def main():
parser = argparse.ArgumentParser(
description="Refine orientation matrix")
parser.add_argument('-d', '--directory', default='./',
help='directory containing the NeXus file')
parser.add_argument('-f', '--filename', required=True,
help='NeXus file name')
parser.add_argument('-e', '--entries', default=['f1', 'f2', 'f3'],
nargs='+', help='names of entries to be oriented')
parser.add_argument('-o', '--omega', default='0.0', help='omega start')
args = parser.parse_args()
name, ext = os.path.splitext(args.filename)
if ext == '':
args.filename = args.filename + '.nxs'
root = nxload(os.path.join(args.directory, args.filename), 'rw')
entries = args.entries
tic=timeit.default_timer()
for e in entries:
entry = root[e]
ref = NXRefine(entry)
old_score = ref.score()
print 'Current lattice parameters: ', ref.a, ref.b, ref.c
print '%s peaks; Old score: %.4f' % (len(ref.idx), old_score)
success, info, msg = refine_orientation(ref)
new_score = ref.score()
print 'Success:', success, ' ', msg
print 'No. of function calls:', info['nfev']
print 'New lattice parameters: ', ref.a, ref.b, ref.c
print '%s peaks; New score: %.4f' % (len(ref.idx), new_score)
if new_score <= old_score and success > 0 and success < 5:
write_parameters(ref)
note = NXnote('nxorient '+' '.join(sys.argv[1:]),
('Current machine: %s\n'
'Current working directory: %s')
% (socket.gethostname(), os.getcwd()))
entry['nxorient'] = NXprocess(program='nxorient',
sequence_index=len(entry.NXprocess)+1,
version=__version__,
note=note)
toc=timeit.default_timer()
print toc-tic, 'seconds for', args.filename
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 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_start, 'Phi Start (deg)')
self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)')
self.parameters.add('chi_start', self.refine.chi_start, 'Chi Start (deg)')
self.parameters.add('chi_step', self.refine.chi_step, 'Chi Step (deg)')
self.parameters.add('omega_start', self.refine.omega_start, 'Omega Start (deg)')
self.parameters.add('omega_step', self.refine.omega_step, 'Omega Step (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 = QtGui.QHBoxLayout()
self.grain_combo = QtGui.QComboBox()
self.grain_combo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
self.grain_combo.currentIndexChanged.connect(self.set_grain)
self.grain_textbox = QtGui.QLabel()
self.grain_layout.addWidget(self.grain_combo)
self.grain_layout.addStretch()
self.grain_layout.addWidget(self.grain_textbox)
bottom_layout = QtGui.QHBoxLayout()
self.result_textbox = QtGui.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_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
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_start'].value,
self.parameters['chi_step'].value)
def set_chi(self):
self.refine.chi_start, self.refine.chi_step = self.get_chi()
def get_omega(self):
return (self.parameters['omega_start'].value,
self.parameters['omega_step'].value)
def set_omega(self):
self.refine.omega_start, self.refine.omega_step = 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_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()
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 = 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)
refine_button = QtGui.QPushButton('Refine')
refine_button.clicked.connect(self.refine_orientation)
restore_button = QtGui.QPushButton('Restore')
restore_button.clicked.connect(self.restore_orientation)
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)
orient_layout.addWidget(refine_button)
orient_layout.addWidget(restore_button)
grid = QtGui.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 = 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.addLayout(grid)
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(message_box.close)
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)
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)