class MaskDialog(BaseDialog):
def __init__(self, parent=None):
super(MaskDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.parameters = GridParameters()
self.parameters.add('mask', 'pilatus_mask/entry/mask', 'Mask Path')
self.action_buttons(('Save Mask', self.save_mask))
self.set_layout(self.entry_layout, self.parameters.grid(),
self.action_buttons(('Save Mask', self.save_mask)),
self.close_buttons())
self.set_title('Mask Data')
def save_mask(self):
try:
mask = self.treeview.tree[self.parameters['mask'].value]
if mask.dtype != np.bool:
raise NeXusError('Mask must be a Boolean array')
elif len(mask.shape) == 1:
raise NeXusError('Mask must be at least two-dimensional')
elif len(mask.shape) > 2:
mask = mask[0]
self.entry['instrument/detector/pixel_mask'] = mask
self.entry['instrument/detector/pixel_mask_applied'] = False
except NeXusError as error:
report_error('Applying Mask', error)
class SampleDialog(BaseDialog):
def __init__(self, parent=None):
super(SampleDialog, self).__init__(parent)
self.sample = GridParameters()
self.sample.add('sample', 'sample', 'Sample Name')
self.sample.add('label', 'label', 'Sample Label')
self.set_layout(self.directorybox('Choose Experiment Directory',
default=False),
self.sample.grid(header=False),
self.close_buttons(save=True))
self.set_title('New Sample')
def accept(self):
home_directory = self.get_directory()
self.mainwindow.default_directory = home_directory
sample_directory = os.path.join(home_directory,
self.sample['sample'].value,
self.sample['label'].value)
if not os.path.exists(sample_directory):
os.makedirs(sample_directory)
super(SampleDialog, self).accept()
class SettingsDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
try:
self.settings = NXSettings()
default_directory = self.settings.directory
except NeXusError:
self.settings = None
default_directory = ""
self.set_layout(
self.directorybox('Choose Settings Directory',
suggestion=default_directory),
self.close_layout(save=True))
if self.settings:
self.define_parameters()
self.set_title('New Settings')
def choose_directory(self):
super().choose_directory()
directory = self.get_directory()
self.settings = NXSettings(directory=directory)
self.define_parameters()
def define_parameters(self):
self.refine_parameters = GridParameters()
defaults = self.settings.settings['nxrefine']
for p in defaults:
self.refine_parameters.add(p, defaults[p], p)
self.reduce_parameters = GridParameters()
defaults = self.settings.settings['nxreduce']
for p in defaults:
self.reduce_parameters.add(p, defaults[p], p)
if self.layout.count() == 2:
self.layout.insertLayout(
1, self.refine_parameters.grid(header=False, title='NXRefine'))
self.layout.insertLayout(
2, self.reduce_parameters.grid(header=False, title='NXReduce'))
def accept(self):
try:
for p in self.refine_parameters:
self.settings.set('nxrefine', p,
self.refine_parameters[p].value)
for p in self.reduce_parameters:
self.settings.set('nxreduce', p,
self.reduce_parameters[p].value)
self.settings.save()
super().accept()
except Exception as error:
report_error("Defining New Settings", error)
class EnergyDialog(BaseDialog):
def __init__(self, parent=None):
super(EnergyDialog, self).__init__(parent)
layout = QtGui.QVBoxLayout()
self.select_entry()
self.parameters = GridParameters()
self.parameters.add('m1', self.entry['monitor1/distance'],
'Monitor 1 Distance')
self.parameters.add('m2', self.entry['monitor2/distance'],
'Monitor 2 Distance')
self.parameters.add('Ei', self.entry['instrument/monochromator/energy'],
'Incident Energy')
self.parameters.add('mod', self.entry['instrument/source/distance'],
'Moderator Distance')
layout.addLayout(self.entry_layout)
layout.addLayout(self.parameters.grid())
layout.addLayout(self.action_buttons(('Get Ei', self.get_ei)))
layout.addWidget(self.close_buttons(save=True))
self.setLayout(layout)
self.setWindowTitle('Get Incident Energy')
self.m1 = self.entry['monitor1']
self.m2 = self.entry['monitor2']
@property
def m1_distance(self):
return self.parameters['m1'].value - self.moderator_distance
@property
def m2_distance(self):
return self.parameters['m2'].value - self.moderator_distance
@property
def Ei(self):
return self.parameters['Ei'].value
@property
def moderator_distance(self):
return self.parameters['mod'].value
def get_ei(self):
t = 2286.26 * self.m1_distance / np.sqrt(self.Ei)
m1_time = self.m1[t-200.0:t+200.0].moment()
t = 2286.26 * self.m2_distance / np.sqrt(self.Ei)
m2_time = self.m2[t-200.0:t+200.0].moment()
self.parameters['Ei'].value = (2286.26 * (self.m2_distance - self.m1_distance) /
(m2_time - m1_time))**2
def accept(self):
try:
self.parameters['Ei'].save()
except NeXusError as error:
report_error("Getting Incident Energy", error)
super(EnergyDialog, self).accept()
class EnergyDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry()
self.parameters = GridParameters()
self.parameters.add('m1', self.entry['monitor1/distance'],
'Monitor 1 Distance')
self.parameters.add('m2', self.entry['monitor2/distance'],
'Monitor 2 Distance')
self.parameters.add('Ei',
self.entry['instrument/monochromator/energy'],
'Incident Energy')
self.parameters.add('mod', self.entry['instrument/source/distance'],
'Moderator Distance')
action_buttons = self.action_buttons(('Get Ei', self.get_ei))
self.set_layout(self.entry_layout, self.parameters.grid(),
action_buttons, self.close_buttons(save=True))
self.set_title('Get Incident Energy')
self.m1 = self.entry['monitor1']
self.m2 = self.entry['monitor2']
@property
def m1_distance(self):
return self.parameters['m1'].value - self.moderator_distance
@property
def m2_distance(self):
return self.parameters['m2'].value - self.moderator_distance
@property
def Ei(self):
return self.parameters['Ei'].value
@property
def moderator_distance(self):
return self.parameters['mod'].value
def get_ei(self):
t = 2286.26 * self.m1_distance / np.sqrt(self.Ei)
m1_time = self.m1[t - 200.0:t + 200.0].moment()
t = 2286.26 * self.m2_distance / np.sqrt(self.Ei)
m2_time = self.m2[t - 200.0:t + 200.0].moment()
self.parameters['Ei'].value = (2286.26 *
(self.m2_distance - self.m1_distance) /
(m2_time - m1_time))**2
def accept(self):
try:
self.parameters['Ei'].save()
except NeXusError as error:
report_error("Getting Incident Energy", error)
super().accept()
class SampleDialog(BaseDialog):
def __init__(self, parent=None):
super(SampleDialog, self).__init__(parent)
self.sample = GridParameters()
self.sample.add('sample', 'sample', 'Sample Name')
self.sample.add('label', 'label', 'Sample Label')
self.set_layout(
self.directorybox('Choose Experiment Directory', default=False),
self.sample.grid(header=False), self.close_buttons(save=True))
self.set_title('New Sample')
def accept(self):
home_directory = self.get_directory()
self.mainwindow.default_directory = home_directory
sample_directory = os.path.join(home_directory,
self.sample['sample'].value,
self.sample['label'].value)
if not os.path.exists(sample_directory):
os.makedirs(sample_directory)
super(SampleDialog, self).accept()
class ExperimentDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.parameters = GridParameters()
self.parameters.add('experiment', 'experiment', 'Experiment')
self.set_layout(
self.directorybox('Choose Home Directory', default=False),
self.parameters.grid(header=False), self.close_layout(save=True))
self.set_title('New Experiment')
def accept(self):
try:
home_directory = self.get_directory()
experiment_directory = os.path.join(
home_directory, self.parameters['experiment'].value)
if not os.path.exists(experiment_directory):
os.makedirs(experiment_directory)
self.mainwindow.default_directory = experiment_directory
configuration_directory = os.path.join(experiment_directory,
'configurations')
if not os.path.exists(configuration_directory):
os.makedirs(configuration_directory)
task_directory = os.path.join(experiment_directory, 'tasks')
if not os.path.exists(task_directory):
os.makedirs(task_directory)
nxdb = NXDatabase(os.path.join(task_directory, 'nxdatabase.db'))
calibration_directory = os.path.join(experiment_directory,
'calibrations')
if not os.path.exists(calibration_directory):
os.makedirs(calibration_directory)
script_directory = os.path.join(experiment_directory, 'scripts')
if not os.path.exists(script_directory):
os.makedirs(script_directory)
super().accept()
except Exception as error:
report_error("Defining New Experiment", error)
class EnergyDialog(BaseDialog):
def __init__(self, parent=None):
super(EnergyDialog, self).__init__(parent)
self.select_entry()
self.parameters = GridParameters()
self.parameters.add("m1", self.entry["monitor1/distance"], "Monitor 1 Distance")
self.parameters.add("m2", self.entry["monitor2/distance"], "Monitor 2 Distance")
self.parameters.add("Ei", self.entry["instrument/monochromator/energy"], "Incident Energy")
self.parameters.add("mod", self.entry["instrument/source/distance"], "Moderator Distance")
action_buttons = self.action_buttons(("Get Ei", self.get_ei))
self.set_layout(self.entry_layout, self.parameters.grid(), action_buttons, self.close_buttons(save=True))
self.set_title("Get Incident Energy")
self.m1 = self.entry["monitor1"]
self.m2 = self.entry["monitor2"]
@property
def m1_distance(self):
return self.parameters["m1"].value - self.moderator_distance
@property
def m2_distance(self):
return self.parameters["m2"].value - self.moderator_distance
@property
def Ei(self):
return self.parameters["Ei"].value
@property
def moderator_distance(self):
return self.parameters["mod"].value
def get_ei(self):
t = 2286.26 * self.m1_distance / np.sqrt(self.Ei)
m1_time = self.m1[t - 200.0 : t + 200.0].moment()
t = 2286.26 * self.m2_distance / np.sqrt(self.Ei)
m2_time = self.m2[t - 200.0 : t + 200.0].moment()
self.parameters["Ei"].value = (2286.26 * (self.m2_distance - self.m1_distance) / (m2_time - m1_time)) ** 2
def accept(self):
try:
self.parameters["Ei"].save()
except NeXusError as error:
report_error("Getting Incident Energy", error)
super(EnergyDialog, self).accept()
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()
class ConvertDialog(BaseDialog):
def __init__(self, parent=None):
super(ConvertDialog, self).__init__(parent)
layout = QtGui.QVBoxLayout()
self.select_entry()
self.parameters = GridParameters()
self.parameters.add('Ei', self.entry['instrument/monochromator/energy'],
'Incident Energy')
self.parameters.add('dQ', self.round(np.sqrt(self.Ei/2)/50), 'Q Step')
self.parameters.add('dE', self.round(self.Ei/50), 'Energy Step')
layout.addLayout(self.entry_layout)
layout.addLayout(self.parameters.grid())
layout.addLayout(self.action_buttons(('Plot', self.plot_data),
('Save', self.save_data)))
layout.addWidget(self.close_buttons())
self.setLayout(layout)
self.setWindowTitle('Converting to (Q,E)')
@property
def Ei(self):
return self.parameters['Ei'].value
@property
def dQ(self):
return self.parameters['dQ'].value
@property
def dE(self):
return self.parameters['dE'].value
def read_parameters(self):
self.L1 = - self.entry['sample/distance']
self.L2 = np.mean(self.entry['instrument/detector/distance'])
self.m1 = self.entry['monitor1']
self.t_m1 = self.m1.moment()
self.d_m1 = self.entry['monitor1/distance']
def convert_tof(self, tof):
ki = np.sqrt(self.Ei / 2.0721)
ts = self.t_m1 + 1588.254 * (self.L1 - self.d_m1) / ki
kf = 1588.254 * self.L2 / (tof - ts)
eps = self.Ei - 2.0721*kf**2
return eps
def convert_QE(self):
"""Convert S(phi,eps) to S(Q,eps)"""
self.read_parameters()
Ei = self.Ei
dQ = self.dQ
dE = self.dE
pol, tof = centers(self.entry['data'].nxsignal, self.entry['data'].nxaxes)
en = self.convert_tof(tof)
idx_max = min(np.where(np.abs(en-0.75*Ei)<0.1)[0])
en = en[:idx_max]
data = self.entry['data'].nxsignal.nxdata[:,:idx_max]
if self.entry['data'].nxerrors:
errors = self.entry['data'].nxerrors.nxdata[:]
Q = np.zeros((len(pol), len(en)))
E = np.zeros((len(pol), len(en)))
for i in range(0,len(pol)):
p = pol[i]
Q[i,:] = np.array(np.sqrt((2*Ei - en - 2*np.sqrt(Ei*(Ei-en))
* np.cos(p*np.pi/180.0))/2.0721))
E[i,:] = np.array(en)
s = Q.shape
Qin = Q.reshape(s[0]*s[1])
Ein = E.reshape(s[0]*s[1])
datain = data.reshape(s[0]*s[1])
if self.entry['data'].nxerrors:
errorsin = errors.reshape(s[0]*s[1])
qmin = Q.min()
qmax = Q.max()
emin = E.min()
emax = E.max()
NQ = int((qmax-qmin)/dQ) + 1
NE = int((emax-emin)/dE) + 1
Qb = np.linspace(qmin, qmax, NQ)
Eb = np.linspace(emin, emax, NE)
#histogram and normalize
norm, nbin = np.histogramdd((Ein,Qin), bins=(Eb,Qb))
hist, hbin = np.histogramdd((Ein,Qin), bins=(Eb,Qb), weights=datain)
if self.entry['data'].nxerrors:
histe, hbin = np.histogramdd((Ein,Qin), bins=(Eb,Qb), weights=errorsin*errorsin)
histe = histe**0.5
err = histe/norm
I = NXfield(hist/norm, name='S(Q,E)')
Qb = NXfield(Qb[:-1]+dQ/2., name='Q')
Eb = NXfield(Eb[:-1]+dE/2., name='E')
result = NXdata(I, (Eb, Qb))
if self.entry.data.nxerrors:
result.errors = NXfield(err)
return result
def round(self, x, prec=2, base=.05):
return round(base * round(float(x)/base), prec)
def plot_data(self):
self.convert_QE().plot()
def save_data(self):
self.entry['sqe'] = self.convert_QE()
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 ConfigurationDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.settings = NXSettings().settings
self.configuration_file = NXroot()
self.configuration_file['entry'] = NXentry()
self.detectors = {}
self.entries = {}
self.setup_groups()
self.setup_configuration()
self.setup_analysis()
self.setup_scan()
self.setup_instrument()
self.set_layout(
self.directorybox('Choose Experiment Directory', default=False),
self.configuration.grid(header=False),
self.analysis.grid(header=False, title='Analysis Settings'),
self.scan.grid(header=False, title='Scan Settings'),
self.instrument.grid(header=False, title='Detector Settings'))
self.set_title('New Configuration')
def setup_groups(self):
entry = self.configuration_file['entry']
entry['nxreduce'] = NXparameters()
entry['instrument'] = NXinstrument()
entry['instrument/monochromator'] = NXmonochromator()
entry['instrument/goniometer'] = NXgoniometer()
entry['instrument/detector'] = NXdetector()
def setup_configuration(self):
default = self.settings['nxrefine']
entry = self.configuration_file['entry']
entry['instrument/monochromator/wavelength'] = NXfield(
default['wavelength'], dtype=np.float32)
entry['instrument/monochromator/wavelength'].attrs['units'] = (
'Angstroms')
entry['instrument/monochromator/energy'] = NXfield(12.398419739640717 /
0.5,
dtype=np.float32)
entry['instrument/monochromator/energy'].attrs['units'] = 'keV'
entry['instrument/goniometer'] = NXgoniometer()
entry['instrument/detector'] = NXdetector()
self.configuration = GridParameters()
self.configuration.add('configuration', 'configuration',
'Configuration Filename')
self.configuration.add('wavelength',
entry['instrument/monochromator/wavelength'],
'Wavelength (Å)')
def setup_analysis(self):
default = self.settings['nxreduce']
entry = self.configuration_file['entry']
entry['nxreduce/threshold'] = NXfield(default['threshold'],
dtype=float)
entry['nxreduce/monitor'] = NXfield(default['monitor'])
entry['nxreduce/norm'] = NXfield(default['norm'], dtype=float)
entry['nxreduce/first_frame'] = NXfield(default['first'], dtype=int)
entry['nxreduce/last_frame'] = NXfield(default['last'], dtype=int)
entry['nxreduce/radius'] = NXfield(default['radius'], dtype=float)
self.analysis = GridParameters()
self.analysis.add('threshold', entry['nxreduce/threshold'],
'Peak Threshold')
self.analysis.add('first', entry['nxreduce/first_frame'],
'First Frame')
self.analysis.add('last', entry['nxreduce/last_frame'], 'Last Frame')
self.analysis.add('monitor', ['monitor1', 'monitor2'],
'Normalization Monitor')
self.analysis['monitor'].value = default['monitor']
self.analysis.add('norm', entry['nxreduce/norm'],
'Normalization Value')
self.analysis.add('radius', entry['nxreduce/radius'],
'Punch Radius (Å)')
def setup_scan(self):
default = self.settings['nxrefine']
entry = self.configuration_file['entry']
entry['instrument/goniometer/chi'] = (NXfield(default['chi'],
dtype=float))
entry['instrument/goniometer/chi'].attrs['units'] = 'degree'
entry['instrument/goniometer/phi'] = (NXfield(default['phi'],
dtype=float))
entry['instrument/goniometer/phi'].attrs['step'] = (NXfield(
default['phi_step'], dtype=float))
entry['instrument/goniometer/phi'].attrs['end'] = (NXfield(
default['phi_end'], dtype=float))
entry['instrument/goniometer/phi'].attrs['units'] = 'degree'
entry['instrument/detector/frame_time'] = (NXfield(
1 / float(default['frame_rate']), dtype=float))
self.scan = GridParameters()
self.scan.add('chi', default['chi'], 'Chi (deg)')
self.scan.add('phi_start', default['phi'], 'Phi Start (deg)')
self.scan.add('phi_end', default['phi_end'], 'Phi End (deg)')
self.scan.add('phi_step', default['phi_step'], 'Phi Step (deg)')
self.scan.add('frame_rate', default['frame_rate'], 'Frame Rate (Hz)')
def setup_instrument(self):
default = self.settings['nxrefine']
entry = self.configuration_file['entry']
entry['instrument/detector/distance'] = NXfield(default['distance'],
dtype=float)
entry['instrument/detector/distance'].attrs['units'] = 'mm'
self.instrument = GridParameters()
self.instrument.add('distance', entry['instrument/detector/distance'],
'Detector Distance (mm)')
detector_list = sorted(
list(set([detector().name
for detector in ALL_DETECTORS.values()])))
self.instrument.add('detector', detector_list, 'Detector')
self.instrument['detector'].value = 'Pilatus CdTe 2M'
self.instrument.add('positions', [0, 1, 2, 3, 4, 5, 6, 7, 8],
'Number of Detector Positions',
slot=self.set_entries)
self.instrument['positions'].value = '0'
def setup_entry(self, position):
default = self.settings['nxrefine']
entry = NXentry()
self.detectors[position] = GridParameters()
self.detectors[position].add('x', default['x'], 'Translation - x (mm)')
self.detectors[position].add('y', default['y'], 'Translation - y (mm)')
self.detectors[position].add('omega', default['omega'], 'Omega (deg)')
self.configuration_file[f'f{position}'] = entry
def get_detector(self):
for detector in ALL_DETECTORS:
if (ALL_DETECTORS[detector]().name ==
self.instrument['detector'].value):
return ALL_DETECTORS[detector]()
@property
def positions(self):
return int(self.instrument['positions'].value)
@property
def position(self):
try:
return int(self.entry_box.currentText())
except ValueError:
return 1
def set_entries(self):
self.entry_box = self.select_box(
[str(i) for i in range(1, self.positions + 1)],
slot=self.choose_position)
self.entry_layout = self.make_layout(
self.labels('Position', header=True), self.entry_box)
self.add_layout(self.entry_layout)
for position in range(1, self.positions + 1):
self.setup_entry(position)
self.add_layout(self.detectors[position].grid(header=False))
if position != 1:
self.detectors[position].hide_grid()
self.add_layout(self.close_buttons(save=True))
def choose_position(self):
for i in self.detectors:
self.detectors[i].hide_grid()
if self.position in self.detectors:
self.detectors[self.position].show_grid()
def get_parameters(self):
entry = self.configuration_file['entry']
entry['nxreduce/threshold'] = self.analysis['threshold'].value
entry['nxreduce/first_frame'] = self.analysis['first'].value
entry['nxreduce/last_frame'] = self.analysis['last'].value
entry['nxreduce/monitor'] = self.analysis['monitor'].value
entry['nxreduce/norm'] = self.analysis['norm'].value
entry['nxreduce/radius'] = self.analysis['radius'].value
entry['instrument/monochromator/wavelength'] = (
self.configuration['wavelength'].value)
entry['instrument/monochromator/energy'] = (
12.398419739640717 / self.configuration['wavelength'].value)
detector = self.get_detector()
entry['instrument/detector/description'] = detector.name
entry['instrument/detector/distance'] = (
self.instrument['distance'].value)
entry['instrument/detector/pixel_size'] = detector.pixel1 * 1000
entry['instrument/detector/pixel_size'].attrs['units'] = 'mm'
entry['instrument/detector/pixel_mask'] = detector.mask
entry['instrument/detector/shape'] = detector.shape
entry['instrument/detector/yaw'] = 0.0
entry['instrument/detector/pitch'] = 0.0
entry['instrument/detector/roll'] = 0.0
for position in range(1, self.positions + 1):
entry = self.configuration_file[f'f{position}']
entry['instrument'] = self.configuration_file['entry/instrument']
entry['instrument/detector/translation_x'] = (
self.detectors[position]['x'].value)
entry['instrument/detector/translation_x'].attrs['units'] = 'mm'
entry['instrument/detector/translation_y'] = (
self.detectors[position]['y'].value)
entry['instrument/detector/translation_y'].attrs['units'] = 'mm'
if self.scan['frame_rate'].value > 0.0:
entry['instrument/detector/frame_time'] = (
1.0 / self.scan['frame_rate'].value)
else:
entry['instrument/detector/frame_time'] = 0.1
entry['instrument/detector/frame_time'].attrs['units'] = 's'
entry['instrument/goniometer/phi'] = self.scan['phi_start'].value
entry['instrument/goniometer/phi'].attrs['step'] = (
self.scan['phi_step'].value)
entry['instrument/goniometer/phi'].attrs['end'] = (
self.scan['phi_end'].value)
entry['instrument/goniometer/chi'] = self.scan['chi'].value
entry['instrument/goniometer/omega'] = (
self.detectors[position]['omega'].value)
def accept(self):
try:
experiment_directory = self.get_directory()
configuration_directory = os.path.join(experiment_directory,
'configurations')
self.mainwindow.default_directory = experiment_directory
self.get_parameters()
self.configuration_file.save(
os.path.join(
configuration_directory,
self.configuration['configuration'].value + '.nxs'))
self.treeview.tree.load(self.configuration_file.nxfilename, 'rw')
super().accept()
except Exception as error:
report_error("Defining New Configuration", error)
class CalculateDialog(BaseDialog):
def __init__(self, parent=None):
super(CalculateDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine(self.entry)
self.refine.read_parameters()
self.parameters = GridParameters()
self.parameters.add('wavelength', self.refine.wavelength, 'Wavelength (Ang)')
self.parameters.add('distance', self.refine.distance, 'Detector Distance (mm)')
self.parameters.add('xc', self.refine.xc, 'Beam Center - x')
self.parameters.add('yc', self.refine.yc, 'Beam Center - y')
self.parameters.add('pixel', self.refine.pixel_size, 'Pixel Size (mm)')
action_buttons = self.action_buttons(('Plot', self.plot_lattice),
('Save', self.write_parameters))
self.set_layout(self.entry_layout, self.parameters.grid(),
action_buttons, self.close_buttons())
self.set_title('Calculate Angles')
def choose_entry(self):
self.refine = NXRefine(self.entry)
self.update_parameters()
def update_parameters(self):
self.parameters['wavelength'].value = self.refine.wavelength
self.parameters['distance'].value = self.refine.distance
self.parameters['xc'].value = self.refine.xc
self.parameters['yc'].value = self.refine.yc
self.parameters['pixel'].value = self.refine.pixel_size
def get_wavelength(self):
return self.parameters['wavelength'].value
def get_distance(self):
return self.parameters['distance'].value
def get_centers(self):
return self.parameters['xc'].value, self.parameters['yc'].value
def get_pixel_size(self):
return self.parameters['pixel'].value
def get_parameters(self):
self.refine.wavelength = self.get_wavelength()
self.refine.distance = self.get_distance()
self.refine.xc, self.refine.yc = self.get_centers()
self.refine.pixel_size = self.get_pixel_size()
self.refine.yaw = self.refine.pitch = self.refine.roll = None
def plot_lattice(self):
try:
self.get_parameters()
self.plot_peaks(self.refine.xp, self.refine.yp)
except NeXusError as error:
report_error('Calculating Angles', error)
def plot_peaks(self, x, y):
try:
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 write_parameters(self):
try:
self.get_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()
except NeXusError as error:
report_error('Calculating Angles', error)
class Mask3DDialog(BaseDialog):
def __init__(self, parent=None):
super(Mask3DDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.parameters = GridParameters()
self.parameters.add('radius', 200, 'Radius')
self.parameters.add('width', 3, 'Frame Width')
self.set_layout(self.entry_layout,
self.parameters.grid(),
self.action_buttons(('Calculate 3D Mask', self.calculate_mask)),
self.progress_layout(save=True))
self.progress_bar.setVisible(False)
self.progress_bar.setValue(0)
self.set_title('Calculate 3D Mask')
self.reduce = None
def choose_entry(self):
self.reduce = NXReduce(self.entry)
@property
def radius(self):
return self.parameters['radius'].value
@property
def width(self):
return self.parameters['width'].value
def calculate_mask(self):
self.check_lock(self.reduce.wrapper_file)
self.thread = QtCore.QThread()
self.reduce = NXReduce(self.entry, radius=self.radius, width=self.width,
mask=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.calculate_mask)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxfind)
self.thread.start(QtCore.QThread.LowestPriority)
def check_lock(self, file_name):
try:
with Lock(file_name, timeout=2):
pass
except LockException as error:
if self.confirm_action('Clear lock?', str(error)):
Lock(file_name).release()
def calculate_mask(self, mask):
self.mask = mask
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.thread.exit()
def accept(self):
try:
with Lock(self.reduce.wrapper_file):
self.reduce.write_peaks(self.peaks)
except LockException as error:
if self.confirm_action('Clear lock?', str(error)):
Lock(self.reduce.wrapper_file).release()
if self.thread:
self.stop()
super(Mask3DDialog, self).accept()
def reject(self):
if self.thread:
self.stop()
super(Mask3DDialog, self).reject()
class MaximumDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
self.parameters = GridParameters()
self.parameters.add('first', '', 'First Frame')
self.parameters.add('last', '', 'Last Frame')
self.output = NXLabel('Maximum Value:')
self.set_layout(
self.entry_layout, self.output, self.parameters.grid(),
self.action_buttons(('Find Maximum', self.find_maximum)),
self.progress_layout(save=True))
self.progress_bar.setVisible(False)
self.progress_bar.setValue(0)
self.set_title('Find Maximum Value')
self.reduce = None
def choose_entry(self):
self.reduce = NXReduce(self.entry)
self.maximum = self.reduce.maximum
if self.reduce.first:
self.parameters['first'].value = self.reduce.first
if self.reduce.last:
self.parameters['last'].value = self.reduce.last
@property
def first(self):
try:
_first = np.int32(self.parameters['first'].value)
if _first >= 0:
return _first
else:
return None
except Exception as error:
return None
@property
def last(self):
try:
_last = np.int32(self.parameters['last'].value)
if _last > 0:
return _last
else:
return None
except Exception as error:
return None
@property
def maximum(self):
return np.float(self.output.text().split()[-1])
@maximum.setter
def maximum(self, value):
self.output.setText(f'Maximum Value: {value}')
def find_maximum(self):
if is_file_locked(self.reduce.data_file):
return
self.start_thread()
self.reduce = NXReduce(self.entry,
first=self.first,
last=self.last,
maxcount=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_maximum)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxmax)
self.thread.finished.connect(self.stop)
self.thread.start(QtCore.QThread.LowestPriority)
def get_maximum(self, maximum):
self.maximum = maximum
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.stop_thread()
def accept(self):
try:
self.reduce.write_maximum(self.maximum)
self.reduce.record('nxmax',
maximum=self.maximum,
first_frame=self.first,
last_frame=self.last)
self.reduce.record_end('nxmax')
self.stop()
super().accept()
except Exception as error:
report_error("Finding Maximum", error)
def reject(self):
self.stop()
super().reject()
class ScanDialog(BaseDialog):
def __init__(self, parent=None):
super(ScanDialog, self).__init__(parent)
self.config_file = None
self.positions = 1
self.entries = {}
self.directory_box = self.directorybox('Choose Experiment Directory',
self.choose_directory,
default=False)
self.configuration_box = self.select_configuration()
self.configuration_layout = self.make_layout(
self.action_buttons(('Choose Experiment Configuration',
self.choose_configuration)),
self.configuration_box)
self.sample_box = self.select_sample()
self.sample_layout = self.make_layout(
self.action_buttons(('Choose Sample', self.choose_sample)),
self.sample_box)
self.scan_box = self.select_box(['1'], slot=self.choose_position)
self.setup_scans()
self.set_layout(self.directory_box,
self.configuration_layout,
self.sample_layout,
self.scan.grid(header=False),
self.make_layout(self.labels('Position'), self.scan_box),
self.entries[1].grid(header=False),
self.entries[2].grid(header=False),
self.entries[3].grid(header=False),
self.entries[4].grid(header=False),
self.entries[5].grid(header=False),
self.action_buttons(('Make Scan File', self.make_scan)),
self.close_buttons(close=True))
for i in self.entries:
self.entries[i].hide_grid()
self.entries[1].show_grid()
self.set_title('New Scan')
@property
def configuration(self):
return self.configuration_box.currentText()
@property
def sample(self):
return self.sample_box.currentText().split('/')[0]
@property
def label(self):
return self.sample_box.currentText().split('/')[1]
@property
def position(self):
try:
return int(self.scan_box.currentText())
except ValueError:
return 1
def choose_directory(self):
super(ScanDialog, self).choose_directory()
self.mainwindow.default_directory = self.get_directory()
self.setup_directory()
def setup_directory(self):
self.configuration_box.clear()
configurations = self.get_configurations()
for configuration in configurations:
self.configuration_box.addItem(configuration)
self.choose_configuration()
self.sample_box.clear()
samples = self.get_samples()
for sample in samples:
self.sample_box.addItem(sample)
self.sample_box.adjustSize()
self.choose_sample()
def select_configuration(self):
return self.select_box(self.get_configurations())
def get_configurations(self):
home_directory = self.get_directory()
if (os.path.exists(home_directory) and
'configurations' in os.listdir(home_directory)):
return [f for f in
os.listdir(os.path.join(home_directory, 'configurations'))
if f.endswith('.nxs')]
else:
return []
def choose_configuration(self):
home_directory = self.get_directory()
config_file = os.path.join(home_directory, 'configurations',
self.configuration)
if os.path.exists(config_file):
self.config_file = nxload(config_file)
self.positions = len(self.config_file.entries) - 1
self.scan_box.clear()
for position in range(1, self.positions+1):
self.scan_box.addItem('%d' % position)
self.scan_box.setCurrentIndex(0)
self.copy_configuration()
def select_sample(self):
return self.select_box(self.get_samples())
def get_samples(self):
home_directory = self.get_directory()
if (os.path.exists(home_directory) and
'configurations' in os.listdir(home_directory)):
sample_directories = [f for f in os.listdir(home_directory)
if (not f.startswith('.') and
os.path.isdir(
os.path.join(home_directory, f)))]
else:
return []
samples = []
for sample_directory in sample_directories:
label_directories = [f for f in
os.listdir(os.path.join(home_directory, sample_directory))
if os.path.isdir(os.path.join(home_directory, sample_directory, f))]
for label_directory in label_directories:
samples.append(os.path.join(sample_directory, label_directory))
return [sample.strip() for sample in samples]
def choose_sample(self):
pass
def setup_scans(self):
self.scan = GridParameters()
self.scan.add('scan', 'scan', 'Scan Label')
self.scan.add('temperature', 300.0, 'Temperature (K)')
self.scan.add('phi_start', -5.0, 'Phi Start (deg)')
self.scan.add('phi_end', 360.0, 'Phi End (deg)')
self.scan.add('phi_step', 0.1, 'Phi Step (deg)')
self.scan.add('frame_rate', 10, 'Frame Rate (Hz)')
for position in range(1, 6):
self.setup_position(position)
def setup_position(self, position):
self.entries[position] = GridParameters()
self.entries[position].add('chi', -90.0, 'Chi (deg)')
self.entries[position].add('omega', 0.0, 'Omega (deg)')
self.entries[position].add('x', 0.0, 'Translation - x (mm)')
self.entries[position].add('y', 0.0, 'Translation - y (mm)')
self.entries[position].add('linkfile', 'f%d.h5' % position, 'Detector Filename')
self.entries[position].add('linkpath', '/entry/data/data', 'Detector Data Path')
def choose_position(self):
for i in self.entries:
self.entries[i].hide_grid()
if self.position in self.entries:
self.entries[self.position].show_grid()
def copy_configuration(self):
self.scan_file = NXroot()
for entry in self.config_file.entries:
self.scan_file[entry] = self.config_file[entry]
self.read_parameters()
def read_parameters(self):
for position in range(1, self.positions+1):
entry = self.scan_file['f%d' % position]
self.entries[position]['x'].value = entry['instrument/detector/translation_x']
self.entries[position]['y'].value = entry['instrument/detector/translation_y']
def get_parameters(self):
entry = self.scan_file['entry']
if 'sample' not in entry:
entry['sample'] = NXsample()
entry['sample/name'] = self.sample
entry['sample/label'] = self.label
entry['sample/temperature'] = self.scan['temperature'].value
entry['sample/temperature'].attrs['units'] = 'K'
y_size, x_size = entry['instrument/detector/shape'].nxvalue
scan = self.scan['scan'].value
for position in range(1, self.positions+1):
entry = self.scan_file['f%d' % position]
entry.makelink(self.scan_file['entry/sample'])
phi_start = self.scan['phi_start'].value
phi_end = self.scan['phi_end'].value
phi_step = self.scan['phi_step'].value
chi = self.entries[position]['chi'].value
omega = self.entries[position]['omega'].value
frame_rate = self.scan['frame_rate'].value
if 'goniometer' not in entry['instrument']:
entry['instrument/goniometer'] = NXgoniometer()
entry['instrument/goniometer/phi'] = phi_start
entry['instrument/goniometer/phi_set'] = phi_start
entry['instrument/goniometer/phi'].attrs['step'] = phi_step
entry['instrument/goniometer/phi'].attrs['end'] = phi_end
entry['instrument/goniometer/chi'] = chi
entry['instrument/goniometer/chi_set'] = chi
entry['instrument/goniometer/omega'] = omega
entry['instrument/goniometer/omega_set'] = omega
if frame_rate > 0.0:
entry['instrument/detector/frame_time'] = 1.0 / frame_rate
linkpath = self.entries[position]['linkpath'].value
linkfile = os.path.join(scan, self.entries[position]['linkfile'].value)
entry['data'] = NXdata()
entry['data'].nxsignal = NXlink(linkpath, linkfile)
entry['data/x_pixel'] = np.arange(x_size, dtype=np.int32)
entry['data/y_pixel'] = np.arange(y_size, dtype=np.int32)
entry['data/frame_number'] = np.arange(
(phi_end-phi_start)/phi_step, dtype=np.int32)
entry['data'].nxaxes = [entry['data/frame_number'],
entry['data/y_pixel'],
entry['data/x_pixel']]
def make_scan(self):
home_directory = self.get_directory()
self.mainwindow.default_directory = home_directory
sample_directory = os.path.join(home_directory, self.sample)
label_directory = os.path.join(home_directory, self.sample, self.label)
scan_directory = os.path.join(label_directory, self.scan['scan'].value)
scan_name = self.sample+'_'+self.scan['scan'].value
try:
os.makedirs(scan_directory)
except Exception:
pass
self.copy_configuration()
self.get_parameters()
self.scan_file.save(os.path.join(label_directory, scan_name+'.nxs'))
self.treeview.tree.load(self.scan_file.nxfilename, 'r')
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 LatticeDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_root(self.choose_entry)
self.refine = NXRefine()
self.parameters = GridParameters()
self.parameters.add('space_group',
self.refine.space_group,
'Space Group',
slot=self.set_groups)
self.parameters.add('laue_group', self.refine.laue_groups,
'Laue Group')
self.parameters.add('symmetry',
self.refine.symmetries,
'Symmetry',
slot=self.set_lattice_parameters)
self.parameters.add('centring', self.refine.centrings, 'Cell Centring')
self.parameters.add('a',
self.refine.a,
'Unit Cell - a (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('b',
self.refine.b,
'Unit Cell - b (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('c',
self.refine.c,
'Unit Cell - c (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('alpha',
self.refine.alpha,
'Unit Cell - alpha (deg)',
slot=self.set_lattice_parameters)
self.parameters.add('beta',
self.refine.beta,
'Unit Cell - beta (deg)',
slot=self.set_lattice_parameters)
self.parameters.add('gamma',
self.refine.gamma,
'Unit Cell - gamma (deg)',
slot=self.set_lattice_parameters)
self.parameters['laue_group'].value = self.refine.laue_group
self.parameters['symmetry'].value = self.refine.symmetry
self.parameters['centring'].value = self.refine.centring
self.import_button = NXPushButton('Import CIF', self.import_cif)
self.import_checkbox = NXCheckBox('Update Lattice Parameters')
self.set_layout(self.root_layout, self.close_buttons(save=True))
self.set_title('Defining Lattice')
def choose_entry(self):
self.refine = NXRefine(self.root['entry'])
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid(header=False))
if sgtbx:
self.insert_layout(
2,
self.make_layout(self.import_button,
self.import_checkbox,
align='center'))
self.update_parameters()
def import_cif(self):
filename = getOpenFileName(self, 'Open CIF File')
if os.path.exists(filename):
cif_info = cif.reader(file_path=filename).model()
for c in cif_info:
s = cif_info[c]
if '_cell_length_a' in s:
break
def value(text):
if '(' in text:
return float(text[:text.index('(')])
else:
return float(text)
if self.import_checkbox.isChecked():
self.refine.a = value(s['_cell_length_a'])
self.refine.b = value(s['_cell_length_b'])
self.refine.c = value(s['_cell_length_c'])
self.refine.alpha = value(s['_cell_angle_alpha'])
self.refine.beta = value(s['_cell_angle_beta'])
self.refine.gamma = value(s['_cell_angle_gamma'])
if '_space_group_IT_number' in s:
sgi = sgtbx.space_group_info(s['_space_group_IT_number'])
elif '_symmetry_Int_Tables_number' in s:
sgi = sgtbx.space_group_info(s['_symmetry_Int_Tables_number'])
elif '_space_group_name_H-M_alt' in s:
sgi = sgtbx.space_group_info(s['_space_group_name_H-M_alt'])
elif '_symmetry_space_group_name_H-M' in s:
sgi = sgtbx.space_group_info(
s['_symmetry_space_group_name_H-M'])
elif '_space_group_name_Hall' in s:
sgi = sgtbx.space_group_info('hall: ' +
s['_space_group_name_Hall'])
elif '_symmetry_space_group_name_Hall' in s:
sgi = sgtbx.space_group_info(
'hall: ' + s['_symmetry_space_group_name_Hall'])
else:
sgi = None
if sgi:
self.refine.space_group = sgi.type().lookup_symbol()
self.refine.symmetry = sgi.group().crystal_system().lower()
self.refine.laue_group = sgi.group().laue_group_type()
self.refine.centring = self.refine.space_group[0]
self.update_parameters()
def update_parameters(self):
self.parameters['space_group'].value = self.refine.space_group
self.parameters['laue_group'].value = self.refine.laue_group
self.parameters['symmetry'].value = self.refine.symmetry
self.parameters['centring'].value = self.refine.centring
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
def set_groups(self):
if self.space_group:
try:
if isinstance(self.space_group, float):
sgi = sgtbx.space_group_info(int(self.space_group))
else:
sgi = sgtbx.space_group_info(self.space_group)
except RuntimeError as error:
report_error("Defining Lattice", error)
return
try:
self.refine.space_group = sgi.type().lookup_symbol()
self.refine.symmetry = sgi.group().crystal_system().lower()
self.refine.laue_group = sgi.group().laue_group_type()
self.refine.centring = self.refine.space_group[0]
self.update_parameters()
except Exception:
pass
@property
def space_group(self):
return self.parameters['space_group'].value
@property
def laue_group(self):
return self.parameters['laue_group'].value
def get_symmetry(self):
return self.parameters['symmetry'].value
def get_centring(self):
return self.parameters['centring'].value
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
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
elif symmetry == 'orthorhombic':
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
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
elif symmetry == 'monoclinic':
self.parameters['alpha'].value = 90.0
self.parameters['gamma'].value = 90.0
def get_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.space_group = self.space_group
self.refine.laue_group = self.laue_group
self.refine.symmetry = self.get_symmetry()
self.refine.centring = self.get_centring()
def write_parameters(self):
self.get_parameters()
self.refine.write_parameters(sample=True)
def accept(self):
try:
self.write_parameters()
super().accept()
except NeXusError as error:
report_error("Defining Lattice", error)
class MakeDialog(BaseDialog):
def __init__(self, parent=None):
super(MakeDialog, self).__init__(parent)
self.scans = None
self.set_layout(self.directorybox("Choose Sample Directory",
self.choose_sample),
self.textboxes(('Scan Command', 'Pil2Mscan')),
self.action_buttons(('Select All', self.select_scans),
('Reverse All', self.reverse_scans),
('Clear All', self.clear_scans),
('Make Scan Macro', self.make_scans)),
self.close_buttons(close=True))
self.set_title('Make Scans')
def choose_sample(self):
super(MakeDialog, self).choose_directory()
self.sample_directory = self.get_directory()
self.experiment_directory = os.path.dirname(os.path.dirname(self.sample_directory))
self.macro_directory = os.path.join(self.experiment_directory, 'macros')
self.label = os.path.basename(self.sample_directory)
self.sample = os.path.basename(os.path.dirname(self.sample_directory))
self.experiment = os.path.basename(self.experiment_directory)
self.experiment_path = self.experiment
self.scan_path = os.path.join(self.experiment, self.sample, self.label)
self.setup_scans()
def setup_scans(self):
if self.scans:
self.scans.delete_grid()
self.scans = GridParameters()
all_files = [self.sample+'_'+d+'.nxs'
for d in os.listdir(self.sample_directory)
if os.path.isdir(os.path.join(self.sample_directory, d))]
filenames = sorted([f for f in all_files
if os.path.exists(os.path.join(self.sample_directory, f))],
key=natural_sort)
for i, f in enumerate(filenames):
scan = 'f%d' % i
self.scans.add(scan, i+1, f, True, self.update_scans)
self.scans[scan].checkbox.stateChanged.connect(self.update_scans)
self.insert_layout(2, self.scans.grid(header=False))
@property
def scan_list(self):
scan_list = []
for scan in self.scans.values():
if scan.checkbox.isChecked() and scan.value > 0:
scan_list.append(scan)
else:
scan.value = 0
return sorted(scan_list, key=attrgetter('value'))
def update_scans(self):
scan_list = self.scan_list
scan_number = 0
for scan in scan_list:
scan_number += 1
scan.value = scan_number
for scan in self.scans.values():
if scan.checkbox.isChecked() and scan.value == 0:
scan.value = scan_number + 1
scan_number += 1
def select_scans(self):
for i, scan in enumerate(self.scans):
self.scans[scan].value = i+1
self.scans[scan].checkbox.setChecked(True)
def reverse_scans(self):
for i, scan in enumerate(reversed(self.scan_list)):
scan.value = i+1
scan.checkbox.setChecked(True)
def clear_scans(self):
for scan in self.scans:
self.scans[scan].value = 0
self.scans[scan].checkbox.setChecked(False)
def make_scans(self):
scans = [scan.label.text() for scan in self.scan_list]
scan_command = self.textbox['Scan Command'].text()
scan_parameters = ['#command path filename temperature detx dety ' +
'phi_start phi_step phi_end chi omega frame_rate']
for scan in self.scan_list:
nexus_file = scan.label.text()
root = nxload(os.path.join(self.sample_directory, nexus_file))
temperature = root.entry.sample.temperature
base_name = os.path.basename(os.path.splitext(nexus_file)[0])
scan_dir = base_name.replace(self.sample+'_', '')
for entry in [root[e] for e in root if e != 'entry']:
if 'phi_set' in entry['instrument/goniometer']:
phi_start = entry['instrument/goniometer/phi_set']
else:
phi_start = entry['instrument/goniometer/phi']
phi_step = entry['instrument/goniometer/phi'].attrs['step']
phi_end = entry['instrument/goniometer/phi'].attrs['end']
if 'chi_set' in entry['instrument/goniometer']:
chi = entry['instrument/goniometer/chi_set']
else:
chi = entry['instrument/goniometer/chi']
if 'omega_set' in entry['instrument/goniometer']:
omega = entry['instrument/goniometer/omega_set']
else:
omega = entry['instrument/goniometer/omega']
dx = entry['instrument/detector/translation_x']
dy = entry['instrument/detector/translation_y']
if ('frame_time' in entry['instrument/detector'] and
entry['instrument/detector/frame_time'] > 0.0):
frame_rate = 1.0 / entry['instrument/detector/frame_time']
else:
frame_rate = 10.0
scan_file = entry.nxname
if scan_command == 'Pil2Mscan':
scan_parameters.append(
'%s %s %s %.6g %.6g %.6g %.6g %.6g %.6g %.6g %.6g %.6g'
% (scan_command, os.path.join(self.scan_path, scan_dir),
scan_file, temperature, dx, dy,
phi_start, phi_step, phi_end,
chi, omega, frame_rate))
if scan_command == 'Pil2Mstring':
scan_parameters.append('Pil2Mstring("%s")' % scan_dir)
elif scan_command != 'Pil2Mscan':
scan_parameters.append('%s %s' % (scan_command, temperature))
if not os.path.exists(self.macro_directory):
os.mkdir(os.path.join(self.experiment_directory, 'macros'))
macro_filter = ';;'.join(("SPEC Macro (*.mac)", "Any Files (*.* *)"))
macro = getSaveFileName(self, 'Open Macro', self.macro_directory,
macro_filter)
if macro:
with open(macro, 'w') as f:
f.write('\n'.join(scan_parameters))
class MaximumDialog(BaseDialog):
def __init__(self, parent=None):
super(MaximumDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.parameters = GridParameters()
self.parameters.add('first', '', 'First Frame')
self.parameters.add('last', '', 'Last Frame')
self.output = QtWidgets.QLabel('Maximum Value:')
self.set_layout(self.entry_layout, self.output,
self.parameters.grid(),
self.action_buttons(('Find Maximum', self.find_maximum)),
self.progress_layout(save=True))
self.progress_bar.setVisible(False)
self.progress_bar.setValue(0)
self.set_title('Find Maximum Value')
self.reduce = None
def choose_entry(self):
self.reduce = NXReduce(self.entry)
self.maximum = self.reduce.maximum
if self.reduce.first:
self.parameters['first'].value = self.reduce.first
if self.reduce.last:
self.parameters['last'].value = self.reduce.last
@property
def first(self):
try:
_first = np.int32(self.parameters['first'].value)
if _first >= 0:
return _first
else:
return None
except Exception as error:
return None
@property
def last(self):
try:
_last = np.int32(self.parameters['last'].value)
if _last > 0:
return _last
else:
return None
except Exception as error:
return None
@property
def maximum(self):
return np.float(self.output.text().split()[-1])
@maximum.setter
def maximum(self, value):
self.output.setText('Maximum Value: %s' % value)
def find_maximum(self):
self.check_lock(self.reduce.data_file)
self.start_thread()
self.reduce = NXReduce(self.entry, first=self.first, last=self.last,
maxcount=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_maximum)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxmax)
self.thread.finished.connect(self.stop)
self.thread.start(QtCore.QThread.LowestPriority)
def check_lock(self, file_name):
try:
with Lock(file_name, timeout=2):
pass
except LockException as error:
if self.confirm_action('Clear lock?', str(error)):
Lock(file_name).release()
def get_maximum(self, maximum):
self.maximum = maximum
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.stop_thread()
def accept(self):
try:
with Lock(self.reduce.wrapper_file):
self.reduce.write_maximum(self.maximum)
except LockException as error:
if self.confirm_action('Clear lock?', str(error)):
Lock(self.reduce.wrapper_file).release()
self.stop()
super(MaximumDialog, self).accept()
def reject(self):
self.stop()
super(MaximumDialog, self).reject()
class ParametersDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_root(self.choose_root)
default = NXSettings().settings['nxreduce']
self.parameters = GridParameters()
self.parameters.add('threshold', default['threshold'],
'Peak Threshold')
self.parameters.add('first', default['first'], 'First Frame')
self.parameters.add('last', default['last'], 'Last Frame')
self.parameters.add('monitor', ['monitor1', 'monitor2'],
'Normalization Monitor')
self.parameters['monitor'].value = default['monitor']
self.parameters.add('norm', default['norm'], 'Normalization Value')
self.parameters.add('radius', default['radius'], 'Punch Radius (Å)')
self.parameters.add('qmax', default['qmax'], 'Maximum Taper Q (Å-1)')
self.set_layout(self.root_layout,
self.close_buttons(save=True))
self.set_title('Choose Parameters')
def choose_root(self):
self.entries = [self.root[entry]
for entry in self.root if entry != 'entry']
if self.layout.count() == 2:
self.layout.insertLayout(1, self.parameters.grid(header=False))
self.read_parameters()
def read_parameters(self):
if 'nxreduce' in self.root['entry']:
reduce = self.root['entry/nxreduce']
if 'threshold' in reduce:
self.parameters['threshold'].value = reduce['threshold']
if 'first_frame' in reduce:
self.parameters['first'].value = reduce['first_frame']
if 'last_frame' in reduce:
self.parameters['last'].value = reduce['last_frame']
if 'monitor' in reduce:
self.parameters['monitor'].value = reduce['monitor']
if 'norm' in reduce:
self.parameters['norm'].value = reduce['norm']
if 'radius' in reduce:
self.parameters['radius'].value = reduce['radius']
if 'qmax' in reduce:
self.parameters['qmax'].value = reduce['qmax']
else:
try:
reduce = NXReduce(self.entries[0])
if reduce.first:
self.parameters['first'].value = reduce.first
if reduce.last:
self.parameters['last'].value = reduce.last
if reduce.threshold:
self.parameters['threshold'].value = reduce.threshold
if reduce.monitor:
self.parameters['monitor'].value = reduce.monitor
if reduce.norm:
self.parameters['norm'].value = reduce.norm
if reduce.radius:
self.parameters['radius'].value = reduce.radius
if reduce.qmax:
self.parameters['qmax'].value = reduce.qmax
except Exception:
pass
def write_parameters(self):
if 'nxreduce' not in self.root['entry']:
self.root['entry/nxreduce'] = NXparameters()
self.root['entry/nxreduce/threshold'] = self.threshold
self.root['entry/nxreduce/first_frame'] = self.first
self.root['entry/nxreduce/last_frame'] = self.last
self.root['entry/nxreduce/monitor'] = self.monitor
self.root['entry/nxreduce/norm'] = self.norm
self.root['entry/nxreduce/radius'] = self.radius
self.root['entry/nxreduce/qmax'] = self.qmax
@property
def threshold(self):
return float(self.parameters['threshold'].value)
@property
def first(self):
return int(self.parameters['first'].value)
@property
def last(self):
return int(self.parameters['last'].value)
@property
def monitor(self):
return self.parameters['monitor'].value
@property
def norm(self):
return float(self.parameters['norm'].value)
@property
def radius(self):
return float(self.parameters['radius'].value)
@property
def qmax(self):
return float(self.parameters['qmax'].value)
def accept(self):
try:
self.write_parameters()
super().accept()
except NeXusError as error:
report_error(error)
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 FindDialog(BaseDialog):
def __init__(self, parent=None):
super(FindDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.parameters = GridParameters()
self.parameters.add('threshold', '', 'Threshold')
self.parameters.add('first', '', 'First Frame')
self.parameters.add('last', '', 'Last Frame')
find_layout = QtWidgets.QHBoxLayout()
self.find_button = QtWidgets.QPushButton('Find Peaks')
self.find_button.clicked.connect(self.find_peaks)
self.peak_count = QtWidgets.QLabel()
self.peak_count.setVisible(False)
find_layout.addStretch()
find_layout.addWidget(self.find_button)
find_layout.addWidget(self.peak_count)
find_layout.addStretch()
self.set_layout(self.entry_layout,
self.parameters.grid(),
find_layout,
self.progress_layout(save=True))
self.progress_bar.setVisible(False)
self.progress_bar.setValue(0)
self.set_title('Find Peaks')
self.reduce = None
def choose_entry(self):
self.reduce = NXReduce(self.entry)
if self.reduce.first:
self.parameters['first'].value = self.reduce.first
if self.reduce.last:
self.parameters['last'].value = self.reduce.last
else:
try:
self.parameters['last'].value = len(self.entry.data.nxaxes[0])
except Exception:
pass
if self.reduce.threshold:
self.parameters['threshold'].value = self.reduce.threshold
@property
def threshold(self):
try:
_threshold = np.int32(self.parameters['threshold'].value)
if _threshold > 0.0:
return _threshold
else:
return None
except Exception:
return None
@property
def first(self):
try:
_first = np.int32(self.parameters['first'].value)
if _first >= 0:
return _first
else:
return None
except Exception as error:
return None
@property
def last(self):
try:
_last = np.int32(self.parameters['last'].value)
if _last > 0:
return _last
else:
return None
except Exception as error:
return None
def find_peaks(self):
self.check_lock(self.reduce.data_file)
self.start_thread()
self.reduce = NXReduce(self.entry, threshold=self.threshold,
first=self.first, last=self.last,
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(QtCore.QThread.LowestPriority)
def check_lock(self, file_name):
try:
with Lock(file_name, timeout=2):
pass
except LockException as error:
if self.confirm_action('Clear lock?', str(error)):
Lock(file_name).release()
def get_peaks(self, peaks):
self.peaks = peaks
self.peak_count.setText('%s peaks found' % len(self.peaks))
self.peak_count.setVisible(True)
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.stop_thread()
def accept(self):
try:
with Lock(self.reduce.wrapper_file):
self.reduce.write_peaks(self.peaks)
except LockException as error:
if self.confirm_action('Clear lock?', str(error)):
Lock(self.reduce.wrapper_file).release()
self.stop()
super(FindDialog, self).accept()
def reject(self):
self.stop()
super(FindDialog, self).reject()
class LatticeDialog(BaseDialog):
def __init__(self, parent=None):
super(LatticeDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine()
self.parameters = GridParameters()
self.parameters.add('symmetry',
self.refine.symmetries,
'Symmetry',
slot=self.set_lattice_parameters)
self.parameters.add('centring', self.refine.centrings, 'Cell Centring')
self.parameters.add('a',
self.refine.a,
'Unit Cell - a (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('b',
self.refine.b,
'Unit Cell - b (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('c',
self.refine.c,
'Unit Cell - c (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('alpha',
self.refine.alpha,
'Unit Cell - alpha (deg)',
slot=self.set_lattice_parameters)
self.parameters.add('beta',
self.refine.beta,
'Unit Cell - beta (deg)',
slot=self.set_lattice_parameters)
self.parameters.add('gamma',
self.refine.gamma,
'Unit Cell - gamma (deg)',
slot=self.set_lattice_parameters)
self.parameters['symmetry'].value = self.refine.symmetry
self.parameters['centring'].value = self.refine.centring
action_buttons = self.action_buttons(('Plot', self.plot_lattice),
('Save', self.write_parameters))
self.set_layout(self.entry_layout, self.parameters.grid(),
action_buttons, self.close_buttons())
self.set_title('Defining Lattice')
def choose_entry(self):
self.refine = NXRefine(self.entry)
self.update_parameters()
def update_parameters(self):
self.parameters['symmetry'].value = self.refine.symmetry
self.parameters['centring'].value = self.refine.centring
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
def get_symmetry(self):
return self.parameters['symmetry'].value
def get_centring(self):
return self.parameters['centring'].value
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
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
elif symmetry == 'orthorhombic':
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
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
elif symmetry == 'monoclinic':
self.parameters['alpha'].value = 90.0
self.parameters['gamma'].value = 90.0
def get_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.symmetry = self.get_symmetry()
self.refine.centring = self.get_centring()
def plot_lattice(self):
try:
self.get_parameters()
self.plot_peaks(self.refine.xp, self.refine.yp)
polar_min, polar_max = plotview.xaxis.get_limits()
self.plot_rings(polar_max)
except NeXusError as error:
report_error('Plotting Lattice', error)
def write_parameters(self):
try:
self.get_parameters()
self.refine.write_parameters()
except NeXusError as error:
report_error('Defining Lattice', error)
def plot_peaks(self, x, y):
try:
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()
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 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 MakeDialog(BaseDialog):
def __init__(self, parent=None):
super(MakeDialog, self).__init__(parent)
self.scans = None
self.set_layout(
self.directorybox("Choose Sample Directory", self.choose_sample),
self.textboxes(('Scan Command', 'Pil2Mscan')),
self.action_buttons(('Select All', self.select_scans),
('Reverse All', self.reverse_scans),
('Clear All', self.clear_scans),
('Make Scan Macro', self.make_scans)),
self.close_buttons(close=True))
self.set_title('Make Scans')
def choose_sample(self):
super(MakeDialog, self).choose_directory()
self.sample_directory = self.get_directory()
self.experiment_directory = os.path.dirname(
os.path.dirname(self.sample_directory))
self.macro_directory = os.path.join(self.experiment_directory,
'macros')
self.label = os.path.basename(self.sample_directory)
self.sample = os.path.basename(os.path.dirname(self.sample_directory))
self.experiment = os.path.basename(self.experiment_directory)
self.experiment_path = self.experiment
self.scan_path = os.path.join(self.experiment, self.sample, self.label)
self.setup_scans()
def setup_scans(self):
if self.scans:
self.scans.delete_grid()
self.scans = GridParameters()
all_files = [
self.sample + '_' + d + '.nxs'
for d in os.listdir(self.sample_directory)
if os.path.isdir(os.path.join(self.sample_directory, d))
]
filenames = sorted([
f for f in all_files
if os.path.exists(os.path.join(self.sample_directory, f))
],
key=natural_sort)
for i, f in enumerate(filenames):
scan = 'f%d' % i
self.scans.add(scan, i + 1, f, True, self.update_scans)
self.scans[scan].checkbox.stateChanged.connect(self.update_scans)
self.insert_layout(2, self.scans.grid(header=False))
@property
def scan_list(self):
scan_list = []
for scan in self.scans.values():
if scan.checkbox.isChecked() and scan.value > 0:
scan_list.append(scan)
else:
scan.value = 0
return sorted(scan_list, key=attrgetter('value'))
def update_scans(self):
scan_list = self.scan_list
scan_number = 0
for scan in scan_list:
scan_number += 1
scan.value = scan_number
for scan in self.scans.values():
if scan.checkbox.isChecked() and scan.value == 0:
scan.value = scan_number + 1
scan_number += 1
def select_scans(self):
for i, scan in enumerate(self.scans):
self.scans[scan].value = i + 1
self.scans[scan].checkbox.setChecked(True)
def reverse_scans(self):
for i, scan in enumerate(reversed(self.scan_list)):
scan.value = i + 1
scan.checkbox.setChecked(True)
def clear_scans(self):
for scan in self.scans:
self.scans[scan].value = 0
self.scans[scan].checkbox.setChecked(False)
def make_scans(self):
scans = [scan.label.text() for scan in self.scan_list]
scan_command = self.textbox['Scan Command'].text()
scan_parameters = [
'#command path filename temperature detx dety ' +
'phi_start phi_step phi_end chi omega frame_rate'
]
for scan in self.scan_list:
nexus_file = scan.label.text()
root = nxload(os.path.join(self.sample_directory, nexus_file))
temperature = root.entry.sample.temperature
base_name = os.path.basename(os.path.splitext(nexus_file)[0])
scan_dir = base_name.replace(self.sample + '_', '')
for entry in [root[e] for e in root if e != 'entry']:
if 'phi_set' in entry['instrument/goniometer']:
phi_start = entry['instrument/goniometer/phi_set']
else:
phi_start = entry['instrument/goniometer/phi']
phi_step = entry['instrument/goniometer/phi'].attrs['step']
phi_end = entry['instrument/goniometer/phi'].attrs['end']
if 'chi_set' in entry['instrument/goniometer']:
chi = entry['instrument/goniometer/chi_set']
else:
chi = entry['instrument/goniometer/chi']
if 'omega_set' in entry['instrument/goniometer']:
omega = entry['instrument/goniometer/omega_set']
else:
omega = entry['instrument/goniometer/omega']
dx = entry['instrument/detector/translation_x']
dy = entry['instrument/detector/translation_y']
if ('frame_time' in entry['instrument/detector']
and entry['instrument/detector/frame_time'] > 0.0):
frame_rate = 1.0 / entry['instrument/detector/frame_time']
else:
frame_rate = 10.0
scan_file = entry.nxname
if scan_command == 'Pil2Mscan':
scan_parameters.append(
'%s %s %s %.6g %.6g %.6g %.6g %.6g %.6g %.6g %.6g %.6g'
%
(scan_command, os.path.join(self.scan_path, scan_dir),
scan_file, temperature, dx, dy, phi_start, phi_step,
phi_end, chi, omega, frame_rate))
if scan_command == 'Pil2Mstring':
scan_parameters.append('Pil2Mstring("%s")' % scan_dir)
elif scan_command != 'Pil2Mscan':
scan_parameters.append('%s %s' % (scan_command, temperature))
if not os.path.exists(self.macro_directory):
os.mkdir(os.path.join(self.experiment_directory, 'macros'))
macro_filter = ';;'.join(("SPEC Macro (*.mac)", "Any Files (*.* *)"))
macro = getSaveFileName(self, 'Open Macro', self.macro_directory,
macro_filter)
if macro:
with open(macro, 'w') as f:
f.write('\n'.join(scan_parameters))
class MaximumDialog(BaseDialog):
def __init__(self, parent=None):
super(MaximumDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.parameters = GridParameters()
self.parameters.add('first', '', 'First Frame')
self.parameters.add('last', '', 'Last Frame')
self.output = QtWidgets.QLabel('Maximum Value:')
self.set_layout(
self.entry_layout, self.output, self.parameters.grid(),
self.action_buttons(('Find Maximum', self.find_maximum)),
self.progress_layout(save=True))
self.progress_bar.setVisible(False)
self.progress_bar.setValue(0)
self.set_title('Find Maximum Value')
self.reduce = None
def choose_entry(self):
self.reduce = NXReduce(self.entry)
self.maximum = self.reduce.maximum
if self.reduce.first:
self.parameters['first'].value = self.reduce.first
if self.reduce.last:
self.parameters['last'].value = self.reduce.last
@property
def first(self):
try:
_first = np.int32(self.parameters['first'].value)
if _first >= 0:
return _first
else:
return None
except Exception as error:
return None
@property
def last(self):
try:
_last = np.int32(self.parameters['last'].value)
if _last > 0:
return _last
else:
return None
except Exception as error:
return None
@property
def maximum(self):
return np.float(self.output.text().split()[-1])
@maximum.setter
def maximum(self, value):
self.output.setText('Maximum Value: %s' % value)
def find_maximum(self):
self.check_lock(self.reduce.data_file)
self.start_thread()
self.reduce = NXReduce(self.entry,
first=self.first,
last=self.last,
maxcount=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_maximum)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxmax)
self.thread.finished.connect(self.stop)
self.thread.start(QtCore.QThread.LowestPriority)
def check_lock(self, file_name):
try:
with Lock(file_name, timeout=2):
pass
except LockException as error:
if self.confirm_action('Clear lock?', str(error)):
Lock(file_name).release()
def get_maximum(self, maximum):
self.maximum = maximum
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.stop_thread()
def accept(self):
try:
with Lock(self.reduce.wrapper_file):
self.reduce.write_maximum(self.maximum)
except LockException as error:
if self.confirm_action('Clear lock?', str(error)):
Lock(self.reduce.wrapper_file).release()
self.stop()
super(MaximumDialog, self).accept()
def reject(self):
self.stop()
super(MaximumDialog, self).reject()
class ScanDialog(BaseDialog):
def __init__(self, parent=None):
super(ScanDialog, self).__init__(parent)
self.scan_file = NXroot()
self.scan_file['entry'] = NXentry()
self.detectors = {}
self.entries = {}
self.setup_sample()
self.setup_instrument()
self.set_layout(self.directorybox('Choose Data Directory'),
self.sample.grid(header=False),
self.instrument.grid(header=False))
self.set_title('New Scan')
def setup_sample(self):
self.scan_file['entry/sample'] = NXsample()
self.scan_file['entry/sample/name'] = 'sample'
self.scan_file['entry/sample/label'] = 'label'
self.scan_file['entry/sample/temperature'] = NXfield(300.0, dtype=np.float32)
self.scan_file['entry/sample/temperature'].attrs['units'] = 'K'
self.sample = GridParameters()
self.sample.add('sample', self.scan_file['entry/sample/name'], 'Sample Name')
self.sample.add('label', self.scan_file['entry/sample/label'], 'Sample Label')
self.sample.add('scan', 'scan', 'Scan Label')
self.sample.add('temperature', self.scan_file['entry/sample/temperature'], 'Temperature (K)')
def setup_instrument(self):
entry = self.scan_file['entry']
entry.instrument = NXinstrument()
entry.instrument.monochromator = NXmonochromator()
entry.instrument.detector = NXdetector()
entry['instrument/monochromator/wavelength'] = NXfield(0.5, dtype=np.float32)
entry['instrument/monochromator/wavelength'].attrs['units'] = 'Angstroms'
entry['instrument/detector/distance'] = NXfield(100.0, dtype=np.float32)
entry['instrument/detector/distance'].attrs['units'] = 'mm'
entry['instrument/detector/pixel_size'] = NXfield(0.172, dtype=np.float32)
entry['instrument/detector/pixel_size'].attrs['units'] = 'mm'
self.instrument = GridParameters()
self.instrument.add('wavelength', entry['instrument/monochromator/wavelength'], 'Wavelength (Ang)')
self.instrument.add('distance', entry['instrument/detector/distance'], 'Detector Distance (mm)')
self.instrument.add('pixel', entry['instrument/detector/pixel_size'], 'Pixel Size (mm)')
self.instrument.add('positions', [0,1,2,3,4], 'Number of Detector Positions', slot=self.set_entries)
self.instrument['positions'].value = '0'
def setup_entry(self, position):
entry = self.scan_file['f%s' % position] = NXentry()
entry.instrument = NXinstrument()
entry.instrument.detector = NXdetector()
entry.instrument.monochromator = NXmonochromator()
entry['instrument/detector/beam_center_x'] = NXfield(1024.0, dtype=np.float32)
entry['instrument/detector/beam_center_y'] = NXfield(1024.0, dtype=np.float32)
self.detectors[position] = GridParameters()
self.detectors[position].add('xc', entry['instrument/detector/beam_center_x'], 'Beam Center - x')
self.detectors[position].add('yc', entry['instrument/detector/beam_center_y'], 'Beam Center - y')
@property
def positions(self):
return int(self.instrument['positions'].value)
def set_entries(self):
for position in range(1,self.positions+1):
self.setup_entry(position)
self.layout.addLayout(self.detectors[position].grid(header=False, title='Position %s'%position))
self.layout.addWidget(self.close_buttons(save=True))
def get_parameters(self):
entry = self.scan_file['entry']
entry['sample/name'] = self.sample['sample'].value
entry['sample/label'] = self.sample['label'].value
entry['sample/temperature'] = self.sample['temperature'].value
entry['instrument/monochromator/wavelength'] = self.instrument['wavelength'].value
entry['instrument/detector/distance'] = self.instrument['distance'].value
entry['instrument/detector/pixel_size'] = self.instrument['pixel'].value
for position in range(1, self.positions+1):
entry = self.scan_file['f%s' % position]
entry['instrument/monochromator/wavelength'] = self.instrument['wavelength'].value
entry['instrument/detector/distance'] = self.instrument['distance'].value
entry['instrument/detector/pixel_size'] = self.instrument['pixel'].value
entry['instrument/detector/beam_center_x'] = self.detectors[position]['xc'].value
entry['instrument/detector/beam_center_y'] = self.detectors[position]['yc'].value
entry.makelink(self.scan_file['entry/sample'])
def accept(self):
home_directory = self.get_directory()
sample_directory = os.path.join(home_directory, self.sample['sample'].value)
label_directory = os.path.join(home_directory, self.sample['sample'].value, self.sample['label'].value)
scan_directory = os.path.join(label_directory, self.sample['scan'].value)
scan_name = self.sample['sample'].value+'_'+self.sample['scan'].value
try:
os.makedirs(scan_directory)
for position in range(1, self.positions+1):
os.mkdir(os.path.join(scan_directory, 'f%s' % position))
except Exception:
pass
self.get_parameters()
self.scan_file.save(os.path.join(label_directory, scan_name+'.nxs'))
self.treeview.tree.load(self.scan_file.nxfilename, 'rw')
super(ScanDialog, self).accept()
class ParametersDialog(BaseDialog):
def __init__(self, parent=None):
super(ParametersDialog, self).__init__(parent)
self.select_root(self.choose_root)
self.parameters = GridParameters()
self.parameters.add('threshold', '', 'Threshold')
self.parameters.add('first', 25, 'First Frame')
self.parameters.add('last', 3625, 'Last Frame')
self.parameters.add('radius', 200, 'Radius')
self.parameters.add('width', 3, 'Frame Width')
self.parameters.add('norm', '', 'Normalization')
self.set_layout(self.root_layout,
self.parameters.grid(),
self.close_buttons(save=True))
self.set_title('Choose Parameters')
def choose_root(self):
self.entries = [self.root[entry]
for entry in self.root if entry != 'entry']
self.update_parameters()
def update_parameters(self):
reduce = NXReduce(self.entries[0])
if reduce.first:
self.parameters['first'].value = reduce.first
if reduce.last:
self.parameters['last'].value = reduce.last
if reduce.threshold:
self.parameters['threshold'].value = reduce.threshold
if reduce.radius:
self.parameters['radius'].value = reduce.radius
if reduce.width:
self.parameters['width'].value = reduce.width
if reduce.norm:
self.parameters['norm'].value = reduce.norm
def write_parameters(self, entry):
if 'peaks' not in entry:
entry['peaks'] = NXreflections()
if self.first:
entry['peaks'].attrs['first'] = np.int(self.first)
elif 'first' in entry['peaks'].attrs:
del entry['peaks'].attrs['first']
if self.last:
entry['peaks'].attrs['last'] = np.int(self.last)
elif 'last' in entry['peaks'].attrs:
del entry['peaks'].attrs['last']
if self.threshold:
entry['peaks'].attrs['threshold'] = self.threshold
elif 'threshold' in entry['peaks'].attrs:
del entry['peaks'].attrs['threshold']
if self.radius:
entry['peaks'].attrs['radius'] = np.int(self.radius)
elif 'radius' in entry['peaks'].attrs:
del entry['peaks'].attrs['radius']
if self.width:
entry['peaks'].attrs['width'] = np.int(self.width)
elif 'width' in entry['peaks'].attrs:
del entry['peaks'].attrs['width']
if self.norm:
entry['peaks'].attrs['norm'] = self.norm
elif 'norm' in entry['peaks'].attrs:
del entry['peaks'].attrs['norm']
def get_value(self, key):
value = self.parameters[key].value
if isinstance(value, float) and value <= 0:
return None
elif isinstance(value, str):
return None
else:
return value
@property
def threshold(self):
return self.get_value('threshold')
@property
def first(self):
return self.get_value('first')
@property
def last(self):
return self.get_value('last')
@property
def radius(self):
return self.get_value('radius')
@property
def width(self):
return self.get_value('width')
@property
def norm(self):
return self.get_value('norm')
def accept(self):
for entry in self.entries:
self.write_parameters(entry)
super(ParametersDialog, self).accept()
class ExperimentDialog(BaseDialog):
def __init__(self, parent=None):
super(ExperimentDialog, self).__init__(parent)
self.experiment_file = NXroot()
self.experiment_file['entry'] = NXentry()
self.detectors = {}
self.entries = {}
self.setup_instrument()
self.set_layout(
self.directorybox('Choose Experiment Directory', default=False),
self.instrument.grid(header=False))
self.set_title('New Experiment')
def setup_instrument(self):
entry = self.experiment_file['entry']
entry.instrument = NXinstrument()
entry.instrument.monochromator = NXmonochromator()
entry.instrument.detector = NXdetector()
entry['instrument/monochromator/wavelength'] = NXfield(
0.5, dtype=np.float32)
entry['instrument/monochromator/wavelength'].attrs[
'units'] = 'Angstroms'
entry['instrument/monochromator/energy'] = NXfield(12.398419739640717 /
0.5,
dtype=np.float32)
entry['instrument/monochromator/energy'].attrs['units'] = 'keV'
entry['instrument/detector/distance'] = NXfield(100.0,
dtype=np.float32)
entry['instrument/detector/distance'].attrs['units'] = 'mm'
self.instrument = GridParameters()
self.instrument.add('experiment', 'experiment', 'Experiment Name')
self.instrument.add('wavelength',
entry['instrument/monochromator/wavelength'],
'Wavelength (Ang)')
self.instrument.add('distance', entry['instrument/detector/distance'],
'Detector Distance (mm)')
detector_list = sorted(
list(set([detector().name
for detector in ALL_DETECTORS.values()])))
self.instrument.add('detector', detector_list, 'Detector')
self.instrument['detector'].value = 'Pilatus CdTe 2M'
self.instrument.add('positions', [0, 1, 2, 3, 4],
'Number of Detector Positions',
slot=self.set_entries)
self.instrument['positions'].value = '0'
def setup_entry(self, position):
entry = NXentry()
self.detectors[position] = GridParameters()
self.detectors[position].add('x', 0.0, 'Translation - x (mm)')
self.detectors[position].add('y', 0.0, 'Translation - y (mm)')
self.experiment_file['f%s' % position] = entry
def get_detector(self):
for detector in ALL_DETECTORS:
if ALL_DETECTORS[detector](
).name == self.instrument['detector'].value:
return ALL_DETECTORS[detector]()
@property
def positions(self):
return int(self.instrument['positions'].value)
def set_entries(self):
for position in range(1, self.positions + 1):
self.setup_entry(position)
self.layout.addLayout(self.detectors[position].grid(
header=False, title='Position %s' % position))
self.layout.addWidget(self.close_buttons(save=True))
def get_parameters(self):
entry = self.experiment_file['entry']
entry['instrument/monochromator/wavelength'] = self.instrument[
'wavelength'].value
entry[
'instrument/monochromator/energy'] = 12.398419739640717 / self.instrument[
'wavelength'].value
detector = self.get_detector()
entry['instrument/detector/description'] = detector.name
entry['instrument/detector/distance'] = self.instrument[
'distance'].value
entry['instrument/detector/pixel_size'] = detector.pixel1 * 1000
entry['instrument/detector/pixel_size'].attrs['units'] = 'mm'
entry['instrument/detector/pixel_mask'] = detector.mask
entry['instrument/detector/shape'] = detector.shape
entry['instrument/detector/yaw'] = 0.0
entry['instrument/detector/pitch'] = 0.0
entry['instrument/detector/roll'] = 0.0
for position in range(1, self.positions + 1):
entry = self.experiment_file['f%s' % position]
entry['instrument'] = self.experiment_file['entry/instrument']
entry['instrument/detector/translation_x'] = self.detectors[
position]['x'].value
entry['instrument/detector/translation_x'].attrs['units'] = 'mm'
entry['instrument/detector/translation_y'] = self.detectors[
position]['y'].value
entry['instrument/detector/translation_y'].attrs['units'] = 'mm'
entry['instrument/detector/frame_time'] = 0.1
entry['instrument/detector/frame_time'].attrs['units'] = 'seconds'
def accept(self):
try:
home_directory = self.get_directory()
self.mainwindow.default_directory = home_directory
self.get_parameters()
configuration_directory = os.path.join(home_directory,
'configurations')
if not os.path.exists(configuration_directory):
os.makedirs(configuration_directory)
self.experiment_file.save(
os.path.join(configuration_directory,
self.instrument['experiment'].value + '.nxs'))
task_directory = os.path.join(home_directory, 'tasks')
if not os.path.exists(task_directory):
os.makedirs(task_directory)
calibration_directory = os.path.join(home_directory,
'calibrations')
if not os.path.exists(calibration_directory):
os.makedirs(calibration_directory)
self.treeview.tree.load(self.experiment_file.nxfilename, 'rw')
super(ExperimentDialog, self).accept()
except Exception as error:
report_error("Defining New Experiment", error)
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 CalculateDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine()
self.parameters = GridParameters()
self.parameters.add('wavelength', self.refine.wavelength,
'Wavelength (Ang)')
self.parameters.add('distance', self.refine.distance,
'Detector Distance (mm)')
self.parameters.add('xc', self.refine.xc, 'Beam Center - x')
self.parameters.add('yc', self.refine.yc, 'Beam Center - y')
self.parameters.add('pixel', self.refine.pixel_size, 'Pixel Size (mm)')
self.action_buttons = self.action_buttons(
('Plot', self.plot_lattice), ('Save', self.write_parameters))
self.set_layout(self.entry_layout, self.close_buttons())
self.set_title('Calculate Angles')
def choose_entry(self):
self.refine = NXRefine(self.entry)
if 'peaks' in self.entry:
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid(header=False))
self.insert_layout(2, self.action_buttons)
self.update_parameters()
else:
self.display_message("Calculating Angles",
"No peaks have been found in this entry")
def update_parameters(self):
self.parameters['wavelength'].value = self.refine.wavelength
self.parameters['distance'].value = self.refine.distance
self.parameters['xc'].value = self.refine.xc
self.parameters['yc'].value = self.refine.yc
self.parameters['pixel'].value = self.refine.pixel_size
def get_wavelength(self):
return self.parameters['wavelength'].value
def get_distance(self):
return self.parameters['distance'].value
def get_centers(self):
return self.parameters['xc'].value, self.parameters['yc'].value
def get_pixel_size(self):
return self.parameters['pixel'].value
def get_parameters(self):
self.refine.wavelength = self.get_wavelength()
self.refine.distance = self.get_distance()
self.refine.xc, self.refine.yc = self.get_centers()
self.refine.pixel_size = self.get_pixel_size()
self.refine.yaw = self.refine.pitch = self.refine.roll = None
def plot_lattice(self):
try:
self.get_parameters()
self.plot_peaks(self.refine.xp, self.refine.yp)
except NeXusError as error:
report_error("Calculating Angles", error)
def plot_peaks(self, x, y):
try:
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 write_parameters(self):
try:
self.get_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()
except NeXusError as error:
report_error("Calculating Angles", error)
class ScanDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.config_file = None
self.positions = 1
self.entries = {}
self.settings = NXSettings()
self.directory_box = self.directorybox('Choose Experiment Directory',
self.choose_directory,
default=False)
self.sample_box = self.select_sample()
self.sample_layout = self.make_layout(
self.action_buttons(('Choose Sample', self.choose_sample)),
self.sample_box)
self.configuration_box = self.select_configuration()
self.configuration_layout = self.make_layout(
self.action_buttons(('Choose Experiment Configuration',
self.choose_configuration)),
self.configuration_box)
self.scan_box = self.select_box(['1'], slot=self.choose_position)
self.scan_layout = self.make_layout(
self.labels('Position', header=True), self.scan_box)
self.set_layout(self.directory_box,
self.close_buttons(close=True))
self.set_title('New Scan')
@property
def configuration(self):
return self.configuration_box.currentText()
@property
def sample(self):
return self.sample_box.currentText().split('/')[0]
@property
def label(self):
return self.sample_box.currentText().split('/')[1]
@property
def position(self):
try:
return int(self.scan_box.currentText())
except ValueError:
return 1
def choose_directory(self):
super().choose_directory()
self.mainwindow.default_directory = self.get_directory()
self.setup_directory()
self.insert_layout(1, self.sample_layout)
def setup_directory(self):
self.sample_box.clear()
samples = self.get_samples()
for sample in samples:
self.sample_box.addItem(sample)
self.sample_box.adjustSize()
configurations = self.get_configurations()
self.configuration_box.clear()
for configuration in configurations:
self.configuration_box.addItem(configuration)
def select_sample(self):
return self.select_box(self.get_samples())
def get_samples(self):
home_directory = self.get_directory()
if os.path.exists(home_directory):
sample_directories = [f for f in os.listdir(home_directory)
if (not f.startswith('.') and
os.path.isdir(
os.path.join(home_directory, f)))]
else:
return []
samples = []
for sample_directory in sample_directories:
label_directories = [
f
for f in os.listdir(
os.path.join(home_directory, sample_directory))
if os.path.isdir(
os.path.join(home_directory, sample_directory, f))]
for label_directory in label_directories:
samples.append(os.path.join(sample_directory, label_directory))
return [sample.strip() for sample in samples]
def choose_sample(self):
self.insert_layout(2, self.configuration_layout)
def select_configuration(self):
return self.select_box(self.get_configurations())
def get_configurations(self):
home_directory = self.get_directory()
if (os.path.exists(home_directory) and
'configurations' in os.listdir(home_directory)):
return sorted(
[f
for f in os.listdir(
os.path.join(home_directory, 'configurations'))
if f.endswith('.nxs')])
else:
return []
def choose_configuration(self):
home_directory = self.get_directory()
config_file = os.path.join(home_directory, 'configurations',
self.configuration)
if os.path.exists(config_file):
self.config_file = nxload(config_file)
self.positions = len(self.config_file.entries) - 1
self.scan_box.clear()
for position in range(1, self.positions+1):
self.scan_box.addItem(f'{position}')
self.scan_box.setCurrentIndex(0)
self.copy_configuration()
self.setup_scans()
self.read_parameters()
self.insert_layout(3, self.scan.grid(header=False))
self.insert_layout(4, self.scan_layout)
for p in range(1, self.positions+1):
self.insert_layout(p+4, self.entries[p].grid_layout)
self.insert_layout(self.positions+5,
self.action_buttons(('Make Scan File',
self.make_scan)))
def setup_scans(self):
default = self.settings['nxrefine']
self.scan = GridParameters()
self.scan.add('scan', 'scan', 'Scan Label')
self.scan.add('temperature', 300.0, 'Temperature (K)')
self.scan.add('phi_start', default['phi'], 'Phi Start (deg)')
self.scan.add('phi_end', default['phi_end'], 'Phi End (deg)')
self.scan.add('phi_step', default['phi_step'], 'Phi Step (deg)')
self.scan.add('frame_rate', default['frame_rate'], 'Frame Rate (Hz)')
for position in range(1, self.positions+1):
self.setup_position(position)
def setup_position(self, position):
default = self.settings['nxrefine']
self.entries[position] = GridParameters()
self.entries[position].add('chi', default['chi'], 'Chi (deg)')
self.entries[position].add('omega', default['omega'], 'Omega (deg)')
self.entries[position].add('x', default['x'], 'Translation - x (mm)')
self.entries[position].add('y', default['y'], 'Translation - y (mm)')
self.entries[position].add('linkfile', f'f{position:d}.h5',
'Detector Filename')
self.entries[position].add(
'linkpath', '/entry/data/data', 'Detector Data Path')
self.entries[position].grid(header=False)
if position != 1:
self.entries[position].hide_grid()
def choose_position(self):
for i in self.entries:
self.entries[i].hide_grid()
if self.position in self.entries:
self.entries[self.position].show_grid()
def copy_configuration(self):
self.scan_file = NXroot()
for entry in self.config_file.entries:
self.scan_file[entry] = self.config_file[entry]
def read_parameters(self):
for position in range(1, self.positions+1):
entry = self.scan_file[f'f{position:d}']
if 'instrument/goniometer/chi' in entry:
self.entries[position]['chi'].value = (
entry['instrument/goniometer/chi'])
if 'instrument/goniometer/omega' in entry:
self.entries[position]['omega'].value = (
entry['instrument/goniometer/omega'])
if 'instrument/detector/translation_x' in entry:
self.entries[position]['x'].value = (
entry['instrument/detector/translation_x'])
if 'instrument/detector/translation_y' in entry:
self.entries[position]['y'].value = (
entry['instrument/detector/translation_y'])
def get_parameters(self):
entry = self.scan_file['entry']
if 'sample' not in entry:
entry['sample'] = NXsample()
entry['sample/name'] = self.sample
entry['sample/label'] = self.label
entry['sample/temperature'] = self.scan['temperature'].value
entry['sample/temperature'].attrs['units'] = 'K'
y_size, x_size = entry['instrument/detector/shape'].nxvalue
scan = self.scan['scan'].value
for position in range(1, self.positions+1):
entry = self.scan_file[f'f{position:d}']
entry.makelink(self.scan_file['entry/sample'])
phi_start = self.scan['phi_start'].value
phi_end = self.scan['phi_end'].value
phi_step = self.scan['phi_step'].value
chi = self.entries[position]['chi'].value
omega = self.entries[position]['omega'].value
frame_rate = self.scan['frame_rate'].value
if 'goniometer' not in entry['instrument']:
entry['instrument/goniometer'] = NXgoniometer()
entry['instrument/goniometer/phi'] = phi_start
entry['instrument/goniometer/phi_set'] = phi_start
entry['instrument/goniometer/phi'].attrs['step'] = phi_step
entry['instrument/goniometer/phi'].attrs['end'] = phi_end
entry['instrument/goniometer/chi'] = chi
entry['instrument/goniometer/chi_set'] = chi
entry['instrument/goniometer/omega'] = omega
entry['instrument/goniometer/omega_set'] = omega
if frame_rate > 0.0:
entry['instrument/detector/frame_time'] = 1.0 / frame_rate
linkpath = self.entries[position]['linkpath'].value
linkfile = os.path.join(
scan, self.entries[position]['linkfile'].value)
entry['data'] = NXdata()
entry['data'].nxsignal = NXlink(linkpath, linkfile)
entry['data/x_pixel'] = np.arange(x_size, dtype=np.int32)
entry['data/y_pixel'] = np.arange(y_size, dtype=np.int32)
entry['data/frame_number'] = np.arange(
(phi_end-phi_start)/phi_step, dtype=np.int32)
entry['data'].nxaxes = [entry['data/frame_number'],
entry['data/y_pixel'],
entry['data/x_pixel']]
def make_scan(self):
home_directory = self.get_directory()
self.mainwindow.default_directory = home_directory
sample_directory = os.path.join(home_directory, self.sample)
label_directory = os.path.join(home_directory, self.sample, self.label)
scan_directory = os.path.join(
label_directory, str(self.scan['scan'].value))
scan_name = self.sample+'_'+self.scan['scan'].value
try:
os.makedirs(scan_directory)
except Exception:
pass
self.copy_configuration()
self.get_parameters()
self.scan_file.save(os.path.join(label_directory, scan_name+'.nxs'))
self.treeview.tree.load(self.scan_file.nxfilename, 'r')
class Mask3DDialog(BaseDialog):
def __init__(self, parent=None):
super(Mask3DDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.parameters = GridParameters()
self.parameters.add('radius', 200, 'Radius')
self.parameters.add('width', 3, 'Frame Width')
self.set_layout(
self.entry_layout, self.parameters.grid(),
self.action_buttons(('Calculate 3D Mask', self.calculate_mask)),
self.progress_layout(save=True))
self.progress_bar.setVisible(False)
self.progress_bar.setValue(0)
self.set_title('Calculate 3D Mask')
self.reduce = None
def choose_entry(self):
self.reduce = NXReduce(self.entry)
@property
def radius(self):
return self.parameters['radius'].value
@property
def width(self):
return self.parameters['width'].value
def calculate_mask(self):
self.check_lock(self.reduce.wrapper_file)
self.thread = QtCore.QThread()
self.reduce = NXReduce(self.entry,
radius=self.radius,
width=self.width,
mask=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.calculate_mask)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxfind)
self.thread.start(QtCore.QThread.LowestPriority)
def check_lock(self, file_name):
try:
with Lock(file_name, timeout=2):
pass
except LockException as error:
if self.confirm_action('Clear lock?', str(error)):
Lock(file_name).release()
def calculate_mask(self, mask):
self.mask = mask
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.thread.exit()
def accept(self):
try:
with Lock(self.reduce.wrapper_file):
self.reduce.write_peaks(self.peaks)
except LockException as error:
if self.confirm_action('Clear lock?', str(error)):
Lock(self.reduce.wrapper_file).release()
if self.thread:
self.stop()
super(Mask3DDialog, self).accept()
def reject(self):
if self.thread:
self.stop()
super(Mask3DDialog, self).reject()
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 ExperimentDialog(BaseDialog):
def __init__(self, parent=None):
super(ExperimentDialog, self).__init__(parent)
self.experiment_file = NXroot()
self.experiment_file['entry'] = NXentry()
self.detectors = {}
self.entries = {}
self.setup_instrument()
self.set_layout(self.directorybox('Choose Home Directory'),
self.instrument.grid(header=False))
self.set_title('New Experiment')
def setup_instrument(self):
entry = self.experiment_file['entry']
entry.instrument = NXinstrument()
entry.instrument.monochromator = NXmonochromator()
entry.instrument.detector = NXdetector()
entry['instrument/monochromator/wavelength'] = NXfield(0.5, dtype=np.float32)
entry['instrument/monochromator/wavelength'].attrs['units'] = 'Angstroms'
entry['instrument/detector/distance'] = NXfield(100.0, dtype=np.float32)
entry['instrument/detector/distance'].attrs['units'] = 'mm'
entry['instrument/detector/pixel_size'] = NXfield(0.172, dtype=np.float32)
entry['instrument/detector/pixel_size'].attrs['units'] = 'mm'
self.instrument = GridParameters()
self.instrument.add('wavelength', entry['instrument/monochromator/wavelength'], 'Wavelength (Ang)')
self.instrument.add('distance', entry['instrument/detector/distance'], 'Detector Distance (mm)')
self.instrument.add('pixel', entry['instrument/detector/pixel_size'], 'Pixel Size (mm)')
self.instrument.add('positions', [0,1,2,3,4], 'Number of Detector Positions', slot=self.set_entries)
self.instrument['positions'].value = '0'
def setup_entry(self, position):
entry = self.experiment_file['f%s' % position] = NXentry()
entry.instrument = NXinstrument()
entry.instrument.detector = NXdetector()
entry.instrument.monochromator = NXmonochromator()
entry['instrument/detector/beam_center_x'] = NXfield(1024.0, dtype=np.float32)
entry['instrument/detector/beam_center_y'] = NXfield(1024.0, dtype=np.float32)
self.detectors[position] = GridParameters()
self.detectors[position].add('xc', entry['instrument/detector/beam_center_x'], 'Beam Center - x')
self.detectors[position].add('yc', entry['instrument/detector/beam_center_y'], 'Beam Center - y')
@property
def positions(self):
return int(self.instrument['positions'].value)
def set_entries(self):
for position in range(1,self.positions+1):
self.setup_entry(position)
self.layout.addLayout(self.detectors[position].grid(header=False, title='Position %s'%position))
self.layout.addWidget(self.close_buttons(save=True))
def get_parameters(self):
entry = self.experiment_file['entry']
entry['instrument/monochromator/wavelength'] = self.instrument['wavelength'].value
entry['instrument/detector/distance'] = self.instrument['distance'].value
entry['instrument/detector/pixel_size'] = self.instrument['pixel'].value
for position in range(1, self.positions+1):
entry = self.experiment_file['f%s' % position]
entry['instrument/monochromator/wavelength'] = self.instrument['wavelength'].value
entry['instrument/detector/distance'] = self.instrument['distance'].value
entry['instrument/detector/pixel_size'] = self.instrument['pixel'].value
entry['instrument/detector/beam_center_x'] = self.detectors[position]['xc'].value
entry['instrument/detector/beam_center_y'] = self.detectors[position]['yc'].value
entry.makelink(self.experiment_file['entry/sample'])
def accept(self):
try:
home_directory = self.get_directory()
self.get_parameters()
self.experiment_file.save(os.path.join(home_directory, experiment+'.nxs'))
self.treeview.tree.load(self.experiment_file.nxfilename, 'rw')
super(ExperimentDialog, self).accept()
except NeXusError as error:
report_error("Defining New Experiment", error)
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 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()
class ConvertDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry()
self.parameters = GridParameters()
self.parameters.add('Ei',
self.entry['instrument/monochromator/energy'],
'Incident Energy')
self.parameters.add('dQ', self.round(np.sqrt(self.Ei / 2) / 50),
'Q Step')
self.parameters.add('dE', self.round(self.Ei / 50), 'Energy Step')
self.set_layout(
self.entry_layout, self.parameters.grid(),
self.action_buttons(
('Plot', self.plot_data), ('Save', self.save_data)),
self.close_buttons())
self.setWindowTitle('Converting to (Q,E)')
@property
def Ei(self):
return self.parameters['Ei'].value
@property
def dQ(self):
return self.parameters['dQ'].value
@property
def dE(self):
return self.parameters['dE'].value
def read_parameters(self):
self.L1 = -self.entry['sample/distance']
self.L2 = np.mean(self.entry['instrument/detector/distance'])
self.m1 = self.entry['monitor1']
self.t_m1 = self.m1.moment()
self.d_m1 = self.entry['monitor1/distance']
def convert_tof(self, tof):
ki = np.sqrt(self.Ei / 2.0721)
ts = self.t_m1 + 1588.254 * (self.L1 - self.d_m1) / ki
kf = 1588.254 * self.L2 / (tof - ts)
eps = self.Ei - 2.0721 * kf**2
return eps
def convert_QE(self):
"""Convert S(phi,eps) to S(Q,eps)"""
self.read_parameters()
Ei = self.Ei
dQ = self.dQ
dE = self.dE
signal = self.entry['data'].nxsignal
pol = centers(self.entry['data/polar_angle'], signal.shape[0])
tof = centers(self.entry['data/time_of_flight'], signal.shape[1])
en = self.convert_tof(tof)
idx_max = min(np.where(np.abs(en - 0.75 * Ei) < 0.1)[0])
en = en[:idx_max]
data = signal.nxdata[:, :idx_max]
if self.entry['data'].nxerrors:
errors = self.entry['data'].nxerrors.nxdata[:]
Q = np.zeros((len(pol), len(en)))
E = np.zeros((len(pol), len(en)))
for i in range(0, len(pol)):
p = pol[i]
Q[i, :] = np.array(
np.sqrt(
(2 * Ei - en -
2 * np.sqrt(Ei * (Ei - en)) * np.cos(p * np.pi / 180.0)) /
2.0721))
E[i, :] = np.array(en)
s = Q.shape
Qin = Q.reshape(s[0] * s[1])
Ein = E.reshape(s[0] * s[1])
datain = data.reshape(s[0] * s[1])
if self.entry['data'].nxerrors:
errorsin = errors.reshape(s[0] * s[1])
qmin = Q.min()
qmax = Q.max()
emin = E.min()
emax = E.max()
NQ = int((qmax - qmin) / dQ) + 1
NE = int((emax - emin) / dE) + 1
Qb = np.linspace(qmin, qmax, NQ)
Eb = np.linspace(emin, emax, NE)
# histogram and normalize
norm, nbin = np.histogramdd((Ein, Qin), bins=(Eb, Qb))
hist, hbin = np.histogramdd((Ein, Qin), bins=(Eb, Qb), weights=datain)
if self.entry['data'].nxerrors:
histe, hbin = np.histogramdd((Ein, Qin),
bins=(Eb, Qb),
weights=errorsin * errorsin)
histe = histe**0.5
err = histe / norm
Ib = NXfield(hist / norm, name='S(Q,E)')
Qb = NXfield(Qb[:-1] + dQ / 2., name='Q')
Eb = NXfield(Eb[:-1] + dE / 2., name='E')
result = NXdata(Ib, (Eb, Qb))
if self.entry.data.nxerrors:
result.errors = NXfield(err)
return result
def round(self, x, prec=2, base=.05):
return round(base * round(float(x) / base), prec)
def plot_data(self):
self.convert_QE().plot()
def save_data(self):
self.entry['sqe'] = self.convert_QE()
class ExperimentDialog(BaseDialog):
def __init__(self, parent=None):
super(ExperimentDialog, self).__init__(parent)
self.experiment_file = NXroot()
self.experiment_file['entry'] = NXentry()
self.detectors = {}
self.entries = {}
self.setup_instrument()
self.set_layout(self.directorybox('Choose Experiment Directory', default=False),
self.instrument.grid(header=False))
self.set_title('New Experiment')
def setup_instrument(self):
entry = self.experiment_file['entry']
entry.instrument = NXinstrument()
entry.instrument.monochromator = NXmonochromator()
entry.instrument.detector = NXdetector()
entry['instrument/monochromator/wavelength'] = NXfield(0.5, dtype=np.float32)
entry['instrument/monochromator/wavelength'].attrs['units'] = 'Angstroms'
entry['instrument/monochromator/energy'] = NXfield(12.398419739640717/0.5, dtype=np.float32)
entry['instrument/monochromator/energy'].attrs['units'] = 'keV'
entry['instrument/detector/distance'] = NXfield(100.0, dtype=np.float32)
entry['instrument/detector/distance'].attrs['units'] = 'mm'
self.instrument = GridParameters()
self.instrument.add('experiment', 'experiment', 'Experiment Name')
self.instrument.add('wavelength', entry['instrument/monochromator/wavelength'], 'Wavelength (Ang)')
self.instrument.add('distance', entry['instrument/detector/distance'], 'Detector Distance (mm)')
detector_list = sorted(list(set([detector().name for detector in ALL_DETECTORS.values()])))
self.instrument.add('detector', detector_list, 'Detector')
self.instrument['detector'].value = 'Pilatus CdTe 2M'
self.instrument.add('positions', [0,1,2,3,4], 'Number of Detector Positions', slot=self.set_entries)
self.instrument['positions'].value = '0'
def setup_entry(self, position):
entry = NXentry()
self.detectors[position] = GridParameters()
self.detectors[position].add('x', 0.0, 'Translation - x (mm)')
self.detectors[position].add('y', 0.0, 'Translation - y (mm)')
self.experiment_file['f%s' % position] = entry
def get_detector(self):
for detector in ALL_DETECTORS:
if ALL_DETECTORS[detector]().name == self.instrument['detector'].value:
return ALL_DETECTORS[detector]()
@property
def positions(self):
return int(self.instrument['positions'].value)
def set_entries(self):
for position in range(1,self.positions+1):
self.setup_entry(position)
self.layout.addLayout(self.detectors[position].grid(header=False, title='Position %s'%position))
self.layout.addWidget(self.close_buttons(save=True))
def get_parameters(self):
entry = self.experiment_file['entry']
entry['instrument/monochromator/wavelength'] = self.instrument['wavelength'].value
entry['instrument/monochromator/energy'] = 12.398419739640717 / self.instrument['wavelength'].value
detector = self.get_detector()
entry['instrument/detector/description'] = detector.name
entry['instrument/detector/distance'] = self.instrument['distance'].value
entry['instrument/detector/pixel_size'] = detector.pixel1 * 1000
entry['instrument/detector/pixel_size'].attrs['units'] = 'mm'
entry['instrument/detector/pixel_mask'] = detector.mask
entry['instrument/detector/shape'] = detector.shape
entry['instrument/detector/yaw'] = 0.0
entry['instrument/detector/pitch'] = 0.0
entry['instrument/detector/roll'] = 0.0
for position in range(1, self.positions+1):
entry = self.experiment_file['f%s' % position]
entry['instrument'] = self.experiment_file['entry/instrument']
entry['instrument/detector/translation_x'] = self.detectors[position]['x'].value
entry['instrument/detector/translation_x'].attrs['units'] = 'mm'
entry['instrument/detector/translation_y'] = self.detectors[position]['y'].value
entry['instrument/detector/translation_y'].attrs['units'] = 'mm'
entry['instrument/detector/frame_time'] = 0.1
entry['instrument/detector/frame_time'].attrs['units'] = 'seconds'
def accept(self):
try:
home_directory = self.get_directory()
self.mainwindow.default_directory = home_directory
self.get_parameters()
configuration_directory = os.path.join(home_directory, 'configurations')
if not os.path.exists(configuration_directory):
os.makedirs(configuration_directory)
self.experiment_file.save(os.path.join(configuration_directory,
self.instrument['experiment'].value+'.nxs'))
task_directory = os.path.join(home_directory, 'tasks')
if not os.path.exists(task_directory):
os.makedirs(task_directory)
calibration_directory = os.path.join(home_directory, 'calibrations')
if not os.path.exists(calibration_directory):
os.makedirs(calibration_directory)
self.treeview.tree.load(self.experiment_file.nxfilename, 'rw')
super(ExperimentDialog, self).accept()
except Exception as error:
report_error("Defining New Experiment", error)
class LatticeDialog(BaseDialog):
def __init__(self, parent=None):
super(LatticeDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine()
self.parameters = GridParameters()
self.parameters.add('symmetry', self.refine.symmetries, 'Symmetry',
slot=self.set_lattice_parameters)
self.parameters.add('centring', self.refine.centrings, 'Cell Centring')
self.parameters.add('a', self.refine.a, 'Unit Cell - a (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('b', self.refine.b, 'Unit Cell - b (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('c', self.refine.c, 'Unit Cell - c (Ang)',
slot=self.set_lattice_parameters)
self.parameters.add('alpha', self.refine.alpha, 'Unit Cell - alpha (deg)',
slot=self.set_lattice_parameters)
self.parameters.add('beta', self.refine.beta, 'Unit Cell - beta (deg)',
slot=self.set_lattice_parameters)
self.parameters.add('gamma', self.refine.gamma, 'Unit Cell - gamma (deg)',
slot=self.set_lattice_parameters)
self.parameters['symmetry'].value = self.refine.symmetry
self.parameters['centring'].value = self.refine.centring
action_buttons = self.action_buttons(('Plot', self.plot_lattice),
('Save', self.write_parameters))
self.set_layout(self.entry_layout, self.parameters.grid(),
action_buttons, self.close_buttons())
self.set_title('Defining Lattice')
def choose_entry(self):
self.refine = NXRefine(self.entry)
self.update_parameters()
def update_parameters(self):
self.parameters['symmetry'].value = self.refine.symmetry
self.parameters['centring'].value = self.refine.centring
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
def get_symmetry(self):
return self.parameters['symmetry'].value
def get_centring(self):
return self.parameters['centring'].value
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
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
elif symmetry == 'orthorhombic':
self.parameters['alpha'].value = 90.0
self.parameters['beta'].value = 90.0
self.parameters['gamma'].value = 90.0
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
elif symmetry == 'monoclinic':
self.parameters['alpha'].value = 90.0
self.parameters['gamma'].value = 90.0
def get_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.symmetry = self.get_symmetry()
self.refine.centring = self.get_centring()
def plot_lattice(self):
try:
self.get_parameters()
self.plot_peaks(self.refine.xp, self.refine.yp)
polar_min, polar_max = plotview.xaxis.get_limits()
self.plot_rings(polar_max)
except NeXusError as error:
report_error('Plotting Lattice', error)
def write_parameters(self):
try:
self.get_parameters()
self.refine.write_parameters()
except NeXusError as error:
report_error('Defining Lattice', error)
def plot_peaks(self, x, y):
try:
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()
class FindDialog(BaseDialog):
def __init__(self, parent=None):
super(FindDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
try:
threshold = np.float32(self.entry.data.attrs["maximum"]) / 20
max_frame = np.int32(len(self.entry.data.nxaxes[0]))
except Exception:
threshold = 5000
max_frame = 0
self.parameters = GridParameters()
self.parameters.add("threshold", threshold, "Threshold")
self.parameters.add("min", 0, "First Frame")
self.parameters.add("max", max_frame, "Last Frame")
self.parameters.add("pixel_tolerance", 50, "Pixel Tolerance")
self.parameters.add("frame_tolerance", 10, "Frame Tolerance")
find_layout = QtGui.QHBoxLayout()
self.find_button = QtGui.QPushButton("Find Peaks")
self.find_button.clicked.connect(self.find_peaks)
self.peak_count = QtGui.QLabel()
self.peak_count.setVisible(False)
find_layout.addStretch()
find_layout.addWidget(self.find_button)
find_layout.addWidget(self.peak_count)
find_layout.addStretch()
self.set_layout(self.entry_layout, self.parameters.grid(), find_layout)
self.set_title("Find Peaks")
self.npk = 0
try:
self.parameters["max"].value = self.entry["data"].nxsignal.shape[0]
self.parameters["threshold"].value = self.entry["data"].attrs["maximum"] / 20
except Exception:
pass
def choose_entry(self):
try:
self.parameters["threshold"].value = self.entry["data"].attrs["maximum"] / 20
self.parameters["max"].value = len(self.entry.data.nxaxes[0])
except Exception:
pass
def get_threshold(self):
return self.parameters["threshold"].value
def get_limits(self):
return np.int32(self.parameters["min"].value), np.int32(self.parameters["max"].value)
def get_tolerance(self):
"""
Return pixel and frame tolerances from the text boxes.
Note that the pixel tolerance is squared to save square-root
calculations in peak comparisons.
"""
return (self.parameters["pixel_tolerance"].value, self.parameters["frame_tolerance"].value)
def find_peaks(self):
field = self.entry["data"].nxsignal
try:
self.mask = self.entry["instrument/detector/pixel_mask"]
except NeXusError:
self.mask = None
self.layout.removeWidget(self.find_button)
self.find_button.setVisible(False)
if len(field.shape) == 2:
self.layout.addWidget(self.close_buttons(save=True))
elif len(field.shape) > 2:
self.layout.addLayout(self.progress_layout(save=True))
threshold = self.get_threshold()
self.blim = np.zeros(field.shape[-2:], np.int32)
self.verbose = 0
lio = labelimage(field.shape[-2:], flipper=flip1)
allpeaks = []
if len(field.shape) == 2:
res = None
else:
chunk_size = field.nxfile[field.nxpath].chunks[0]
z_min, z_max = self.get_limits()
pixel_tolerance, frame_tolerance = self.get_tolerance()
self.progress_bar.setRange(z_min, z_max)
for i in range(0, field.shape[0], chunk_size):
try:
if i + chunk_size > z_min and i < z_max:
self.progress_bar.setValue(i)
self.update_progress()
v = field[i : i + chunk_size, :, :].nxdata
for j in range(chunk_size):
if i + j >= z_min and i + j <= z_max:
omega = np.float32(i + j)
lio.peaksearch(v[j], threshold, omega)
if lio.res is not None:
blob_moments(lio.res)
for k in range(lio.res.shape[0]):
res = lio.res[k]
peak = NXpeak(
res[0],
res[22],
res[23],
res[24],
omega,
res[27],
res[26],
res[29],
threshold,
pixel_tolerance,
frame_tolerance,
)
if peak.isvalid(self.mask):
allpeaks.append(peak)
except IndexError as error:
pass
if not allpeaks:
self.reject()
report_error("Finding peaks", "No peaks found")
allpeaks = sorted(allpeaks)
self.progress_bar.reset()
self.progress_bar.setRange(z_min, z_max)
merged_peaks = []
for z in range(z_min, z_max + 1):
self.progress_bar.setValue(z)
self.update_progress()
frame = [peak for peak in allpeaks if peak.z == z]
if not merged_peaks:
merged_peaks.extend(frame)
else:
for peak1 in frame:
combined = False
for peak2 in last_frame:
if peak1 == peak2:
for idx in range(len(merged_peaks)):
if peak1 == merged_peaks[idx]:
break
peak1.combine(merged_peaks[idx])
merged_peaks[idx] = peak1
combined = True
break
if not combined:
reversed_peaks = [p for p in reversed(merged_peaks) if p.z >= peak1.z - frame_tolerance]
for peak2 in reversed_peaks:
if peak1 == peak2:
for idx in range(len(merged_peaks)):
if peak1 == merged_peaks[idx]:
break
peak1.combine(merged_peaks[idx])
merged_peaks[idx] = peak1
combined = True
break
if not combined:
merged_peaks.append(peak1)
if frame:
last_frame = frame
merged_peaks = sorted(merged_peaks)
for peak in merged_peaks:
peak.merge()
merged_peaks = sorted(merged_peaks)
self.peaks = merged_peaks
self.progress_bar.setVisible(False)
self.peak_count.setText("%s peaks found" % len(self.peaks))
self.peak_count.setVisible(True)
def accept(self):
try:
if "peaks" in self.entry.entries:
del self.entry["peaks"]
self.entry.peaks = NXdata()
shape = (len(self.peaks),)
self.entry.peaks.npixels = NXfield([peak.np for peak in self.peaks], dtype=np.float32)
self.entry.peaks.intensity = NXfield([peak.intensity for peak in self.peaks], dtype=np.float32)
self.entry.peaks.x = NXfield([peak.x for peak in self.peaks], dtype=np.float32)
self.entry.peaks.y = NXfield([peak.y for peak in self.peaks], dtype=np.float32)
self.entry.peaks.z = NXfield([peak.z for peak in self.peaks], dtype=np.float32)
self.entry.peaks.sigx = NXfield([peak.sigx for peak in self.peaks], dtype=np.float32)
self.entry.peaks.sigy = NXfield([peak.sigy for peak in self.peaks], dtype=np.float32)
self.entry.peaks.covxy = NXfield([peak.covxy for peak in self.peaks], dtype=np.float32)
super(FindDialog, self).accept()
except NeXusError as error:
report_error("Finding peaks", error)
