters.result = self.refine.result
self.parameters.fit_report = self.refine.fit_report
self.fit_report.append(self.refine.fit_report)
self.update_parameters()
self.parameters.status_message.setText(self.parameters.result.message)
if self.peaks_box and self.peaks_box.isVisible():
self.update_table()
def restore_parameters(self):
self.refine.restore_parameters()
self.update_parameters()
try:
self.fit_report.pop()
except IndexError:
pass
def reset_parameters(self):
self.refine.read_parameters()
self.update_parameters()
self.set_symmetry()
try:
self.fit_report.pop()
except IndexError:
pass
def list_peaks(self):
if self.peaks_box is not None and self.table_model is not None:
self.update_table()
return
self.peaks_box = BaseDialog(self)
self.peaks_box.setMinimumWidth(600)
self.peaks_box.setMinimumHeight(600)
header = [
'i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity', 'H', 'K', 'L',
'Diff'
]
peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
orient_layout = QtWidgets.QHBoxLayout()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = QtWidgets.QLineEdit(str(self.refine.primary))
self.primary_box.setAlignment(QtCore.Qt.AlignRight)
self.primary_box.setFixedWidth(80)
self.secondary_box = QtWidgets.QLineEdit(str(self.refine.secondary))
self.secondary_box.setAlignment(QtCore.Qt.AlignRight)
self.secondary_box.setFixedWidth(80)
orient_button = QtWidgets.QPushButton('Orient')
orient_button.clicked.connect(self.orient)
orient_layout.addStretch()
orient_layout.addWidget(QtWidgets.QLabel('Primary'))
orient_layout.addWidget(self.primary_box)
orient_layout.addWidget(QtWidgets.QLabel('Secondary'))
orient_layout.addWidget(self.secondary_box)
orient_layout.addStretch()
orient_layout.addWidget(orient_button)
self.table_view = QtWidgets.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(
QtWidgets.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
layout = QtWidgets.QVBoxLayout()
layout.addLayout(orient_layout)
layout.addWidget(self.table_view)
close_layout = QtWidgets.QHBoxLayout()
self.status_text = QtWidgets.QLabel('Score: %.4f' %
self.refine.score())
self.tolerance_box = QtWidgets.QLineEdit(str(
self.refine.hkl_tolerance))
self.tolerance_box.setAlignment(QtCore.Qt.AlignRight)
self.tolerance_box.setMaxLength(5)
self.tolerance_box.editingFinished.connect(self.update_table)
self.tolerance_box.setFixedWidth(80)
save_button = QtWidgets.QPushButton('Save Orientation')
save_button.clicked.connect(self.save_orientation)
close_button = QtWidgets.QPushButton('Close Window')
close_button.clicked.connect(self.close_peaks_box)
close_layout.addWidget(self.status_text)
close_layout.addStretch()
close_layout.addWidget(QtWidgets.QLabel('Threshold'))
close_layout.addWidget(self.tolerance_box)
close_layout.addStretch()
close_layout.addWidget(save_button)
close_layout.addStretch()
close_layout.addWidget(close_button)
layout.addLayout(close_layout)
self.peaks_box.setLayout(layout)
self.peaks_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
def update_table(self):
if self.peaks_box is None:
self.list_peaks()
self.transfer_parameters()
self.refine.hkl_tolerance = self.get_hkl_tolerance()
self.table_model.peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
rows, columns = len(self.table_model.peak_list), 11
self.table_model.dataChanged.emit(
self.table_model.createIndex(0, 0),
self.table_model.createIndex(rows - 1, columns - 1))
self.table_view.resizeColumnsToContents()
self.status_text.setText('Score: %.4f' % self.refine.score())
self.peaks_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
self.peaks_box.setVisible(True)
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
i, x, y, z = [
self.table_view.model().peak_list[row][i] for i in range(4)
]
signal = data.nxsignal
xmin, xmax = max(0, x - 200), min(x + 200, signal.shape[2])
ymin, ymax = max(0, y - 200), min(y + 200, signal.shape[1])
zmin, zmax = max(0, z - 20), min(z + 20, signal.shape[0])
zslab = np.s_[zmin:zmax, ymin:ymax, xmin:xmax]
if self.plotview is None:
self.plotview = NXPlotView('Peak Plot')
self.plotview.plot(data[zslab], log=True)
self.plotview.ax.set_title('%s: Peak %s' % (data.nxtitle, i))
self.plotview.ztab.maxbox.setValue(z)
self.plotview.aspect = 'equal'
self.plotview.crosshairs(x, y, color='r', linewidth=0.5)
def orient(self):
self.refine.primary = int(self.primary_box.text())
self.refine.secondary = int(self.secondary_box.text())
self.refine.Umat = (
self.refine.get_UBmat(self.refine.primary, self.refine.secondary) *
self.refine.Bimat)
self.update_table()
def save_orientation(self):
self.write_parameters()
def close_peaks_box(self):
self.peaks_box.close()
self.peaks_box = None
class CalibrateDialog(BaseDialog):
def __init__(self, parent=None):
super(CalibrateDialog, self).__init__(parent)
self.plotview = None
self.data = None
self.counts = None
self.points = []
self.pattern_geometry = None
self.cake_geometry = None
self.is_calibrated = False
cstr = str(ALL_CALIBRANTS)
calibrants = sorted(cstr[cstr.index(':')+2:].split(', '))
self.parameters = GridParameters()
self.parameters.add('calibrant', calibrants, 'Calibrant')
self.parameters['calibrant'].value = 'CeO2'
self.parameters.add('wavelength', 0.5, 'Wavelength (Ang)', False)
self.parameters.add('distance', 100.0, 'Detector Distance (mm)', True)
self.parameters.add('xc', 512, 'Beam Center - x', True)
self.parameters.add('yc', 512, 'Beam Center - y', True)
self.parameters.add('yaw', 0.0, 'Yaw (degrees)', True)
self.parameters.add('pitch', 0.0, 'Pitch (degrees)', True)
self.parameters.add('roll', 0.0, 'Roll (degrees)', True)
self.parameters.add('search_size', 10, 'Search Size (pixels)')
rings = ['Ring%s' % i for i in range(1,21)]
self.rings_box = self.select_box(rings)
self.set_layout(self.select_entry(self.choose_entry),
self.action_buttons(('Plot Calibration', self.plot_data)),
self.parameters.grid(header=False),
self.make_layout(
self.action_buttons(('Select Points', self.select)),
self.rings_box),
self.action_buttons(('Calibrate', self.calibrate),
('Plot Cake', self.plot_cake),
('Restore', self.restore_parameters),
('Save', self.save_parameters)),
self.close_buttons(close=True))
self.set_title('Calibrating Powder')
def choose_entry(self):
if 'calibration' not in self.entry['instrument']:
raise NeXusError('Please load calibration data to this entry')
self.update_parameters()
self.plot_data()
def update_parameters(self):
self.parameters['wavelength'].value = self.entry['instrument/monochromator/wavelength']
detector = self.entry['instrument/detector']
self.parameters['distance'].value = detector['distance']
self.parameters['yaw'].value = detector['yaw']
self.parameters['pitch'].value = detector['pitch']
self.parameters['roll'].value = detector['roll']
if 'beam_center_x' in detector:
self.parameters['xc'].value = detector['beam_center_x']
if 'beam_center_y' in detector:
self.parameters['yc'].value = detector['beam_center_y']
self.data = self.entry['instrument/calibration']
self.counts = self.data.nxsignal.nxvalue
@property
def search_size(self):
return int(self.parameters['search_size'].value)
@property
def ring(self):
return int(self.rings_box.currentText()[4:]) - 1
@property
def ring_color(self):
colors = ['r', 'b', 'g', 'c', 'm'] * 4
return colors[self.ring]
def plot_data(self):
if self.plotview is None:
if 'Powder Calibration' in plotviews:
self.plotview = plotviews['Powder Calibration']
else:
self.plotview = NXPlotView('Powder Calibration')
self.plotview.plot(self.data, log=True)
self.plotview.aspect='equal'
self.plotview.ytab.flipped = True
self.clear_peaks()
def on_button_press(self, event):
self.plotview.make_active()
if event.inaxes:
self.xp, self.yp = event.x, event.y
else:
self.xp, self.yp = 0, 0
def on_button_release(self, event):
if event.inaxes:
if abs(event.x - self.xp) > 5 or abs(event.y - self.yp) > 5:
return
x, y = self.plotview.inverse_transform(event.xdata, event.ydata)
for i, point in enumerate(self.points):
circle = point[0]
if circle.contains_point(self.plotview.ax.transData.transform((x,y))):
circle.remove()
for circle in point[2]:
circle.remove()
del self.points[i]
return
idx, idy = self.find_peak(x, y)
points = [(idy, idx)]
circles = []
massif = Massif(self.counts)
extra_points = massif.find_peaks((idy, idx))
for point in extra_points:
points.append(point)
circles.append(self.circle(point[1], point[0], alpha=0.3))
self.points.append([self.circle(idx, idy), points, circles, self.ring])
def circle(self, idx, idy, alpha=1.0):
return self.plotview.circle(idx, idy, self.search_size,
facecolor=self.ring_color, edgecolor='k',
alpha=alpha)
def select(self):
self.plotview.cidpress = self.plotview.mpl_connect(
'button_press_event', self.on_button_press)
self.plotview.cidrelease = self.plotview.mpl_connect(
'button_release_event', self.on_button_release)
def find_peak(self, x, y):
s = self.search_size
left = int(np.round(x - s * 0.5))
if left < 0:
left = 0
top = int(np.round(y - s * 0.5))
if top < 0:
top = 0
region = self.counts[top:(top+s),left:(left+s)]
idy, idx = np.where(region == region.max())
idx = left + idx[0]
idy = top + idy[0]
return idx, idy
def clear_peaks(self):
self.points = []
@property
def calibrant(self):
return ALL_CALIBRANTS[self.parameters['calibrant'].value]
@property
def point_array(self):
points = []
for point in self.points:
for p in point[1]:
points.append((p[0], p[1], point[3]))
return np.array(points)
def prepare_parameters(self):
self.parameters.set_parameters()
self.wavelength = self.parameters['wavelength'].value * 1e-10
self.distance = self.parameters['distance'].value * 1e-3
self.yaw = np.radians(self.parameters['yaw'].value)
self.pitch = np.radians(self.parameters['pitch'].value)
self.roll = np.radians(self.parameters['roll'].value)
self.pixel_size = self.entry['instrument/detector/pixel_size'].nxvalue * 1e-3
self.xc = self.parameters['xc'].value
self.yc = self.parameters['yc'].value
def calibrate(self):
self.prepare_parameters()
self.orig_pixel1 = self.pixel_size
self.orig_pixel2 = self.pixel_size
self.pattern_geometry = GeometryRefinement(self.point_array,
dist=self.distance,
wavelength=self.wavelength,
pixel1=self.pixel_size,
pixel2=self.pixel_size,
calibrant=self.calibrant)
self.refine()
self.create_cake_geometry()
self.pattern_geometry.reset()
def refine(self):
self.pattern_geometry.data = self.point_array
if self.parameters['wavelength'].vary:
self.pattern_geometry.refine2()
fix = []
else:
fix = ['wavelength']
if not self.parameters['distance'].vary:
fix.append('dist')
self.pattern_geometry.refine2_wavelength(fix=fix)
self.read_parameters()
self.is_calibrated = True
self.create_cake_geometry()
self.pattern_geometry.reset()
def create_cake_geometry(self):
self.cake_geometry = AzimuthalIntegrator()
pyFAI_parameter = self.pattern_geometry.getPyFAI()
pyFAI_parameter['wavelength'] = self.pattern_geometry.wavelength
self.cake_geometry.setPyFAI(dist=pyFAI_parameter['dist'],
poni1=pyFAI_parameter['poni1'],
poni2=pyFAI_parameter['poni2'],
rot1=pyFAI_parameter['rot1'],
rot2=pyFAI_parameter['rot2'],
rot3=pyFAI_parameter['rot3'],
pixel1=pyFAI_parameter['pixel1'],
pixel2=pyFAI_parameter['pixel2'])
self.cake_geometry.wavelength = pyFAI_parameter['wavelength']
def plot_cake(self):
if 'Cake Plot' in plotviews:
plotview = plotviews['Cake Plot']
else:
plotview = NXPlotView('Cake Plot')
if not self.is_calibrated:
raise NeXusError('No refinement performed')
res = self.cake_geometry.integrate2d(self.counts,
1024, 1024,
method='csr',
unit='2th_deg',
correctSolidAngle=True)
self.cake_data = NXdata(res[0], (NXfield(res[2], name='azimumthal_angle'),
NXfield(res[1], name='polar_angle')))
self.cake_data['title'] = self.entry['instrument/calibration/title']
plotview.plot(self.cake_data, log=True)
wavelength = self.parameters['wavelength'].value
polar_angles = [2 * np.degrees(np.arcsin(wavelength/(2*d)))
for d in self.calibrant.dSpacing]
plotview.vlines([polar_angle for polar_angle in polar_angles
if polar_angle < plotview.xaxis.max],
linestyle=':', color='r')
def read_parameters(self):
pyFAI = self.pattern_geometry.getPyFAI()
fit2d = self.pattern_geometry.getFit2D()
self.parameters['wavelength'].value = self.pattern_geometry.wavelength * 1e10
self.parameters['distance'].value = pyFAI['dist'] * 1e3
self.parameters['yaw'].value = np.degrees(pyFAI['rot1'])
self.parameters['pitch'].value = np.degrees(pyFAI['rot2'])
self.parameters['roll'].value = np.degrees(pyFAI['rot3'])
self.parameters['xc'].value = fit2d['centerX']
self.parameters['yc'].value = fit2d['centerY']
def restore_parameters(self):
self.parameters.restore_parameters()
def save_parameters(self):
if not self.is_calibrated:
raise NeXusError('No refinement performed')
elif 'refinement' in self.entry['instrument/calibration']:
if confirm_action('Overwrite previous refinement?'):
del self.entry['instrument/calibration/refinement']
else:
return
self.entry['instrument/calibration/calibrant'] = self.parameters['calibrant'].value
process = NXprocess()
process.program = 'pyFAI'
process.version = pyFAI.version
process.parameters = NXcollection()
process.parameters['Detector'] = self.entry['instrument/detector/description']
pyFAI_parameter = self.pattern_geometry.getPyFAI()
process.parameters['PixelSize1'] = pyFAI_parameter['pixel1']
process.parameters['PixelSize2'] = pyFAI_parameter['pixel2']
process.parameters['Distance'] = pyFAI_parameter['dist']
process.parameters['Poni1'] = pyFAI_parameter['poni1']
process.parameters['Poni2'] = pyFAI_parameter['poni2']
process.parameters['Rot1'] = pyFAI_parameter['rot1']
process.parameters['Rot2'] = pyFAI_parameter['rot2']
process.parameters['Rot3'] = pyFAI_parameter['rot3']
process.parameters['Wavelength'] = pyFAI_parameter['wavelength']
self.entry['instrument/calibration/refinement'] = process
self.entry['instrument/monochromator/wavelength'] = self.parameters['wavelength'].value
self.entry['instrument/monochromator/energy'] = 12.398419739640717 / self.parameters['wavelength'].value
detector = self.entry['instrument/detector']
detector['distance'] = self.parameters['distance'].value
detector['yaw'] = self.parameters['yaw'].value
detector['pitch'] = self.parameters['pitch'].value
detector['roll'] = self.parameters['roll'].value
detector['beam_center_x'] = self.parameters['xc'].value
detector['beam_center_y'] = self.parameters['yc'].value
def reject(self):
super(CalibrateDialog, self).reject()
if 'Powder Calibration' in plotviews:
plotviews['Powder Calibration'].close_view()
if 'Cake Plot' in plotviews:
plotviews['Cake Plot'].close_view()
class RefineLatticeDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine()
self.parameters = GridParameters()
self.parameters.add('symmetry', self.refine.symmetries, 'Symmetry',
None, self.set_lattice_parameters)
self.parameters.add('a',
self.refine.a,
'Unit Cell - a (Ang)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('b',
self.refine.b,
'Unit Cell - b (Ang)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('c',
self.refine.c,
'Unit Cell - c (Ang)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('alpha',
self.refine.alpha,
'Unit Cell - alpha (deg)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('beta',
self.refine.beta,
'Unit Cell - beta (deg)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('gamma',
self.refine.gamma,
'Unit Cell - gamma (deg)',
False,
slot=self.set_lattice_parameters)
self.parameters.add('wavelength', self.refine.wavelength,
'Wavelength (Ang)', False)
self.parameters.add('distance', self.refine.distance, 'Distance (mm)',
False)
self.parameters.add('yaw', self.refine.yaw, 'Yaw (deg)', False)
self.parameters.add('pitch', self.refine.pitch, 'Pitch (deg)', False)
self.parameters.add('roll', self.refine.roll, 'Roll (deg)')
self.parameters.add('xc', self.refine.xc, 'Beam Center - x', False)
self.parameters.add('yc', self.refine.yc, 'Beam Center - y', False)
self.parameters.add('phi', self.refine.phi, 'Phi Start (deg)', False)
self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)')
self.parameters.add('chi', self.refine.chi, 'Chi (deg)', False)
self.parameters.add('omega', self.refine.omega, 'Omega (deg)', False)
self.parameters.add('twotheta', self.refine.twotheta,
'Two Theta (deg)')
self.parameters.add('gonpitch', self.refine.gonpitch,
'Goniometer Pitch (deg)', False)
self.parameters.add('polar', self.refine.polar_max,
'Max. Polar Angle (deg)', None, self.set_polar_max)
self.parameters.add('polar_tolerance', self.refine.polar_tolerance,
'Polar Angle Tolerance')
self.parameters.add('peak_tolerance', self.refine.peak_tolerance,
'Peak Angle Tolerance')
self.parameters.grid()
self.set_symmetry()
self.refine_buttons = self.action_buttons(
('Refine Angles', self.refine_angles),
('Refine HKLs', self.refine_hkls),
('Restore', self.restore_parameters),
('Reset', self.reset_parameters))
self.orientation_buttons = self.action_buttons(
('Refine Orientation Matrix', self.refine_orientation),
('Remove Orientation Matrix', self.remove_orientation))
self.lattice_buttons = self.action_buttons(
('Plot', self.plot_lattice), ('List', self.list_peaks),
('Update', self.update_scaling), ('Save', self.write_parameters))
self.set_layout(self.entry_layout, self.close_layout())
self.parameters.grid_layout.setVerticalSpacing(1)
self.layout.setSpacing(2)
self.set_title('Refining Lattice')
self.peaks_box = None
self.table_model = None
self.orient_box = None
self.update_box = None
self.fit_report = []
def choose_entry(self):
try:
refine = NXRefine(self.entry)
if refine.xp is None:
raise NeXusError("No peaks in entry")
except NeXusError as error:
report_error("Refining Lattice", error)
return
self.refine = refine
self.set_title(f"Refining {self.refine.name}")
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid_layout)
self.insert_layout(2, self.refine_buttons)
self.insert_layout(3, self.orientation_buttons)
self.insert_layout(4, self.parameters.report_layout())
self.insert_layout(5, self.lattice_buttons)
self.update_parameters()
self.update_table()
def report_score(self):
try:
self.status_message.setText(f'Score: {self.refine.score():.4f}')
if self.peaks_box in self.mainwindow.dialogs:
self.status_text.setText(f'Score: {self.refine.score():.4f}')
except Exception as error:
pass
def update_parameters(self):
self.parameters['a'].value = self.refine.a
self.parameters['b'].value = self.refine.b
self.parameters['c'].value = self.refine.c
self.parameters['alpha'].value = self.refine.alpha
self.parameters['beta'].value = self.refine.beta
self.parameters['gamma'].value = self.refine.gamma
self.parameters['wavelength'].value = self.refine.wavelength
self.parameters['distance'].value = self.refine.distance
self.parameters['yaw'].value = self.refine.yaw
self.parameters['pitch'].value = self.refine.pitch
self.parameters['roll'].value = self.refine.roll
self.parameters['xc'].value = self.refine.xc
self.parameters['yc'].value = self.refine.yc
self.parameters['phi'].value = self.refine.phi
self.parameters['phi_step'].value = self.refine.phi_step
self.parameters['chi'].value = self.refine.chi
self.parameters['omega'].value = self.refine.omega
self.parameters['twotheta'].value = self.refine.twotheta
self.parameters['gonpitch'].value = self.refine.gonpitch
self.parameters['polar'].value = self.refine.polar_max
self.parameters['polar_tolerance'].value = self.refine.polar_tolerance
self.parameters['peak_tolerance'].value = self.refine.peak_tolerance
self.parameters['symmetry'].value = self.refine.symmetry
try:
self.refine.polar_angles, self.refine.azimuthal_angles = \
self.refine.calculate_angles(self.refine.xp, self.refine.yp)
except Exception:
pass
self.report_score()
def transfer_parameters(self):
self.refine.a, self.refine.b, self.refine.c, \
self.refine.alpha, self.refine.beta, self.refine.gamma = \
self.get_lattice_parameters()
self.refine.set_symmetry()
self.refine.wavelength = self.get_wavelength()
self.refine.distance = self.get_distance()
self.refine.yaw, self.refine.pitch, self.refine.roll = self.get_tilts()
self.refine.xc, self.refine.yc = self.get_centers()
self.refine.phi, self.refine.phi_step = self.get_phi()
self.refine.chi, self.refine.omega, self.refine.twotheta, \
self.refine.gonpitch = self.get_angles()
self.refine.polar_max = self.get_polar_max()
self.refine.polar_tolerance = self.get_polar_tolerance()
self.refine.peak_tolerance = self.get_peak_tolerance()
def write_parameters(self):
if self.entry.nxfilemode == 'r':
display_message("NeXus file opened as readonly")
return
elif ('nxrefine' in self.entry
or 'orientation_matrix' in self.entry['instrument/detector']):
if not self.confirm_action('Overwrite existing refinement?'):
return
self.transfer_parameters()
polar_angles, azimuthal_angles = self.refine.calculate_angles(
self.refine.xp, self.refine.yp)
self.refine.write_angles(polar_angles, azimuthal_angles)
self.refine.write_parameters()
reduce = NXReduce(self.entry)
reduce.record_start('nxrefine')
reduce.record('nxrefine', fit_report='\n'.join(self.fit_report))
reduce.logger.info('Orientation refined in NeXpy')
reduce.record_end('nxrefine')
root = self.entry.nxroot
entries = [
entry for entry in root.entries
if entry != 'entry' and entry != self.entry.nxname
]
if entries and self.confirm_action(
f'Copy orientation to other entries? ({", ".join(entries)})',
answer='yes'):
om = self.entry['instrument/detector/orientation_matrix']
for entry in entries:
root[entry]['instrument/detector/orientation_matrix'] = om
self.define_data()
if len(self.paths) > 0:
self.update_scaling()
def update_scaling(self):
self.define_data()
if len(self.paths) == 0:
display_message("Refining Lattice", "No data groups to update")
if self.update_box in self.mainwindow.dialogs:
try:
self.update_box.close()
except Exception:
pass
self.update_box = NXDialog(parent=self)
self.update_box.set_title('Update Scaling Factors')
self.update_box.setMinimumWidth(300)
self.update_box.set_layout(
self.paths.grid(header=('', 'Data Groups', '')),
self.update_box.close_layout())
self.update_box.close_box.accepted.connect(self.update_data)
self.update_box.show()
def define_data(self):
def is_valid(data):
try:
valid_axes = [['Ql', 'Qk', 'Qh'], ['l', 'k', 'h'],
['z', 'y', 'x']]
axis_names = [axis.nxname for axis in data.nxaxes]
return axis_names in valid_axes
except Exception:
return False
root = self.entry.nxroot
self.paths = GridParameters()
i = 0
for entry in root.NXentry:
for data in [d for d in entry.NXdata if is_valid(d)]:
i += 1
self.paths.add(i, data.nxpath, i, True, width=200)
def update_data(self):
try:
for path in [
self.paths[p].value for p in self.paths
if self.paths[p].vary
]:
data = self.entry.nxroot[path]
if [axis.nxname for axis in data.nxaxes] == ['z', 'y', 'x']:
lp = self.refine.lattice_parameters
else:
lp = self.refine.reciprocal_lattice_parameters
for i, axis in enumerate(data.nxaxes):
data[axis.nxname].attrs['scaling_factor'] = lp[2 - i]
data.attrs['angles'] = lp[5:2:-1]
self.update_box.close()
except NeXusError as error:
report_error("Updating Groups", error)
def get_symmetry(self):
return self.parameters['symmetry'].value
def set_symmetry(self):
self.refine.symmetry = self.get_symmetry()
self.refine.set_symmetry()
self.update_parameters()
if self.refine.symmetry == 'cubic':
self.parameters['b'].vary = False
self.parameters['c'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'tetragonal':
self.parameters['b'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'orthorhombic':
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'hexagonal':
self.parameters['b'].vary = False
self.parameters['alpha'].vary = False
self.parameters['beta'].vary = False
self.parameters['gamma'].vary = False
elif self.refine.symmetry == 'monoclinic':
self.parameters['alpha'].vary = False
self.parameters['gamma'].vary = False
def get_lattice_parameters(self):
return (self.parameters['a'].value, self.parameters['b'].value,
self.parameters['c'].value, self.parameters['alpha'].value,
self.parameters['beta'].value, self.parameters['gamma'].value)
def set_lattice_parameters(self):
symmetry = self.get_symmetry()
if symmetry == 'cubic':
self.parameters['b'].value = self.parameters['a'].value
self.parameters['c'].value = self.parameters['a'].value
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].disable(vary=False)
self.parameters['c'].disable(vary=False)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'tetragonal':
self.parameters['b'].value = self.parameters['a'].value
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].disable(vary=False)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'orthorhombic':
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].enable(vary=True)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'hexagonal':
self.parameters['b'].value = self.parameters['a'].value
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 120.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].disable(vary=False)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].disable(vary=False)
self.parameters['gamma'].disable(vary=False)
elif symmetry == 'monoclinic':
self.parameters['alpha'].value = 90.0
self.parameters['gamma'].value = 90.0
self.parameters['a'].enable(vary=True)
self.parameters['b'].enable(vary=True)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].disable(vary=False)
self.parameters['beta'].enable(vary=True)
self.parameters['gamma'].disable(vary=False)
else:
self.parameters['a'].enable(vary=True)
self.parameters['b'].enable(vary=True)
self.parameters['c'].enable(vary=True)
self.parameters['alpha'].enable(vary=True)
self.parameters['beta'].enable(vary=True)
self.parameters['gamma'].enable(vary=True)
def get_wavelength(self):
return self.parameters['wavelength'].value
def get_distance(self):
return self.parameters['distance'].value
def get_tilts(self):
return (self.parameters['yaw'].value, self.parameters['pitch'].value,
self.parameters['roll'].value)
def get_centers(self):
return self.parameters['xc'].value, self.parameters['yc'].value
def get_phi(self):
return (self.parameters['phi'].value,
self.parameters['phi_step'].value)
def get_angles(self):
return (self.parameters['chi'].value, self.parameters['omega'].value,
self.parameters['twotheta'].value,
self.parameters['gonpitch'].value)
def get_polar_max(self):
return self.parameters['polar'].value
def set_polar_max(self):
self.refine.polar_max = self.get_polar_max()
def get_polar_tolerance(self):
return self.parameters['polar_tolerance'].value
def get_peak_tolerance(self):
return self.parameters['peak_tolerance'].value
def get_hkl_tolerance(self):
try:
return np.float32(self.tolerance_box.text())
except Exception:
return self.refine.hkl_tolerance
def plot_lattice(self):
self.transfer_parameters()
self.set_polar_max()
self.plot_peaks()
self.plot_rings()
def plot_peaks(self):
try:
x, y = (self.refine.xp[self.refine.idx],
self.refine.yp[self.refine.idx])
polar_angles, azimuthal_angles = self.refine.calculate_angles(x, y)
if polar_angles[0] > polar_angles[-1]:
polar_angles = polar_angles[::-1]
azimuthal_angles = azimuthal_angles[::-1]
azimuthal_field = NXfield(azimuthal_angles, name='azimuthal_angle')
azimuthal_field.long_name = 'Azimuthal Angle'
polar_field = NXfield(polar_angles, name='polar_angle')
polar_field.long_name = 'Polar Angle'
plotview = get_plotview()
plotview.plot(NXdata(azimuthal_field,
polar_field,
title=f'{self.refine.name} Peak Angles'),
xmax=self.get_polar_max())
except NeXusError as error:
report_error('Plotting Lattice', error)
def plot_rings(self):
plotview = get_plotview()
plotview.vlines(self.refine.two_thetas,
colors='r',
linestyles='dotted')
plotview.draw()
@property
def refined(self):
refined = {}
for p in self.parameters:
if self.parameters[p].vary:
refined[p] = True
return refined
def refine_angles(self):
self.parameters.status_message.setText('Fitting...')
self.parameters.status_message.repaint()
self.mainwindow.app.app.processEvents()
self.parameters['phi'].vary = False
self.transfer_parameters()
self.set_lattice_parameters()
try:
self.refine.refine_angles(**self.refined)
except NeXusError as error:
report_error('Refining Lattice', error)
self.parameters.status_message.setText('')
return
self.parameters.result = self.refine.result
self.parameters.fit_report = self.refine.fit_report
self.fit_report.append(self.refine.fit_report)
self.update_parameters()
self.parameters.status_message.setText(self.parameters.result.message)
self.update_table()
def refine_hkls(self):
self.parameters.status_message.setText('Fitting...')
self.parameters.status_message.repaint()
self.mainwindow.app.app.processEvents()
self.transfer_parameters()
try:
self.refine.refine_hkls(**self.refined)
except NeXusError as error:
report_error('Refining Lattice', error)
self.parameters.status_message.setText('')
return
self.parameters.result = self.refine.result
self.parameters.fit_report = self.refine.fit_report
self.fit_report.append(self.refine.fit_report)
self.update_parameters()
self.parameters.status_message.setText(self.parameters.result.message)
self.update_table()
def refine_orientation(self):
self.parameters.status_message.setText('Fitting...')
self.parameters.status_message.repaint()
self.mainwindow.app.app.processEvents()
self.transfer_parameters()
self.refine.refine_orientation_matrix()
self.parameters.result = self.refine.result
self.parameters.fit_report = self.refine.fit_report
self.fit_report.append(self.refine.fit_report)
self.update_parameters()
self.parameters.status_message.setText(self.parameters.result.message)
self.update_table()
def remove_orientation(self):
self.refine.Umat = None
self.report_score()
def restore_parameters(self):
self.refine.restore_parameters()
self.update_parameters()
try:
self.fit_report.pop()
except IndexError:
pass
def reset_parameters(self):
self.refine.read_parameters()
self.update_parameters()
self.set_symmetry()
try:
self.fit_report.pop()
except IndexError:
pass
def list_peaks(self):
if self.peaks_box in self.mainwindow.dialogs:
self.update_table()
return
self.peaks_box = NXDialog(self)
self.peaks_box.setMinimumWidth(600)
self.peaks_box.setMinimumHeight(600)
header = [
'i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity', 'H', 'K', 'L',
'Diff'
]
peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.make_rings()
self.ring_list = self.refine.get_ring_list()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = NXLineEdit(self.refine.primary,
width=80,
align='right')
self.secondary_box = NXLineEdit(self.refine.secondary,
width=80,
align='right')
orient_button = NXPushButton('Orient', self.choose_peaks)
orient_layout = self.make_layout(NXLabel('Primary'),
self.primary_box,
NXLabel('Secondary'),
self.secondary_box,
'stretch',
orient_button,
align='right')
self.table_view = QtWidgets.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(
QtWidgets.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
self.status_text = NXLabel(f'Score: {self.refine.score():.4f}')
self.tolerance_box = NXLineEdit(self.refine.hkl_tolerance,
width=80,
slot=self.update_table,
align='right')
self.tolerance_box.setMaxLength(5)
export_button = NXPushButton('Export', self.export_peaks)
save_button = NXPushButton('Save', self.save_orientation)
close_button = NXPushButton('Close', self.close_peaks_box)
close_layout = self.make_layout(self.status_text, 'stretch',
NXLabel('Threshold'),
self.tolerance_box, 'stretch',
export_button, save_button,
close_button)
self.peaks_box.set_layout(orient_layout, self.table_view, close_layout)
self.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
def update_table(self):
if self.peaks_box not in self.mainwindow.dialogs:
return
elif self.table_model is None:
self.close_peaks_box()
self.list_peaks()
self.transfer_parameters()
self.refine.hkl_tolerance = self.get_hkl_tolerance()
self.table_model.peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.ring_list = self.refine.get_ring_list()
rows, columns = len(self.table_model.peak_list), 11
self.table_model.dataChanged.emit(
self.table_model.createIndex(0, 0),
self.table_model.createIndex(rows - 1, columns - 1))
self.table_view.resizeColumnsToContents()
self.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
self.peaks_box.setVisible(True)
self.report_score()
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
i, x, y, z = [
self.table_view.model().peak_list[row][i] for i in range(4)
]
signal = data.nxsignal
xmin, xmax = max(0, x - 200), min(x + 200, signal.shape[2])
ymin, ymax = max(0, y - 200), min(y + 200, signal.shape[1])
zmin, zmax = max(0, z - 20), min(z + 20, signal.shape[0])
zslab = np.s_[zmin:zmax, ymin:ymax, xmin:xmax]
if 'Peak Plot' in self.plotviews:
self.plotview = self.plotviews['Peak Plot']
else:
self.plotview = NXPlotView('Peak Plot')
self.plotview.plot(data[zslab], log=True)
self.plotview.ax.set_title(f'{data.nxtitle}: Peak {i}')
self.plotview.ztab.maxbox.setValue(z)
self.plotview.aspect = 'equal'
self.plotview.crosshairs(x, y, color='r', linewidth=0.5)
@property
def primary(self):
return int(self.primary_box.text())
@property
def secondary(self):
return int(self.secondary_box.text())
def choose_peaks(self):
try:
if self.orient_box in self.mainwindow.dialogs:
self.orient_box.close()
except Exception:
pass
self.orient_box = NXDialog(self)
self.peak_parameters = GridParameters()
self.peak_parameters.add('primary',
self.primary,
'Primary',
readonly=True)
self.peak_parameters.add('secondary',
self.secondary,
'Secondary',
readonly=True)
self.peak_parameters.add('angle',
self.refine.angle_peaks(
self.primary, self.secondary),
'Angle (deg)',
readonly=True)
self.peak_parameters.add('primary_hkl',
self.ring_list[self.refine.rp[self.primary]],
'Primary HKL',
slot=self.choose_secondary_grid)
self.orient_box.set_layout(
self.peak_parameters.grid(header=False, spacing=5),
self.action_buttons(('Orient', self.orient)),
self.orient_box.close_buttons(close=True))
self.orient_box.set_title('Orient Lattice')
self.orient_box.show()
try:
self.setup_secondary_grid()
except NeXusError as error:
report_error("Refining Lattice", error)
self.orient_box.close()
def setup_secondary_grid(self):
ps_angle = self.refine.angle_peaks(self.primary, self.secondary)
n_phkl = len(self.ring_list[self.refine.rp[self.primary]])
self.hkl_parameters = [GridParameters() for i in range(n_phkl)]
min_diff = self.get_peak_tolerance()
min_p = None
min_hkl = None
for i in range(n_phkl):
phkl = eval(self.peak_parameters['primary_hkl'].box.items()[i])
for hkls in self.rings[self.refine.rp[self.secondary]][1]:
for hkl in hkls:
hkl_angle = self.refine.angle_hkls(phkl, hkl)
diff = abs(ps_angle - hkl_angle)
if diff < self.get_peak_tolerance():
self.hkl_parameters[i].add(str(hkl),
hkl_angle,
str(hkl),
vary=False,
readonly=True)
if diff < min_diff:
min_diff = diff
min_p = i
min_hkl = str(hkl)
self.orient_box.insert_layout(
i + 1, self.hkl_parameters[i].grid(
header=['HKL', 'Angle (deg)', 'Select'], spacing=5))
if min_hkl is None:
raise NeXusError("No matching peaks found")
self.peak_parameters['primary_hkl'].box.setCurrentIndex(min_p)
self.hkl_parameters[min_p][min_hkl].vary = True
self.choose_secondary_grid()
def choose_secondary_grid(self):
box = self.peak_parameters['primary_hkl'].box
for i in [i for i in range(box.count()) if i != box.currentIndex()]:
self.hkl_parameters[i].hide_grid()
self.hkl_parameters[box.currentIndex()].show_grid()
@property
def primary_hkl(self):
return eval(self.peak_parameters['primary_hkl'].value)
@property
def secondary_hkl(self):
for hkls in self.hkl_parameters:
for hkl in hkls:
if hkls[hkl].vary is True:
return eval(hkls[hkl].name)
def orient(self):
self.refine.primary = self.primary
self.refine.secondary = self.secondary
self.refine.Umat = self.refine.get_UBmat(self.primary, self.secondary,
self.primary_hkl,
self.secondary_hkl)
self.update_table()
def export_peaks(self):
peaks = list(
zip(*[
p for p in self.table_model.peak_list
if p[-1] < self.get_hkl_tolerance()
]))
idx = NXfield(peaks[0], name='index')
x = NXfield(peaks[1], name='x')
y = NXfield(peaks[2], name='y')
z = NXfield(peaks[3], name='z')
pol = NXfield(peaks[4], name='polar_angle', units='degree')
azi = NXfield(peaks[5], name='azimuthal_angle', units='degree')
polarization = self.refine.get_polarization()
intensity = NXfield(peaks[6] / polarization[y, x], name='intensity')
H = NXfield(peaks[7], name='H', units='rlu')
K = NXfield(peaks[8], name='K', units='rlu')
L = NXfield(peaks[9], name='L', units='rlu')
diff = NXfield(peaks[10], name='diff')
peaks_data = NXdata(intensity, idx, diff, H, K, L, pol, azi, x, y, z)
export_dialog = ExportDialog(peaks_data, parent=self)
export_dialog.show()
def save_orientation(self):
self.write_parameters()
def close_peaks_box(self):
try:
self.peaks_box.close()
except Exception:
pass
self.peaks_box = None
def accept(self):
if 'transform' not in self.entry:
if self.confirm_action("Set up transforms?", answer="yes"):
self.treeview.select_node(self.entry)
from . import transform_data
transform_data.show_dialog()
super().accept()
