def __init__(self, default_simulation_name="simulation_1"):
super(SimulatorFinalFragment, self).__init__()
self.simulation_length = FloatField(
SimulatorAdapterModel.simulation_length)
self.simulation_name = StrField(Attr(
str,
doc='Name for the current simulation configuration',
default=default_simulation_name,
label='Simulation name'),
name='input_simulation_name_id')
def __init__(self):
super(EquationForm, self).__init__()
self.equation = StrField(self.get_traited_equation().equation,
disabled=True)
for param_key, param in self.get_traited_equation().parameters.default(
).items():
setattr(
self, param_key,
FloatField(Float(label=param_key, default=param),
name=param_key))
class EquationPlotForm(Form):
def __init__(self):
super(EquationPlotForm, self).__init__()
self.min_x = FloatField(Float(
label='Min distance(mm)',
default=0,
doc="The minimum value of the x-axis for spatial equation plot."),
name='min_x')
self.max_x = FloatField(Float(
label='Max distance(mm)',
default=100,
doc="The maximum value of the x-axis for spatial equation plot."),
name='max_x')
def fill_from_post(self, form_data):
if self.min_x.name in form_data:
self.min_x.fill_from_post(form_data)
if self.max_x.name in form_data:
self.max_x.fill_from_post(form_data)
def __init__(self):
super(FFTAdapterForm, self).__init__()
self.time_series = TraitDataTypeSelectField(
FFTAdapterModel.time_series,
name='time_series',
conditions=self.get_filters(),
has_all_option=True)
self.segment_length = FloatField(FFTAdapterModel.segment_length)
self.window_function = SelectField(FFTAdapterModel.window_function)
self.detrend = BoolField(FFTAdapterModel.detrend)
def __init__(self):
super(LocalConnectivityCreatorForm, self).__init__()
self.surface = TraitDataTypeSelectField(LocalConnectivityCreatorModel.surface, name=self.get_input_name(),
conditions=self.get_filters())
self.spatial = SelectField(EnumAttr(field_type=SpatialEquationsEnum,
default=SpatialEquationsEnum.GAUSSIAN.instance, required=True),
name='spatial', display_none_choice=False, subform=GaussianEquationForm)
self.cutoff = FloatField(LocalConnectivityCreatorModel.cutoff)
self.display_name = StrField(LocalConnectivityCreatorModel.display_name, name='display_name')
del self.spatial.choices[-1]
def __init__(self, session_stored_simulator=None):
super(BoldMonitorForm, self).__init__(session_stored_simulator)
self.hrf_kernel_choices = get_ui_name_to_monitor_equation_dict()
default_hrf_kernel = list(self.hrf_kernel_choices.values())[0]
self.period = FloatField(Bold.period)
self.hrf_kernel = SelectField(Attr(HRFKernelEquation,
label='Equation',
default=default_hrf_kernel),
name='hrf_kernel',
choices=self.hrf_kernel_choices)
def __init__(self, prefix=''):
super(RangeForm, self).__init__(prefix)
self.lo = FloatField(Float(
label='Lo',
default=ContinuousWaveletTransform.frequencies.default.lo,
doc='start of range'),
self,
name='Lo')
self.hi = FloatField(Float(
label='Hi',
default=ContinuousWaveletTransform.frequencies.default.hi,
doc='end of range'),
self,
name='Hi')
self.step = FloatField(Float(
label='Step',
default=ContinuousWaveletTransform.frequencies.default.step,
doc='step of range'),
self,
name='Step')
def _add_fields_for_float(self, param, param_key):
# type: (RangeParameter, str) -> None
pse_param_lo = FloatField(Float(label='LO for {}'.format(param.name),
default=param.range_definition.lo,
required=True),
self.project_id,
name=self.LO_FIELD.format(param_key))
self.__setattr__(self.LO_FIELD.format(param_key), pse_param_lo)
pse_param_hi = FloatField(Float(label='HI for {}'.format(param.name),
default=param.range_definition.hi,
required=True),
self.project_id,
name=self.HI_FIELD.format(param_key))
self.__setattr__(self.HI_FIELD.format(param_key), pse_param_hi)
pse_param_step = FloatField(Float(label='STEP for {}'.format(
param.name),
default=param.range_definition.step,
required=True),
self.project_id,
name=self.STEP_FIELD.format(param_key))
self.__setattr__(self.STEP_FIELD.format(param_key), pse_param_step)
def __init__(self, session_stored_simulator=None):
super(MonitorForm, self).__init__()
self.session_stored_simulator = session_stored_simulator
self.period = FloatField(Monitor.period)
self.variables_of_interest_indexes = {}
if session_stored_simulator is not None:
self.variables_of_interest_indexes = session_stored_simulator.determine_indexes_for_chosen_vars_of_interest()
self.variables_of_interest = MultiSelectField(List(of=str, label='Model Variables to watch',
choices=tuple(self.variables_of_interest_indexes.keys())),
name='variables_of_interest')
def __init__(self, prefix='', project_id=None):
super(SimulatorAdapterForm, self).__init__(prefix, project_id)
self.coupling_choices = get_ui_name_to_coupling_dict()
default_coupling = list(self.coupling_choices.values())[0]
self.connectivity = TraitDataTypeSelectField(SimulatorAdapterModel.connectivity, self,
name=self.get_input_name(), conditions=self.get_filters())
self.coupling = SelectField(
Attr(Coupling, default=default_coupling, label="Coupling", doc=Simulator.coupling.doc), self,
name='coupling', choices=self.coupling_choices)
self.conduction_speed = FloatField(Simulator.conduction_speed, self)
self.ordered_fields = (self.connectivity, self.conduction_speed, self.coupling)
self.range_params = [Simulator.connectivity, Simulator.conduction_speed]
def __init__(self, project_id=None):
super(ContinuousWaveletTransformAdapterForm, self).__init__(project_id)
self.time_series = TraitDataTypeSelectField(
WaveletAdapterModel.time_series,
self.project_id,
name=self.get_input_name(),
conditions=self.get_filters(),
has_all_option=True)
self.mother = StrField(ContinuousWaveletTransform.mother,
self.project_id)
self.sample_period = FloatField(
ContinuousWaveletTransform.sample_period, self.project_id)
self.normalisation = StrField(ContinuousWaveletTransform.normalisation,
self.project_id)
self.q_ratio = FloatField(ContinuousWaveletTransform.q_ratio,
self.project_id)
self.frequencies = FormField(
RangeForm,
self.project_id,
name='frequencies',
label=ContinuousWaveletTransform.frequencies.label,
doc=ContinuousWaveletTransform.frequencies.doc)
def __init__(self, session_stored_simulator=None):
super(iEEGMonitorForm, self).__init__(session_stored_simulator)
sensor_filter = FilterChain(fields=[FilterChain.datatype + '.sensors_type'], operations=["=="],
values=[SensorTypes.TYPE_INTERNAL.value])
projection_filter = FilterChain(fields=[FilterChain.datatype + '.projection_type'], operations=["=="],
values=[ProjectionsType.SEEG.value])
self.projection = TraitDataTypeSelectField(iEEGViewModel.projection, name='projection',
conditions=projection_filter)
self.sigma = FloatField(iEEG.sigma)
self.sensors = TraitDataTypeSelectField(iEEGViewModel.sensors, name='sensors', conditions=sensor_filter)
def __init__(self, prefix='', project_id=None):
super(SimulatorAdapterForm, self).__init__(prefix, project_id)
self.connectivity = DataTypeSelectField(self.get_required_datatype(), self, name=self.get_input_name(),
required=True, label="Connectivity",
doc=Simulator.connectivity.doc,
conditions=self.get_filters())
self.coupling_choices = get_ui_name_to_coupling_dict()
self.coupling = SimpleSelectField(choices=self.coupling_choices, form=self, name='coupling', required=True,
label="Coupling", doc=Simulator.coupling.doc)
self.coupling.template = 'form_fields/select_field.html'
self.conduction_speed = FloatField(Simulator.conduction_speed, self)
self.ordered_fields = (self.connectivity, self.conduction_speed, self.coupling)
self.range_params = [Simulator.connectivity, Simulator.conduction_speed]
def __init__(self):
super(LocalConnectivityCreatorForm, self).__init__()
self.surface = TraitDataTypeSelectField(
LocalConnectivityCreatorModel.surface,
name=self.get_input_name(),
conditions=self.get_filters())
self.spatial = SelectField(LocalConnectivityCreatorModel.equation,
name='spatial',
choices=self.possible_equations,
display_none_choice=False,
subform=GaussianEquationForm)
self.cutoff = FloatField(LocalConnectivityCreatorModel.cutoff)
self.display_name = StrField(
LocalConnectivityCreatorModel.display_name, name='display_name')
class EquationSpatialPlotForm(Form):
def __init__(self):
super(EquationSpatialPlotForm, self).__init__()
self.min_space_x = FloatField(Float(
label='Spatial Start Distance(mm)',
default=0,
doc="The minimum value of"
" the x-axis for spatial equation plot."),
self.project_id,
name='min_space_x')
self.max_space_x = FloatField(Float(
label='Spatial End Distance(mm)',
default=100,
doc="The maximum value of "
"the x-axis for spatial equation plot."),
self.project_id,
name='max_space_x')
def fill_from_post(self, form_data):
if self.min_space_x.name in form_data:
self.min_space_x.fill_from_post(form_data)
if self.max_space_x.name in form_data:
self.max_space_x.fill_from_post(form_data)
def __init__(self, project_id=None):
super(TimeseriesMetricsAdapterForm, self).__init__(project_id)
self.time_series = TraitDataTypeSelectField(
TimeseriesMetricsAdapterModel.time_series,
self.project_id,
name="time_series")
self.start_point = FloatField(
TimeseriesMetricsAdapterModel.start_point, self.project_id)
self.segment = IntField(TimeseriesMetricsAdapterModel.segment,
self.project_id)
self.algorithms = MultiSelectField(
TimeseriesMetricsAdapterModel.algorithms,
self.project_id,
name="algorithms")
class EquationTemporalPlotForm(Form):
def __init__(self):
super(EquationTemporalPlotForm, self).__init__()
self.min_tmp_x = FloatField(Float(
label='Temporal Start Time(ms)',
default=0,
doc="The minimum value of the "
"x-axis for temporal equation plot. Not persisted, used only for "
"visualization."),
name='min_tmp_x')
self.max_tmp_x = FloatField(Float(
label='Temporal End Time(ms)',
default=100,
doc="The maximum value of the"
" x-axis for temporal equation plot. Not persisted, used only for"
" visualization."),
name='max_tmp_x')
def fill_from_post(self, form_data):
if self.min_tmp_x.name in form_data:
self.min_tmp_x.fill_from_post(form_data)
if self.max_tmp_x.name in form_data:
self.max_tmp_x.fill_from_post(form_data)
def __init__(self, session_stored_simulator=None, project_id=None):
super(EEGMonitorForm, self).__init__(session_stored_simulator, project_id)
sensor_filter = FilterChain(fields=[FilterChain.datatype + '.sensors_type'], operations=["=="],
values=[SensorTypes.TYPE_EEG.value])
projection_filter = FilterChain(fields=[FilterChain.datatype + '.projection_type'], operations=["=="],
values=[ProjectionsType.EEG.value])
self.projection = TraitDataTypeSelectField(EEGViewModel.projection, self.project_id, name='projection',
conditions=projection_filter)
self.reference = StrField(EEG.reference, self.project_id)
self.sensors = TraitDataTypeSelectField(EEGViewModel.sensors, self.project_id, name='sensors',
conditions=sensor_filter)
self.sigma = FloatField(EEG.sigma, self.project_id)
def __init__(self):
super(ConnectivityViewerForm, self).__init__()
self.connectivity = TraitDataTypeSelectField(ConnectivityViewerModel.connectivity, name='input_data',
conditions=self.get_filters())
surface_conditions = FilterChain(fields=[FilterChain.datatype + '.surface_type'], operations=["=="],
values=['Cortical Surface'])
self.surface_data = TraitDataTypeSelectField(ConnectivityViewerModel.surface_data, name='surface_data',
conditions=surface_conditions)
self.step = FloatField(ConnectivityViewerModel.step, name='step')
colors_conditions = FilterChain(fields=[FilterChain.datatype + '.ndim'], operations=["=="], values=[1])
self.colors = TraitDataTypeSelectField(ConnectivityViewerModel.colors, name='colors',
conditions=colors_conditions)
rays_conditions = FilterChain(fields=[FilterChain.datatype + '.ndim'], operations=["=="], values=[1])
self.rays = TraitDataTypeSelectField(ConnectivityViewerModel.rays, name='rays', conditions=rays_conditions)
def __init__(self, prefix='', project_id=None):
super(ConnectivityViewerForm, self).__init__(prefix, project_id)
# filters_ui = [UIFilter(linked_elem_name="colors",
# linked_elem_field=FilterChain.datatype + "._connectivity"),
# UIFilter(linked_elem_name="rays",
# linked_elem_field=FilterChain.datatype + "._connectivity")]
# json_ui_filter = json.dumps([ui_filter.to_dict() for ui_filter in filters_ui])
# KWARG_FILTERS_UI: json_ui_filter
self.connectivity = TraitDataTypeSelectField(
ConnectivityViewerModel.connectivity,
self,
name='input_data',
conditions=self.get_filters())
surface_conditions = FilterChain(
fields=[FilterChain.datatype + '.surface_type'],
operations=["=="],
values=['Cortical Surface'])
self.surface_data = TraitDataTypeSelectField(
ConnectivityViewerModel.surface_data,
self,
name='surface_data',
conditions=surface_conditions)
self.step = FloatField(ConnectivityViewerModel.step, self, name='step')
colors_conditions = FilterChain(
fields=[FilterChain.datatype + '.ndim'],
operations=["=="],
values=[1])
self.colors = TraitDataTypeSelectField(ConnectivityViewerModel.colors,
self,
name='colors',
conditions=colors_conditions)
rays_conditions = FilterChain(fields=[FilterChain.datatype + '.ndim'],
operations=["=="],
values=[1])
self.rays = TraitDataTypeSelectField(ConnectivityViewerModel.rays,
self,
name='rays',
conditions=rays_conditions)
def __init__(self):
super(SimulatorAdapterForm, self).__init__()
default_coupling = CouplingFunctionsEnum.LINEAR
self.connectivity = TraitDataTypeSelectField(
SimulatorAdapterModel.connectivity,
name=self.get_input_name(),
conditions=self.get_filters())
self.coupling = SelectField(EnumAttr(default=default_coupling,
label="Coupling",
doc=Simulator.coupling.doc),
name='coupling')
self.conduction_speed = FloatField(Simulator.conduction_speed)
self.ordered_fields = (self.connectivity, self.conduction_speed,
self.coupling)
self.range_params = [
Simulator.connectivity, Simulator.conduction_speed
]
def __init__(self):
super(EquationSpatialPlotForm, self).__init__()
self.min_space_x = FloatField(Float(label='Spatial Start Distance(mm)', default=0, doc="The minimum value of"
" the x-axis for spatial equation plot."), name='min_space_x')
self.max_space_x = FloatField(Float(label='Spatial End Distance(mm)', default=100, doc="The maximum value of "
"the x-axis for spatial equation plot."), name='max_space_x')
def __init__(self):
super(IntegratorForm, self).__init__()
self.dt = FloatField(IntegratorViewModel.dt)
def __init__(self, is_dt_disabled=False):
super(IntegratorForm, self).__init__()
self.is_dt_disabled = is_dt_disabled
self.dt = FloatField(IntegratorViewModel.dt)
def __init__(self):
super(NoiseForm, self).__init__()
self.ntau = FloatField(NoiseViewModel.ntau)
self.noise_seed = IntField(NoiseViewModel.noise_seed)
def __init__(self):
super(AllenConnectomeBuilderForm, self).__init__()
self.resolution = SelectField(AllenConnectModel.resolution)
self.weighting = SelectField(AllenConnectModel.weighting)
self.inj_f_thresh = FloatField(AllenConnectModel.inj_f_thresh)
self.vol_thresh = FloatField(AllenConnectModel.vol_thresh)
