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()