def setup(self, ctx):
self._append_view(TextView(f"Remove {self.noun}?"))
featuresettings = set(feature.setting
for feature in ctx.spec.features
if hasattr(feature, "setting"))
self.confs = set(
frozenset(
setting.get("confounds_removal", []) +
(["ICA-AROMA"] if setting.get("ica_aroma") is True else [])
) for setting in ctx.spec.settings[:-1]
# only include active settings
if setting.get("output_image", False)
or setting["name"] in featuresettings)
suggestion = ["ICA-AROMA"]
if len(self.confs) > 0:
inverse_options = {v: k for k, v in self.options.items()}
suggestion = [
inverse_options[s] for s in first(self.confs)
if s in inverse_options
]
self.input_view = MultipleChoiceInputView(list(
self.options.keys()),
checked=suggestion,
isVertical=True)
self._append_view(self.input_view)
self._append_view(SpacerView(1))
self.valuedict = None
def setup(self, ctx):
self.choice = None
self._append_view(
TextView(
"Specify the variables for which to calculate interaction terms"
))
self.variables = ctx.database.metadata(ctx.spec.models[-1].spreadsheet,
"variables")
self.variables = apply_filters_to_variables(
ctx.spec.models[-1].filters, self.variables)
contrastvariables = set(
ravel(contrast["variable"]
for contrast in ctx.spec.models[-1].contrasts
if contrast.get("type") == "infer")
) # names of all variables added to the model in the previous step
self.variables = [
variable for variable in self.variables
if variable["name"] in contrastvariables
]
assert len(
self.variables) > 0, "No variables to calculate interaction terms"
varnames = [variable["name"] for variable in self.variables]
options = [format_column(varname) for varname in varnames]
self.str_by_varname = dict(zip(varnames, options))
self.input_view = MultipleChoiceInputView(options, isVertical=True)
self._append_view(self.input_view)
self._append_view(SpacerView(1))
def setup(self, ctx):
self._append_view(TextView("Select which interaction terms to add to the model"))
nvar = len(self.variables)
terms = list(
chain.from_iterable(combinations(self.variables, i) for i in range(2, nvar + 1))
)
self.term_by_str = {" * ".join(termtpl): termtpl for termtpl in terms}
self.options = list(self.term_by_str.keys())
self.input_view = MultipleChoiceInputView(self.options, isVertical=True)
self._append_view(self.input_view)
self._append_view(SpacerView(1))
def setup(self, ctx):
self._append_view(TextView("Specify the variables to add to the model"))
self.variables = [
variable for variable in ctx.spec.analyses[-1].variables if variable.type != "id"
]
self.varname_by_str = {
_format_column(variable.name): variable.name for variable in self.variables
}
options = list(self.varname_by_str.keys())
self.input_view = MultipleChoiceInputView(options, checked=options)
self._append_view(self.input_view)
self._append_view(SpacerView(1))
def setup(self, ctx):
self._append_view(
TextView("Specify the variables for which to calculate interaction terms")
)
assert (
len(ctx.spec.analyses[-1].variables) > 0
), "No variables to calculate interaction terms"
self.varname_by_str = {
_format_column(variable.name): variable.name
for variable in ctx.spec.analyses[-1].variables
if variable.type != "id"
}
self.options = list(self.varname_by_str.keys())
self.input_view = MultipleChoiceInputView(self.options, isVertical=True)
self._append_view(self.input_view)
self._append_view(SpacerView(1))
def setup(self, ctx):
self._append_view(TextView("Select subject-level analyses to include in this analysis"))
assert ctx.spec.analyses is not None
namesset = set()
for analysis in ctx.spec.analyses:
assert analysis.level is not None
if (
analysis.level == "first"
and analysis.type != "atlas_based_connectivity"
and analysis.type != "image_output"
):
namesset.add(analysis.name)
names = list(namesset)
self.input_view = MultipleChoiceInputView(names, checked=names)
self._append_view(self.input_view)
self._append_view(SpacerView(1))
def setup(self, ctx):
self.is_first_run = True
self.entities_by_analysis = self._resolve_tags(ctx)
entitiesset = set.union(*[set(entities) for entities in self.entities_by_analysis.values()])
entitiesset &= set(self.aggregate_order)
across = ctx.spec.analyses[-1].across
if across in entitiesset:
entitiesset.remove(across)
self.entities = list(entitiesset)
self.options = [
p.inflect(f"Aggregate across plural('{entity}')") for entity in self.entities
]
self.optionstr_by_entity = {k: v for k, v in zip(self.entities, self.options)}
if len(self.options) > 0:
self._append_view(TextView("Aggregate scan-level statistics before analysis?"))
self.input_view = MultipleChoiceInputView(self.options, checked=self.options)
self._append_view(self.input_view)
self._append_view(SpacerView(1))
def setup(self, ctx):
self._append_view(TextView("ICA-AROMA will be performed"))
self._append_view(SpacerView(1))
self._append_view(TextView("Remove other nuisance regressors?"))
self.confs = set(
analysis.tags.confounds_removed.as_tupl()
for analysis in ctx.spec.analyses
if analysis.tags is not None
and analysis.tags.confounds_removed is not None
and analysis.type != "image_output"
)
suggestion = []
if len(self.confs) > 0:
revopts = {v: k for k, v in self.options.items()}
suggestion = [revopts[s] for s in ravel(first(self.confs))[1:] if s in revopts]
self.input_view = MultipleChoiceInputView(
list(self.options.keys()), checked=suggestion, isVertical=True
)
self._append_view(self.input_view)
self._append_view(SpacerView(1))
def setup(self, ctx):
self._append_view(
TextView("Specify the variables to add to the model"))
self.variables = ctx.database.metadata(ctx.spec.models[-1].spreadsheet,
"variables")
self.variables = apply_filters_to_variables(
ctx.spec.models[-1].filters, self.variables)
self.variables = [
variable for variable in self.variables if variable["type"] != "id"
]
varnames = [variable["name"] for variable in self.variables]
options = [format_column(varname) for varname in varnames]
self.varname_by_str = dict(zip(options, varnames))
self.input_view = MultipleChoiceInputView(options, checked=options)
self._append_view(self.input_view)
self._append_view(SpacerView(1))
def setup(self, ctx):
self.result = None
if (not hasattr(ctx.spec.features[-1], "conditions")
or ctx.spec.features[-1].conditions is None
or len(ctx.spec.features[-1].conditions) == 0):
_get_conditions(ctx)
self._append_view(TextView("Select conditions to add to the model"))
conditions = ctx.spec.features[-1].conditions
assert len(conditions) > 0, "No conditions found"
self.options = [
_format_variable(condition) for condition in conditions
]
self.str_by_varname = dict(zip(conditions, self.options))
self.input_view = MultipleChoiceInputView(self.options,
checked=[*self.options])
self._append_view(self.input_view)
self._append_view(SpacerView(1))
def setup(self, ctx):
self.choice = None
self.should_run = False
self.is_first_run = True
assert ctx.spec.features is not None
self.namesset = set(
feature.name for feature in ctx.spec.features
if feature.type not in ["atlas_based_connectivity"])
assert len(self.namesset) > 0
if len(self.namesset) > 1:
self.should_run = True
self._append_view(TextView("Specify features to use"))
names = sorted(list(self.namesset))
self.input_view = MultipleChoiceInputView(names, checked=names)
self._append_view(self.input_view)
self._append_view(SpacerView(1))
def setup(self, ctx):
self.is_first_run = True
self.choice = None
# get entities to ask for
model_obj = ctx.spec.models[-1]
inputs = set(model_obj.inputs)
assert inputs is not None and len(inputs) > 0
featureobjs = []
for obj in ctx.spec.features:
if obj.name in inputs:
if obj.type not in ["atlas_based_connectivity"]:
featureobjs.append(obj)
filepaths = ctx.database.get(**bold_filedict)
setting_filters = dict()
for setting in ctx.spec.settings:
setting_filters[setting["name"]] = setting.get("filters")
self.feature_entities = dict()
for obj in featureobjs:
filters = setting_filters[obj.setting]
feature_filepaths = [*filepaths]
if filters is not None and len(filters) > 0:
feature_filepaths = ctx.database.applyfilters(
feature_filepaths, filters)
self.feature_entities[obj.name], _ = ctx.database.multitagvalset(
aggregate_order, filepaths=feature_filepaths)
entitiesset = set.union(
*
[set(entitylist) for entitylist in self.feature_entities.values()])
across = ctx.spec.models[-1].across
assert across not in entitiesset
self.entities = [
entity for entity in aggregate_order if entity in entitiesset
] # maintain order
display_strs = [
entity_display_aliases[entity]
if entity in entity_display_aliases else entity
for entity in self.entities
]
self.options = [
humanize(p.plural(display_str)) for display_str in display_strs
]
self.optionstr_by_entity = dict(zip(self.entities, self.options))
if len(self.options) > 0:
self._append_view(
TextView("Aggregate scan-level statistics before analysis?"))
self.input_view = MultipleChoiceInputView(
self.options,
checked=[
option for option in self.options if option != "task"
])
self._append_view(self.input_view)
self._append_view(SpacerView(1))