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()
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 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'
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)
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 __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 __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 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_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 __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')
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()
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')
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()
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 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 __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)')
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 __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 __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 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 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 __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 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 __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 __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 __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 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 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))
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 __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 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_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'f{i}'
self.scans.add(scan, i+1, f, True, self.update_scans)
self.scans[scan].checkbox.stateChanged.connect(self.update_scans)
scroll_widget = NXWidget()
scroll_widget.set_layout(self.scans.grid(header=False))
scroll_area = NXScrollArea(scroll_widget)
scroll_area.setMinimumHeight(min(scroll_widget.sizeHint().height(),
600))
scroll_area.setWidgetResizable(True)
self.insert_layout(2, scroll_area)
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 __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 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 __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']
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 __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 __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 __init__(self, parent=None):
super(ConvertDialog, self).__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)')
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))
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"]
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 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 __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 __init__(self, parent=None):
super(CalculateDialog, self).__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)')
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')
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()
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 __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']
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 __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 __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
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 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 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 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 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 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)
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
