class BIDSGrabInputSpec(BaseInterfaceInputSpec):
# TODO: Check this inteface, why are there 'either file or list'? ~Mateusz
fmri_prep_files = List()
fmri_prep_aroma_files = Either(List(ImageFile()), File())
conf_raw_files = Either(List(File(exists=True)), File(exists=True))
conf_json_files = Either(List(File(exists=True)), File(exists=True))
subject = Str()
task = Str()
session = Str()
run = Int()
class DBAnalysis(Analysis):
meas_analysis_id = Long
analysis_view_klass = ('pychron.processing.analyses.analysis_view',
'DBAnalysisView')
uuid = Str
persisted_age = None
experiment_txt = Str
xyz_position = Str
snapshots = List
beam_diameter = Either(Float, Str)
pattern = Str
mask_position = Either(Float, Str)
mask_name = Str
attenuator = Either(Float, Str)
ramp_duration = Either(Float, Str)
ramp_rate = Either(Float, Str)
reprate = Either(Float, Str)
timestamp = Float
rundate = Date
collection_time_zero_offset = Float
peak_center = Any
peak_center_data = Any
ic_factors = Dict
blank_changes = List
fit_changes = List
extraction_script_name = Str
measurement_script_name = Str
extraction_script_blob = Str
measurement_script_blob = Str
selected_blanks_id = Long
source_parameters = List
deflections = List
def get_db_fit(self, meas_analysis, name, kind, selected_histories):
try:
if selected_histories is None:
selected_histories = meas_analysis.selected_histories
sel_fithist = selected_histories.selected_fits
fits = sel_fithist.fits
return next((fi for fi in fits if fi.isotope.kind == kind
and fi.isotope.molecular_weight.name == name), None)
except AttributeError, e:
print 'exception', e
class DBAnalysis(Analysis):
meas_analysis_id = Long
analysis_view_klass = ('pychron.processing.analyses.analysis_view',
'DBAnalysisView')
uuid = Str
persisted_age = None
experiment_txt = Str
xyz_position = Str
snapshots = List
beam_diameter = Either(Float, Str)
pattern = Str
mask_position = Either(Float, Str)
mask_name = Str
attenuator = Either(Float, Str)
ramp_duration = Either(Float, Str)
ramp_rate = Either(Float, Str)
reprate = Either(Float, Str)
timestamp = Float
rundate = Date
collection_time_zero_offset = Float
peak_center = Any
peak_center_data = Any
ic_factors = Dict
blank_changes = List
fit_changes = List
extraction_script_name = Str
measurement_script_name = Str
extraction_script_blob = Str
measurement_script_blob = Str
selected_blanks_id = Long
source_parameters = List
deflections = List
def set_ic_factor(self, det, v, e):
for iso in self.get_isotopes(det):
iso.ic_factor = ufloat(v, e)
def set_temporary_ic_factor(self, k, v, e):
iso = self.get_isotope(detector=k)
if iso:
iso.temporary_ic_factor = (v, e)
def set_temporary_blank(self, k, v, e):
self.debug('setting temporary blank iso={}, v={}, e={}'.format(
k, v, e))
if self.isotopes.has_key(k):
iso = self.isotopes[k]
iso.temporary_blank = Blank(value=v, error=e)
def get_baseline_corrected_signal_dict(self):
get = lambda iso: iso.get_baseline_corrected_value()
return self._get_isotope_dict(get)
def get_baseline_dict(self):
get = lambda iso: iso.baseline.uvalue
return self._get_isotope_dict(get)
def get_ic_factor(self, det):
iso = next(
(i for i in self.isotopes.itervalues() if i.detector == det), None)
if iso:
r = iso.ic_factor
else:
r = ufloat(1, 0)
# if det in self.ic_factors:
# r = self.ic_factors[det]
# else:
# r = ufloat(1, 1e-20)
return r
def get_db_fit(self, meas_analysis, name, kind, selected_histories):
try:
if selected_histories is None:
selected_histories = meas_analysis.selected_histories
sel_fithist = selected_histories.selected_fits
fits = sel_fithist.fits
return next((fi for fi in fits
if fi.isotope.kind == kind and \
fi.isotope.molecular_weight.name == name), None)
except AttributeError, e:
print 'exception', e
class A(HasTraits):
foo = RaisingValidator()
bar = Either(None, RaisingValidator())
class MultiArrayDataSource(HasTraits):
data = Either(None, Array)
class CUDSItemModelView(ModelView):
"""Wraps the CUDSItem node in a ModelView for easier representation
and access."""
traits_view = View(
VGroup(
VGroup(
Item("model.name", resizable=True, enabled_when="False"),
label="CUDS Item Data",
show_border=True,
),
Tabbed(
HGroup(
VGroup(
UItem(
"all_fixed_properties",
editor=ListStrEditor(
adapter=PropertyAdapter(),
selected="selected_fixed_property"),
),
UItem("selected_fixed_property_model_view",
style="custom",
enabled_when="fixed_property_model_view_enabled",
full_size=True),
show_border=False),
label="Fixed Properties",
show_border=False,
),
HGroup(
VGroup(
UItem(
"all_variable_properties",
editor=ListStrEditor(
adapter=PropertyAdapter(),
selected="selected_variable_property"),
),
UItem(
"selected_variable_property_model_view",
style="custom",
enabled_when=
"variable_property_model_view_enabled", # noqa
),
show_border=False),
label="Variable Properties",
show_border=False,
),
)))
#: A list of the fixed and variable properties on the CUDSItem
#: we are visualising, and only that object.
obj_fixed_properties = Property(List(FixedProperty), depends_on="model")
obj_variable_properties = Property(List(VariableProperty),
depends_on="model")
#: A list of the fixed and variable properties on the CUDSItem
#: we are visualising. This includes all those that we inherit
all_fixed_properties = Property(List(FixedProperty), depends_on="model")
all_variable_properties = Property(List(VariableProperty),
depends_on="model")
#: The properties that we inherit from the base CUDSItems.
inherited_properties = Property(Either(List(FixedProperty),
List(VariableProperty)),
depends_on="model")
#: The properties that are selected by the user when they click
selected_fixed_property = Instance(FixedProperty)
selected_variable_property = Instance(VariableProperty)
#: The ModelViews of the above, to allow controlled presentation.
selected_variable_property_model_view = Instance(VariablePropertyModelView)
selected_fixed_property_model_view = Instance(FixedPropertyModelView)
#: State that says if the editor window should be enabled or not
#: Inherited variables cannot be edited on a derived class.
fixed_property_model_view_enabled = Bool()
variable_property_model_view_enabled = Bool()
def _get_obj_fixed_properties(self):
"""Gets the fixed properties, only local to the object"""
return [
p for p in self.model.properties.values()
if isinstance(p, FixedProperty)
]
def _get_obj_variable_properties(self):
"""Gets the variable properties, only local to the object"""
return [
p for p in self.model.properties.values()
if isinstance(p, VariableProperty)
]
def _get_all_fixed_properties(self):
"""Gets all the fixed properties, both local to the object
and from its hierarchy"""
inherited_properties = [
p for p in self.inherited_properties
if isinstance(p, FixedProperty)
]
return self.obj_fixed_properties + inherited_properties
def _get_all_variable_properties(self):
"""Gets all the variable properties, both local to the object
and from its hierarchy"""
inherited_properties = [
p for p in self.inherited_properties
if isinstance(p, VariableProperty)
]
return self.obj_variable_properties + inherited_properties
def _get_inherited_properties(self):
"""Gets all the inherited properties."""
parent_classes = list(traverse_to_root(self.model))[1:]
inherited_properties = []
for parent in parent_classes:
inherited_properties += [p for p in parent.properties.values()]
return inherited_properties
@on_trait_change("selected_variable_property")
def _update_selected_variable_property_model_view(self, value):
"""Syncs the modelview with the changed selected property"""
self.selected_variable_property_model_view = VariablePropertyModelView(
model=self.selected_variable_property)
self.variable_property_model_view_enabled = \
self.selected_variable_property in self.obj_variable_properties
@on_trait_change("selected_fixed_property")
def _update_selected_fixed_property_model_view(self, value):
"""Syncs the modelview with the changed selected property"""
self.selected_fixed_property_model_view = FixedPropertyModelView(
model=self.selected_fixed_property)
self.fixed_property_model_view_enabled = \
self.selected_fixed_property in self.obj_fixed_properties