class TEMParametersUI(t.HasTraits):
beam_energy = t.Float(t.Undefined,
label='Beam energy (keV)')
real_time = t.Float(t.Undefined,
label='Real time (s)')
tilt_stage = t.Float(t.Undefined,
label='Stage tilt (degree)')
live_time = t.Float(t.Undefined,
label='Live time (s)')
probe_area = t.Float(t.Undefined,
label='Beam/probe area (nm^2)')
azimuth_angle = t.Float(t.Undefined,
label='Azimuth angle (degree)')
elevation_angle = t.Float(t.Undefined,
label='Elevation angle (degree)')
energy_resolution_MnKa = t.Float(t.Undefined,
label='Energy resolution MnKa (eV)')
beam_current = t.Float(t.Undefined,
label='Beam current (nA)')
traits_view = tu.View(
tu.Group('beam_energy',
'tilt_stage',
'probe_area',
'beam_current',
label='TEM', show_border=True),
tu.Group('real_time', 'live_time', 'azimuth_angle',
'elevation_angle', 'energy_resolution_MnKa',
label='EDS', show_border=True),
kind='modal', buttons=[OKButton, CancelButton],
title='TEM parameters definition wizard')
def get_data_axis_view(navigate, label):
group_args = [
tui.Item(name='name'),
tui.Item(name='size', style='readonly'),
tui.Item(name='index_in_array', style='readonly'),
tui.Item(name='units'),
]
if navigate:
group_args.extend([
tui.Item(name='index'),
tui.Item(name='value', style='readonly'), ])
data_axis_view = tui.View(
tui.Group(
tui.Group(*group_args,
show_border=True,),
tui.Group(
tui.Item(name='scale'),
tui.Item(name='offset'),
label='Calibration',
show_border=True,),
# label="Data Axis properties",
show_border=True,),
title=label,)
return data_axis_view
def get_axis_group(n, label=''):
group = tui.Group(
tui.Group(
tui.Item('axis%i.name' % n),
tui.Item('axis%i.size' % n, style='readonly'),
tui.Item('axis%i.index_in_array' % n, style='readonly'),
tui.Item('axis%i.low_index' % n, style='readonly'),
tui.Item('axis%i.high_index' % n, style='readonly'),
# The style of the index is chosen to be readonly because of
# a bug in Traits 4.0.0 when using context with a Range traits
# where the limits are defined by another traits_view
tui.Item('axis%i.index' % n, style='readonly'),
tui.Item('axis%i.value' % n, style='readonly'),
tui.Item('axis%i.units' % n),
tui.Item('axis%i.navigate' % n, label='navigate'),
show_border=True,
),
tui.Group(
tui.Item('axis%i.scale' % n),
tui.Item('axis%i.offset' % n),
label='Calibration',
show_border=True,
),
label=label,
show_border=True,
)
return group
def spikes_removal_traitsui(obj, **kwargs):
thisOKButton = tu.Action(name="OK",
action="OK",
tooltip="Close the spikes removal tool")
thisApplyButton = tu.Action(name="Remove spike",
action="apply",
tooltip="Remove the current spike by "
"interpolating\n"
"with the specified settings (and find\n"
"the next spike automatically)")
thisFindButton = tu.Action(
name="Find next",
action="find",
tooltip="Find the next (in terms of navigation\n"
"dimensions) spike in the data.")
thisPreviousButton = tu.Action(name="Find previous",
action="back",
tooltip="Find the previous (in terms of "
"navigation\n"
"dimensions) spike in the data.")
view = tu.View(
tu.Group(
tu.Group(
tu.Item(
'click_to_show_instructions',
show_label=False,
),
tu.Item('show_derivative_histogram',
show_label=False,
tooltip="To determine the appropriate threshold,\n"
"plot the derivative magnitude histogram, \n"
"and look for outliers at high magnitudes \n"
"(which represent sudden spikes in the data)"),
'threshold',
show_border=True,
),
tu.Group('add_noise',
'interpolator_kind',
'default_spike_width',
tu.Group('spline_order',
enabled_when='interpolator_kind == "Spline"'),
show_border=True,
label='Advanced settings'),
),
buttons=[
thisOKButton,
thisPreviousButton,
thisFindButton,
thisApplyButton,
],
handler=SpikesRemovalHandler,
title='Spikes removal tool',
resizable=False,
)
return obj, {"view": view}
def make_plugin_view(model_name, model_nodes, selection_view, model_view):
node_label = '=' + model_name
container_nodes = [
_traitsui.TreeNode(
node_for=[CalcContainer],
label=node_label,
children='',
auto_open=True,
menu=[],
),
_traitsui.TreeNode(
node_for=[CalcContainer],
label=node_label,
children='calculations',
auto_open=True,
menu=[],
),
]
plugin_tree = _traitsui.TreeEditor(
nodes=container_nodes + model_nodes,
# refresh='controller.update_tree',
selected='controller.selected_object',
editable=False,
hide_root=True,
)
plugin_view = _traitsui.View(
_traitsui.Group(
# Left side tree
_traitsui.Item('controller.model',
editor=plugin_tree,
show_label=False),
# Right side
_traitsui.Group(
# Upper right side data set selection panel
selection_view,
# Lower right side calc settings panel
_traitsui.Group(
_traitsui.Item(
'controller.edit_node',
editor=_traitsui.InstanceEditor(view=model_view),
style='custom',
show_label=False),
show_border=True,
),
orientation='vertical',
),
_traitsui.Spring(width=10),
orientation='horizontal',
),
resizable=True,
buttons=['OK'],
)
return plugin_view
class NoPlotControl(_traitsui.ModelView):
model = _traits.Instance(_chaco.DataView)
plot_controllers = _traitsui.Group()
traits_view = _traitsui.View(
_traitsui.Group(_traitsui.Item(
'model',
editor=_enable.ComponentEditor(bgcolor=bg_color),
show_label=False),
_traitsui.Include('plot_controllers'),
orientation="vertical"))
def microscope_parameters_EELS(obj, **kwargs):
view = tu.View(tu.Group('beam_energy',
'convergence_angle',
label='TEM',
show_border=True),
tu.Group('collection_angle', label='EELS',
show_border=True),
buttons=[StoreButton],
title='TEM parameters definition wizard')
return obj, {"view": view}
def get_axis_group(n, navigate, label='', attribs=[], **kwargs):
group_args = [
tui.Item(f'axis{n}.name'),
tui.Item(f'axis{n}.size', style='readonly'),
tui.Item(f'axis{n}.index_in_array', style='readonly'),
tui.Item(f'axis{n}.low_index', style='readonly'),
tui.Item(f'axis{n}.high_index', style='readonly'),
tui.Item(f'axis{n}.units'),
]
cal_args = [ ]
if 'is_binned' in attribs:
group_args.append(tui.Item(f'axis{n}.is_binned'))
if navigate:
group_args.extend([
tui.Item(f'axis{n}.index', editor=tui.RangeEditor(
low_name=f'axis{n}.low_index',
high_name=f'axis{n}.high_index',
label_width=28,
format_str='%i',
mode='auto')),
tui.Item(f'axis{n}.value', style='readonly', format_str='%5g'), ])
if 'scale' in attribs:
cal_args.extend([
tui.Item(f'axis{n}.scale'),
tui.Item(f'axis{n}.offset'), ])
if '_expression' in attribs:
cal_args.extend([
tui.Item(f'axis{n}._expression', style='readonly'), ])
for j in range(len(kwargs['parameters_list'])):
p = kwargs['parameters_list'][j]
cal_args.extend([
tui.Item(f'axis{n}.{p}', label=p), ])
if 'xscale' in kwargs.keys():
cal_args.extend([
tui.Item(f'axis{n}.x.scale', label='x scale'),
tui.Item(f'axis{n}.x.offset', label='x offset'), ])
if cal_args == [ ]:
group = tui.Group(
tui.Group(*group_args,
show_border=True,),
label=label,
show_border=True,)
else:
group = tui.Group(
tui.Group(*group_args,
show_border=True,),
tui.Group(*cal_args,
label='Calibration', show_border=True, ),
label=label,
show_border=True,)
return group
class EELSConfig(t.HasTraits):
eels_gos_files_path = t.Directory(
guess_gos_path(),
label='GOS directory',
desc='The GOS files are required to create the EELS edge components')
fine_structure_width = t.CFloat(
30,
label='Fine structure lenght',
desc='The default lenght of the fine structure from the edge onset')
fine_structure_active = t.CBool(
False,
label='Enable fine structure',
desc="If enabled, the regions of the EELS spectrum defined as fine "
"structure will be fitted with a spline. Please note that it "
"enabling this feature only makes sense when the model is "
"convolved to account for multiple scattering")
fine_structure_smoothing = t.Range(
0.,
1.,
value=0.3,
label='Fine structure smoothing factor',
desc='The lower the value the smoother the fine structure spline fit')
synchronize_cl_with_ll = t.CBool(False)
preedge_safe_window_width = t.CFloat(
2,
label='Pre-onset region (in eV)',
desc='Some functions needs to define the regions between two '
'ionisation edges. Due to limited energy resolution or chemical '
'shift, the region is limited on its higher energy side by '
'the next ionisation edge onset minus an offset defined by this '
'parameters')
min_distance_between_edges_for_fine_structure = t.CFloat(
0,
label='Minimum distance between edges',
desc='When automatically setting the fine structure energy regions, '
'the fine structure of an EELS edge component is automatically '
'disable if the next ionisation edge onset distance to the '
'higher energy side of the fine structure region is lower that '
'the value of this parameter')
view = tui.View(
tui.Group('synchronize_cl_with_ll', label='General'),
tui.Group('eels_gos_files_path',
'preedge_safe_window_width',
tui.Group('fine_structure_width',
'fine_structure_active',
'fine_structure_smoothing',
'min_distance_between_edges_for_fine_structure',
label='Fine structure'),
label='Model'))
def remove_background_traitsui(obj, **kwargs):
view = tu.View(
tu.Group(
'background_type',
'fast',
tu.Group('polynomial_order',
visible_when='background_type == \'Polynomial\''),
),
buttons=[OKButton, CancelButton],
handler=SpanSelectorInSignal1DHandler,
title='Background removal tool',
resizable=True,
width=300,
)
return obj, {"view": view}
def microscope_parameters_EDS_SEM(obj, **kwargs):
view = tu.View(tu.Group('beam_energy',
'tilt_stage',
label='SEM',
show_border=True),
tu.Group('live_time',
'azimuth_angle',
'elevation_angle',
'energy_resolution_MnKa',
label='EDS',
show_border=True),
buttons=[StoreButton],
handler=SetMetadataItemsHandler,
title='SEM parameters definition wizard')
return obj, {"view": view}
class TEMParametersUI(t.HasTraits):
convergence_angle = t.Float(t.Undefined, label='Convergence angle (mrad)')
beam_energy = t.Float(t.Undefined, label='Beam energy (keV)')
collection_angle = t.Float(t.Undefined, label='Collection angle (mrad)')
traits_view = tu.View(tu.Group('beam_energy',
'convergence_angle',
label='TEM',
show_border=True),
tu.Group('collection_angle',
label='EELS',
show_border=True),
kind='modal',
buttons=[OKButton, CancelButton],
title='TEM parameters definition wizard')
class Preferences(t.HasTraits):
EELS = t.Instance(EELSConfig)
EDS = t.Instance(EDSConfig)
Model = t.Instance(ModelConfig)
General = t.Instance(GeneralConfig)
MachineLearning = t.Instance(MachineLearningConfig)
view = tui.View(
tui.Group(tui.Item(
'General',
style='custom',
show_label=False,
),
label='General'),
tui.Group(tui.Item(
'Model',
style='custom',
show_label=False,
),
label='Model'),
tui.Group(tui.Item(
'EELS',
style='custom',
show_label=False,
),
label='EELS'),
tui.Group(tui.Item(
'EDS',
style='custom',
show_label=False,
),
label='EDS'),
tui.Group(tui.Item(
'MachineLearning',
style='custom',
show_label=False,
),
label='Machine Learning'),
title='Preferences',
handler=PreferencesHandler,
)
def gui(self):
self.edit_traits()
def save(self):
config = ConfigParser.SafeConfigParser(allow_no_value=True)
template2config(template, config)
config.write(open(defaults_file, 'w'))
def load(obj, **kwargs):
view = tu.View(tu.Group(
tu.Item('filename', editor=FileEditor(dialog_style='open')), "lazy"),
kind='livemodal',
buttons=[OKButton, CancelButton],
title='Load file')
return obj, {"view": view}
class ButterworthFilter(Smoothing):
cutoff_frequency_ratio = t.Range(0., 1., 0.05)
type = t.Enum('low', 'high')
order = t.Int(2)
view = tu.View(
tu.Group('cutoff_frequency_ratio', 'order', 'type'),
kind='live',
handler=SmoothingHandler,
buttons=OKCancelButtons,
title='Butterworth filter',
)
def _cutoff_frequency_ratio_changed(self, old, new):
self.update_lines()
def _type_changed(self, old, new):
self.update_lines()
def _order_changed(self, old, new):
self.update_lines()
def model2plot(self, axes_manager=None):
b, a = sp.signal.butter(self.order, self.cutoff_frequency_ratio,
self.type)
smoothed = sp.signal.filtfilt(b, a, self.signal())
return smoothed
class _H5Trees(api.HasTraits):
h5_trees = api.Instance(Hdf5FilesNode)
node = api.Any()
path = api.Str()
traits_view = ui.View(
ui.Group(
ui.Item(
'h5_trees',
editor=_hdf5_tree_editor(selected='node'),
resizable=True,
),
ui.Item('path', label='Selected node'),
orientation='vertical',
),
title='Multiple HDF5 file Tree Example',
buttons=['OK', 'Cancel'],
resizable=True,
width=0.3,
height=0.3,
)
def _node_changed(self):
self.path = self.node.path
print(self.node.path)
class AutoRefreshDialog(traits.HasTraits):
minutes = traits.Float(1.0)
autoRefreshBool = traits.Bool()
emailAlertBool = traits.Bool(False)
soundAlertBool = traits.Bool(False)
linesOfDataFrame = traits.Range(1, 10)
alertCode = traits.Code(
DEFAULT_ALERT_CODE,
desc="python code for finding alert worthy elements")
basicGroup = traitsui.Group("minutes", "autoRefreshBool")
alertGroup = traitsui.VGroup(
traitsui.HGroup(traitsui.Item("emailAlertBool"),
traitsui.Item("soundAlertBool")),
traitsui.Item("linesOfDataFrame",
visible_when="emailAlertBool or soundAlertBool"),
traitsui.Item("alertCode",
visible_when="emailAlertBool or soundAlertBool"))
traits_view = traitsui.View(traitsui.VGroup(basicGroup, alertGroup),
title="auto refresh",
buttons=[OKButton],
kind='livemodal',
resizable=True)
class Load(t.HasTraits):
filename = t.File
traits_view = tu.View(
tu.Group('filename'),
kind='livemodal',
buttons=[OKButton, CancelButton],
title='Load file')
class SmoothingTV(Smoothing):
smoothing_parameter = t.Float(200)
view = tu.View(
tu.Group(
'smoothing_parameter',
'line_color'),
kind='live',
handler=SmoothingHandler,
buttons=OKCancelButtons,
title='Total Variation Smoothing',)
def _smoothing_parameter_changed(self, old, new):
self.update_lines()
def _number_of_iterations_changed(self, old, new):
self.update_lines()
def model2plot(self, axes_manager=None):
self.single_spectrum.data = self.signal().copy()
self.single_spectrum.smooth_tv(
smoothing_parameter=self.smoothing_parameter,
show_progressbar=False)
return self.single_spectrum.data
def rectangular_roi_traitsui(obj, **kwargs):
view = tu.View(
tu.Group(
tu.Item(
'left',
label='Left',
format_str='%5g',
),
tu.Item(
'right',
label='Right',
format_str='%5g',
),
tu.Item(
'top',
label='Top',
format_str='%5g',
),
tu.Item(
'bottom',
label='Bottom',
format_str='%5g',
),
), )
return obj, {"view": view}
def line2d_roi_traitsui(obj, **kwargs):
view = tu.View(
tu.Group(
tu.Item(
'x1',
label='x1',
format_str='%5g',
),
tu.Item(
'y1',
label='y1',
format_str='%5g',
),
tu.Item(
'x2',
label='x2',
format_str='%5g',
),
tu.Item(
'y2',
label='y2',
format_str='%5g',
),
tu.Item(
'linewidth',
label='linewidth',
format_str='%5g',
),
), )
return obj, {"view": view}
class SmoothingSavitzkyGolay(Smoothing):
polynomial_order = t.Int(3)
number_of_points = t.Int(5)
crop_diff_axis = False
view = tu.View(
tu.Group('polynomial_order', 'number_of_points', 'differential_order',
'line_color'),
kind='live',
handler=SmoothingHandler,
buttons=OKCancelButtons,
title='Savitzky-Golay Smoothing',
)
def _polynomial_order_changed(self, old, new):
self.update_lines()
def _number_of_points_changed(self, old, new):
self.update_lines()
def _differential_order(self, old, new):
self.update_lines()
def diff_model2plot(self, axes_manager=None):
smoothed = spectrum_tools.sg(self.signal(), self.number_of_points,
self.polynomial_order,
self.differential_order)
return smoothed
def model2plot(self, axes_manager=None):
smoothed = spectrum_tools.sg(self.signal(), self.number_of_points,
self.polynomial_order, 0)
return smoothed
class cash_flow_series(trapi.HasTraits):
name = trapi.Str
short_rate = trapi.Range(0.0, 0.5, 0.05)
time_list = trapi.Array(dtype=np.float, shape=(1, 6))
cash_flows = trapi.Array(dtype=np.float, shape=(1, 6))
disc_values = trapi.Array(dtype=np.float, shape=(1, 6))
present_values = trapi.Array(dtype=np.float, shape=(1, 6))
net_present_value = trapi.Float
update = trapi.Button
def _update_fired(self):
self.disc_values = np.exp(-self.short_rate * self.time_list)
self.present_values = self.disc_values * self.cash_flows
self.net_present_value = np.sum(self.present_values)
v = trui.View(trui.Group(trui.Item(name='name'),
trui.Item(name='short_rate'),
trui.Item(name='time_list', label='Time List'),
trui.Item(name='cash_flows', label='Cash Flows'),
trui.Item('update', show_label=False),
trui.Item(name='disc_values',
label='Discount Factors'),
trui.Item(name='present_values',
label='Present Values'),
trui.Item(name='net_present_value',
label='Net Present Value'),
show_border=True,
label='Calculate Present Values'),
buttons=[trui.OKButton, trui.CancelButton],
resizable=True)
def get_navigation_sliders_group(obj):
"""Raises a windows with sliders to control the index of DataAxis
Parameters
----------
obj : list of DataAxis instances
"""
axis_group_args = []
context = {}
def get_axis_label(axis):
return (axis.name if axis.name != t.Undefined
else f"Axis {axis.index_in_axes_manager}")
for i, axis in enumerate(obj):
axis_group_args.append(tui.Item(f'axis{i}.value',
label=get_axis_label(axis),
editor=tui.RangeEditor(
low_name=f'axis{i}.low_value',
high_name=f'axis{i}.high_value',
label_width=28,
format='%i',
mode='auto')))
context[f'axis{i}'] = axis
axis_group = tui.Group(*axis_group_args,
show_border=False,)
return axis_group, context
class SmoothingLowess(Smoothing):
smoothing_parameter = t.Float(2 / 3.)
number_of_iterations = t.Int(3)
differential_order = t.Int(0)
view = tu.View(
tu.Group('smoothing_parameter', 'number_of_iterations',
'differential_order', 'line_color'),
kind='live',
handler=SmoothingHandler,
buttons=OKCancelButtons,
title='Lowess Smoothing',
)
def _smoothing_parameter_changed(self, old, new):
self.update_lines()
def _number_of_iterations_changed(self, old, new):
self.update_lines()
def model2plot(self, axes_manager=None):
smoothed = utils.lowess(self.axis, self.signal(),
self.smoothing_parameter,
self.number_of_iterations)
return smoothed
class StackedPlotControl(NoPlotControl):
percent = _traits.Bool(False)
plot_controllers = _traitsui.Group(_traitsui.Item('percent'))
@_traits.on_trait_change('percent')
def flip_interaction(self, obj, name, new):
obj.model.plot_stacked(new)
obj.model.invalidate_and_redraw()
def point1d_roi_traitsui(obj, **kwargs):
view = tu.View(
tu.Group(tu.Item(
'value',
label='value',
format_str='%5g',
), ), )
return obj, {"view": view}
def microscope_parameters_EDS_TEM(obj, **kwargs):
view = tu.View(tu.Group('beam_energy',
'tilt_stage',
'probe_area',
'beam_current',
label='TEM',
show_border=True),
tu.Group('real_time',
'live_time',
'azimuth_angle',
'elevation_angle',
'energy_resolution_MnKa',
label='EDS',
show_border=True),
buttons=[StoreButton],
title='TEM parameters definition wizard')
return obj, {"view": view}
def smooth_butterworth(obj, **kwargs):
view = tu.View(
tu.Group('cutoff_frequency_ratio', 'order', 'type'),
kind='live',
handler=SmoothingHandler,
buttons=OKCancelButtons,
title='Butterworth filter',
)
return obj, {"view": view}
class MultiMeshMorpher(ta.HasTraits):
visible = ta.Enum(values='_names')
morph_target = ta.Enum(values='_names')
morph_alpha = ta.Range(0.0, 1.0, 0.0)
show_edges = ta.Bool(False)
_names = ta.List()
def __init__(self, list_verts, tris, names=None, fig=None, **kw):
super(MultiMeshMorpher, self).__init__(**kw)
self._list_verts = list_verts
self._tris = tris
if fig is None:
self._fig = mlab.figure(bgcolor=(1, 1, 1))
else:
self._fig = fig
if names is None:
names = map(str, range(len(list_verts)))
self._names = list(names)
self._verts_by_name = dict(zip(self._names, list_verts))
self._actor, self._pd = mesh_as_vtk_actor(list_verts[0], tris, return_polydata=True)
self._actor.property.set(
ambient=0.0,
specular=0.15,
specular_power=128.,
diffuse=0.8,
)
self._fig.scene.add_actor(self._actor)
self.visible = self._names[0]
if len(self._names) > 1:
self.morph_target = self._names[1]
@ta.on_trait_change('visible, show_edges, morph_target, morph_alpha')
def _update(self):
self._actor.property.edge_visibility = self.show_edges
v1 = self._verts_by_name[self.visible]
if self.morph_alpha > 0:
v2 = self._verts_by_name[self.morph_target]
self._pd.points = v1 * (1 - self.morph_alpha) + v2 * self.morph_alpha
else:
self._pd.points = v1
self._fig.scene.render()
view = tu.View(
tu.Group(
tu.Item('visible'),
tu.Item('morph_target'),
tu.Item('morph_alpha'),
tu.Item('show_edges', name='Wireframe'),
label="Viewer"),
title="MultiMeshMorpher"
)
