def __call__(self, **params):
p = ParamOverrides(self, params)
measured_sheets = [
s for s in topo.sim.objects(CFSheet).values()
if hasattr(s, 'measure_maps') and s.measure_maps
]
results = AttrTree()
# Could easily be extended to measure CoG of all projections
# and e.g. register them using different names (e.g. "Afferent
# XCoG"), but then it's not clear how the PlotGroup would be
# able to find them automatically (as it currently supports
# only a fixed-named plot).
requested_proj = p.proj_name
for sheet in measured_sheets:
for proj in sheet.in_connections:
if (proj.name == requested_proj) or \
(requested_proj == '' and (proj.src != sheet)):
cog_data = self._update_proj_cog(p, proj)
for key, data in cog_data.items():
name = proj.name[0].upper() + proj.name[1:]
results.set_path((key, name), data)
if p.measurement_storage_hook:
p.measurement_storage_hook(results)
return results
def __call__(self, **params):
p = ParamOverrides(self, params)
measured_sheets = [s for s in topo.sim.objects(CFSheet).values()
if hasattr(s,'measure_maps') and s.measure_maps]
results = AttrTree()
# Could easily be extended to measure CoG of all projections
# and e.g. register them using different names (e.g. "Afferent
# XCoG"), but then it's not clear how the PlotGroup would be
# able to find them automatically (as it currently supports
# only a fixed-named plot).
requested_proj=p.proj_name
for sheet in measured_sheets:
for proj in sheet.in_connections:
if (proj.name == requested_proj) or \
(requested_proj == '' and (proj.src != sheet)):
cog_data = self._update_proj_cog(p, proj)
for key, data in cog_data.items():
name = proj.name[0].upper() + proj.name[1:]
results.set_path((key, name), data)
if p.measurement_storage_hook:
p.measurement_storage_hook(results)
return results
def _filter_attrtree(self, attrtree, path_filters):
"""
Filters the loaded AttrTree using the supplied path_filters.
"""
if not path_filters: return attrtree
# Convert string path filters
path_filters = [tuple(pf.split('.')) if not isinstance(pf, tuple)
else pf for pf in path_filters]
# Search for substring matches between paths and path filters
new_attrtree = AttrTree()
for path, item in attrtree.path_items.items():
if any([all([subpath in path for subpath in pf]) for pf in path_filters]):
new_attrtree.set_path(path, item)
return new_attrtree
def _filter_attrtree(self, attrtree, path_filters):
"""
Filters the loaded AttrTree using the supplied path_filters.
"""
if not path_filters: return attrtree
# Convert string path filters
path_filters = [
tuple(pf.split('.')) if not isinstance(pf, tuple) else pf
for pf in path_filters
]
# Search for substring matches between paths and path filters
new_attrtree = AttrTree()
for path, item in attrtree.path_items.items():
if any([
all([subpath in path for subpath in pf])
for pf in path_filters
]):
new_attrtree.set_path(path, item)
return new_attrtree
class Model(param.Parameterized):
"""
The available setup options are:
:'training_patterns': fills the training_patterns AttrTree
with pattern generator instances. The path is the name of the
input sheet. Usually calls PatternCoordinator to do this.
:'setup_sheets': determines the number of sheets, their types
and names sets sheet parameters according to the registered
methods in level sets sheet matchconditions according to the
registered methods in matchconditions
:'projections': determines which connections should be present
between the sheets according to the matchconditions of
SheetSpec objects, using connect to specify the
connection type and sets their parameters according to the
registered methods in connect
The available instantiate options are:
:'sheets': instantiates all sheets and registers them in
topo.sim
:'projections': instantiates all projections and registers
them in topo.sim
"""
__abstract = True
matchconditions = MatchConditions()
sheet_decorators = set()
projection_decorators = set()
@classmethod
def register_decorator(cls, object_type):
name = object_type.name
decorator = ClassDecorator(name, object_type)
setattr(cls, name, decorator)
if issubclass(object_type, topo.sheet.Sheet):
cls.sheet_decorators.add(decorator)
if issubclass(object_type, topo.projection.Projection):
cls.projection_decorators.add(decorator)
@classmethod
def _collect(cls, decorators, name):
"""
Given a list of ClassDecorators (e.g self.sheet_decorators or
self.projection_decorators), collate the named attribute
(i.e. 'types' or 'labels') across the decorators according to
priority.
"""
flattened = [el for d in decorators for el in getattr(d, name).items()]
return dict(
(k, v) for (k, (_, v)) in sorted(flattened, key=lambda x: x[1][0]))
@property
def sheet_labels(self):
"The mapping of level method to corresponding label"
return self._collect(self.sheet_decorators, 'labels')
@property
def sheet_types(self):
"The mapping of level label to sheet type"
return self._collect(self.sheet_decorators, 'types')
@property
def projection_labels(self):
"The mapping of projection method to corresponding label"
return self._collect(self.projection_decorators, 'labels')
@property
def projection_types(self):
"The mapping of projection label to projection type"
return self._collect(self.projection_decorators, 'types')
@property
def modified_parameters(self):
"Dictionary of modified model parameters"
return {k: v for k, v in self.get_param_values(onlychanged=True)}
def __init__(self,
setup_options=True,
register=True,
time_dependent=True,
**params):
numbergen.TimeAware.time_dependent = time_dependent
if register:
self._register_global_params(params)
super(Model, self).__init__(**params)
self._sheet_types = {}
self._projection_types = {}
self.attrs = AttrTree()
self.training_patterns = AttrTree()
self.sheets = AttrTree()
self.projections = AttrTree()
self.setup(setup_options)
def _register_global_params(self, params):
"""
Register the parameters of this object as global parameters
available for users to set from the command line. Values
supplied as global parameters will override those of the given
dictionary of params.
"""
for name, obj in self.params().items():
global_params.add(**{name: obj})
for name, val in params.items():
global_params.params(name).default = val
params.update(global_params.get_param_values())
params["name"] = self.name
#==============================================#
# Public methods to be implemented by modelers #
#==============================================#
def setup_attributes(self, attrs):
"""
Method to precompute any useful attributes from the class
parameters. For instance, if there is a ``num_lags``
parameter, this method could compute the actual projection
delays and store it as attrs.lags. The return value is the
updated attrs AttrTree.
In addition, this method can be used to configure class
attributes of the model components.
"""
return attrs
def setup_training_patterns(self, **overrides):
"""
Returns a dictionary of PatternGenerators to be added to
self.training_patterns, with the target sheet name keys and
pattern generator values.
The overrides keywords can be used by a subclass to
parameterize the training patterns e.g. override the default
parameters of a PatternCoordinator object.
"""
raise NotImplementedError
def setup_sheets(self):
"""
Returns a dictionary of properties or equivalent Lancet.Args
object. Each outer key must be the level name and the values
are lists of property dictionaries for the sheets at that
level (or equivalent Lancet Args object). For instance, two
LGN sheets at the 'LGN' level could be defined by either:
{'LGN':[{'polarity':'ON'}, {'polarity':'OFF'}]}
OR
{'LGN':lancet.List('polarity', ['ON', 'OFF'])}
The specified properties are used to initialize the sheets
AttrTree with SheetSpec objects.
"""
raise NotImplementedError
def setup_analysis(self):
"""
Set up appropriate defaults for analysis functions in
topo.analysis.featureresponses.
"""
pass
#====================================================#
# Remaining methods should not need to be overridden #
#====================================================#
def setup(self, setup_options):
"""
This method can be used to setup certain parts of the
submodel. If setup_options=True, all setup methods are
called. setup_options can also be a list, whereas all list
items of available_setup_options are accepted.
Available setup options are:
'training_patterns','sheets','projections' and 'analysis'.
Please consult the docstring of the Model class for more
information about each setup option.
"""
available_setup_options = [
'attributes', 'training_patterns', 'sheets', 'projections',
'analysis'
]
if setup_options == True:
setup_options = available_setup_options
if 'attributes' in setup_options:
self.attrs = self.setup_attributes(self.attrs)
if 'training_patterns' in setup_options:
training_patterns = self.setup_training_patterns()
for name, training_pattern in training_patterns.items():
self.training_patterns.set_path(name, training_pattern)
if 'sheets' in setup_options:
sheet_properties = self.setup_sheets()
enumeration = enumerate(sheet_properties.items())
for (ordering, (level, property_list)) in enumeration:
sheet_type = self.sheet_types[level]
if isinstance(property_list, lancet.Identity):
property_list = [{}]
elif isinstance(property_list, lancet.Args):
property_list = property_list.specs
# If an empty list or Args()
elif not property_list:
continue
for properties in property_list:
spec_properties = dict(level=level, **properties)
sheet_spec = SheetSpec(sheet_type, spec_properties)
sheet_spec.sort_precedence = ordering
self.sheets.set_path(str(sheet_spec), sheet_spec)
self._update_sheet_spec_parameters()
if 'projections' in setup_options:
self._compute_projection_specs()
if 'analysis' in setup_options:
self._setup_analysis()
def _update_sheet_spec_parameters(self):
for sheet_spec in self.sheets.path_items.values():
param_method = self.sheet_labels.get(sheet_spec.level, None)
if not param_method:
raise Exception("Parameters for sheet level %r not specified" %
sheet_spec.level)
updated_params = param_method(self, sheet_spec.properties)
sheet_spec.update(**updated_params)
def _matchcondition_holds(self, matchconditions, src_sheet):
"""
Given a dictionary of properties to match and a target sheet
spec, return True if the matchcondition holds else False.
"""
matches = True
if matchconditions is None:
return False
for incoming_key, incoming_value in matchconditions.items():
if incoming_key in src_sheet.properties and \
str(src_sheet.properties[incoming_key]) not in str(incoming_value):
matches = False
break
return matches
def _compute_projection_specs(self):
"""
Loop through all possible combinations of SheetSpec objects in
self.sheets If the src_sheet fulfills all criteria specified
in dest_sheet.matchconditions, create a new ProjectionSpec
object and add this item to self.projections.
"""
sheetspec_product = itertools.product(self.sheets.path_items.values(),
self.sheets.path_items.values())
for src_sheet, dest_sheet in sheetspec_product:
has_matchcondition = (dest_sheet.level in self.matchconditions)
conditions = (self.matchconditions.compute_conditions(
dest_sheet.level, self, dest_sheet.properties)
if has_matchcondition else {})
for matchname, matchconditions in conditions.items():
if self._matchcondition_holds(matchconditions, src_sheet):
proj = ProjectionSpec(self.projection_types[matchname],
src_sheet, dest_sheet)
paramsets = self.projection_labels[matchname](
self, src_sheet.properties, dest_sheet.properties)
paramsets = [paramsets] if isinstance(paramsets,
dict) else paramsets
for paramset in paramsets:
proj = ProjectionSpec(self.projection_types[matchname],
src_sheet, dest_sheet)
proj.update(**paramset)
# Only used when time_dependent=False
# (which is to be deprecated)
proj.matchname = matchname
path = (str(dest_sheet), paramset['name'])
self.projections.set_path(path, proj)
def __call__(self, instantiate_options=True, verbose=False):
"""
Instantiates all sheets or projections in self.sheets or
self.projections and registers them in the topo.sim instance.
If instantiate_options=True, all items are initialised
instantiate_options can also be a list, whereas all list items
of available_instantiate_options are accepted.
Available instantiation options are: 'sheets' and
'projections'.
Please consult the docstring of the Model class for more
information about each instantiation option.
"""
msglevel = self.message if verbose else self.debug
available_instantiate_options = ['sheets', 'projections']
if instantiate_options == True:
instantiate_options = available_instantiate_options
if 'sheets' in instantiate_options:
for sheet_spec in self.sheets.path_items.itervalues():
msglevel('Level ' + sheet_spec.level + ': Sheet ' +
str(sheet_spec))
sheet_spec()
if 'projections' in instantiate_options:
for proj in sorted(self.projections):
msglevel('Match: ' + proj.matchname + ': Connection ' + str(proj.src) + \
'->' + str(proj.dest) + ' ' + proj.parameters['name'])
proj()
def summary(self, printed=True):
heading_line = '=' * len(self.name)
summary = [heading_line, self.name, heading_line, '']
for sheet_spec in sorted(self.sheets):
summary.append(sheet_spec.summary(printed=False))
projections = [
proj for proj in self.projections
if str(proj).startswith(str(sheet_spec))
]
for projection_spec in sorted(projections, key=lambda p: str(p)):
summary.append(" " + projection_spec.summary(printed=False))
summary.append('')
if printed: print "\n".join(summary)
else: return "\n".join(summary)
def __str__(self):
return self.name
def _repr_pretty_(self, p, cycle):
p.text(self.summary(printed=False))
def modifications(self, components=['model', 'sheets', 'projections']):
"""
Display the names of all modified parameters for the specified
set of components.
By default all modified parameters are listed - first with the
model parameters, then the sheet parameters and lastly the
projection parameters.
"""
mapping = {
'model': [self],
'sheets': self.sheets,
'projections': self.projections
}
lines = []
for component in components:
heading = "=" * len(component)
lines.extend([heading, component.capitalize(), heading, ''])
specs = mapping[component]
padding = max(len(str(spec)) for spec in specs)
for spec in sorted(specs):
modified = [str(el) for el in sorted(spec.modified_parameters)]
lines.append("%s : [%s]" %
(str(spec).ljust(padding), ", ".join(modified)))
lines.append('')
print "\n".join(lines)
class Model(param.Parameterized):
"""
The available setup options are:
:'training_patterns': fills the training_patterns AttrTree
with pattern generator instances. The path is the name of the
input sheet. Usually calls PatternCoordinator to do this.
:'setup_sheets': determines the number of sheets, their types
and names sets sheet parameters according to the registered
methods in level sets sheet matchconditions according to the
registered methods in matchconditions
:'projections': determines which connections should be present
between the sheets according to the matchconditions of
SheetSpec objects, using connect to specify the
connection type and sets their parameters according to the
registered methods in connect
The available instantiate options are:
:'sheets': instantiates all sheets and registers them in
topo.sim
:'projections': instantiates all projections and registers
them in topo.sim
"""
__abstract = True
matchconditions = MatchConditions()
sheet_decorators = set()
projection_decorators = set()
@classmethod
def register_decorator(cls, object_type):
name = object_type.name
decorator = ClassDecorator(name, object_type)
setattr(cls, name, decorator)
if issubclass(object_type, topo.sheet.Sheet):
cls.sheet_decorators.add(decorator)
if issubclass(object_type, topo.projection.Projection):
cls.projection_decorators.add(decorator)
@classmethod
def _collect(cls, decorators, name):
"""
Given a list of ClassDecorators (e.g self.sheet_decorators or
self.projection_decorators), collate the named attribute
(i.e. 'types' or 'labels') across the decorators according to
priority.
"""
flattened = [el for d in decorators for el in getattr(d, name).items()]
return dict((k,v) for (k, (_, v)) in sorted(flattened, key=lambda x: x[1][0]))
@property
def sheet_labels(self):
"The mapping of level method to corresponding label"
return self._collect(self.sheet_decorators, 'labels')
@property
def sheet_types(self):
"The mapping of level label to sheet type"
return self._collect(self.sheet_decorators, 'types')
@property
def projection_labels(self):
"The mapping of projection method to corresponding label"
return self._collect(self.projection_decorators, 'labels')
@property
def projection_types(self):
"The mapping of projection label to projection type"
return self._collect(self.projection_decorators, 'types')
@property
def modified_parameters(self):
"Dictionary of modified model parameters"
return {k:v for k,v in self.get_param_values(onlychanged=True)}
def __init__(self, setup_options=True, register=True, time_dependent=True, **params):
numbergen.TimeAware.time_dependent = time_dependent
if register:
self._register_global_params(params)
super(Model,self).__init__(**params)
self._sheet_types = {}
self._projection_types = {}
self.attrs = AttrTree()
self.training_patterns = AttrTree()
self.sheets = AttrTree()
self.projections = AttrTree()
self.setup(setup_options)
def _register_global_params(self, params):
"""
Register the parameters of this object as global parameters
available for users to set from the command line. Values
supplied as global parameters will override those of the given
dictionary of params.
"""
for name,obj in self.params().items():
global_params.add(**{name:obj})
for name,val in params.items():
global_params.params(name).default=val
params.update(global_params.get_param_values())
params["name"]=self.name
#==============================================#
# Public methods to be implemented by modelers #
#==============================================#
def setup_attributes(self, attrs):
"""
Method to precompute any useful attributes from the class
parameters. For instance, if there is a ``num_lags``
parameter, this method could compute the actual projection
delays and store it as attrs.lags. The return value is the
updated attrs AttrTree.
In addition, this method can be used to configure class
attributes of the model components.
"""
return attrs
def setup_training_patterns(self, **overrides):
"""
Returns a dictionary of PatternGenerators to be added to
self.training_patterns, with the target sheet name keys and
pattern generator values.
The overrides keywords can be used by a subclass to
parameterize the training patterns e.g. override the default
parameters of a PatternCoordinator object.
"""
raise NotImplementedError
def setup_sheets(self):
"""
Returns a dictionary of properties or equivalent Lancet.Args
object. Each outer key must be the level name and the values
are lists of property dictionaries for the sheets at that
level (or equivalent Lancet Args object). For instance, two
LGN sheets at the 'LGN' level could be defined by either:
{'LGN':[{'polarity':'ON'}, {'polarity':'OFF'}]}
OR
{'LGN':lancet.List('polarity', ['ON', 'OFF'])}
The specified properties are used to initialize the sheets
AttrTree with SheetSpec objects.
"""
raise NotImplementedError
def setup_analysis(self):
"""
Set up appropriate defaults for analysis functions in
topo.analysis.featureresponses.
"""
pass
#====================================================#
# Remaining methods should not need to be overridden #
#====================================================#
def setup(self,setup_options):
"""
This method can be used to setup certain parts of the
submodel. If setup_options=True, all setup methods are
called. setup_options can also be a list, whereas all list
items of available_setup_options are accepted.
Available setup options are:
'training_patterns','sheets','projections' and 'analysis'.
Please consult the docstring of the Model class for more
information about each setup option.
"""
available_setup_options = ['attributes',
'training_patterns',
'sheets',
'projections',
'analysis']
if setup_options==True:
setup_options = available_setup_options
if 'attributes' in setup_options:
self.attrs = self.setup_attributes(self.attrs)
if 'training_patterns' in setup_options:
training_patterns = self.setup_training_patterns()
for name, training_pattern in training_patterns.items():
self.training_patterns.set_path(name, training_pattern)
if 'sheets' in setup_options:
sheet_properties = self.setup_sheets()
enumeration = enumerate(sheet_properties.items())
for (ordering, (level, property_list)) in enumeration:
sheet_type = self.sheet_types[level]
if isinstance(property_list, lancet.Identity):
property_list = [{}]
elif isinstance(property_list, lancet.Args):
property_list = property_list.specs
# If an empty list or Args()
elif not property_list:
continue
for properties in property_list:
spec_properties = dict(level=level, **properties)
sheet_spec = SheetSpec(sheet_type, spec_properties)
sheet_spec.sort_precedence = ordering
self.sheets.set_path(str(sheet_spec), sheet_spec)
self._update_sheet_spec_parameters()
if 'projections' in setup_options:
self._compute_projection_specs()
if 'analysis' in setup_options:
self._setup_analysis()
def _update_sheet_spec_parameters(self):
for sheet_spec in self.sheets.path_items.values():
param_method = self.sheet_labels.get(sheet_spec.level, None)
if not param_method:
raise Exception("Parameters for sheet level %r not specified" % sheet_spec.level)
updated_params = param_method(self,sheet_spec.properties)
sheet_spec.update(**updated_params)
def _matchcondition_holds(self, matchconditions, src_sheet):
"""
Given a dictionary of properties to match and a target sheet
spec, return True if the matchcondition holds else False.
"""
matches=True
if matchconditions is None:
return False
for incoming_key, incoming_value in matchconditions.items():
if incoming_key in src_sheet.properties and \
str(src_sheet.properties[incoming_key]) not in str(incoming_value):
matches=False
break
return matches
def _compute_projection_specs(self):
"""
Loop through all possible combinations of SheetSpec objects in
self.sheets If the src_sheet fulfills all criteria specified
in dest_sheet.matchconditions, create a new ProjectionSpec
object and add this item to self.projections.
"""
sheetspec_product = itertools.product(self.sheets.path_items.values(),
self.sheets.path_items.values())
for src_sheet, dest_sheet in sheetspec_product:
has_matchcondition = (dest_sheet.level in self.matchconditions)
conditions = (self.matchconditions.compute_conditions(
dest_sheet.level, self,dest_sheet.properties)
if has_matchcondition else {})
for matchname, matchconditions in conditions.items():
if self._matchcondition_holds(matchconditions, src_sheet):
proj = ProjectionSpec(self.projection_types[matchname],
src_sheet, dest_sheet)
paramsets = self.projection_labels[matchname](self, src_sheet.properties,
dest_sheet.properties)
paramsets = [paramsets] if isinstance(paramsets, dict) else paramsets
for paramset in paramsets:
proj = ProjectionSpec(self.projection_types[matchname],
src_sheet, dest_sheet)
proj.update(**paramset)
# Only used when time_dependent=False
# (which is to be deprecated)
proj.matchname = matchname
path = (str(dest_sheet), paramset['name'])
self.projections.set_path(path, proj)
def __call__(self,instantiate_options=True, verbose=False):
"""
Instantiates all sheets or projections in self.sheets or
self.projections and registers them in the topo.sim instance.
If instantiate_options=True, all items are initialised
instantiate_options can also be a list, whereas all list items
of available_instantiate_options are accepted.
Available instantiation options are: 'sheets' and
'projections'.
Please consult the docstring of the Model class for more
information about each instantiation option.
"""
msglevel = self.message if verbose else self.debug
available_instantiate_options = ['sheets','projections']
if instantiate_options==True:
instantiate_options=available_instantiate_options
if 'sheets' in instantiate_options:
for sheet_spec in self.sheets.path_items.itervalues():
msglevel('Level ' + sheet_spec.level + ': Sheet ' + str(sheet_spec))
sheet_spec()
if 'projections' in instantiate_options:
for proj in sorted(self.projections):
msglevel('Match: ' + proj.matchname + ': Connection ' + str(proj.src) + \
'->' + str(proj.dest) + ' ' + proj.parameters['name'])
proj()
def summary(self, printed=True):
heading_line = '=' * len(self.name)
summary = [heading_line, self.name, heading_line, '']
for sheet_spec in sorted(self.sheets):
summary.append(sheet_spec.summary(printed=False))
projections = [proj for proj in self.projections
if str(proj).startswith(str(sheet_spec))]
for projection_spec in sorted(projections, key=lambda p: str(p)):
summary.append(" " + projection_spec.summary(printed=False))
summary.append('')
if printed: print "\n".join(summary)
else: return "\n".join(summary)
def __str__(self):
return self.name
def _repr_pretty_(self, p, cycle):
p.text(self.summary(printed=False))
def modifications(self, components=['model', 'sheets', 'projections']):
"""
Display the names of all modified parameters for the specified
set of components.
By default all modified parameters are listed - first with the
model parameters, then the sheet parameters and lastly the
projection parameters.
"""
mapping = {'model': [self],
'sheets':self.sheets,
'projections':self.projections}
lines = []
for component in components:
heading = "=" * len(component)
lines.extend([heading, component.capitalize(), heading, ''])
specs = mapping[component]
padding = max(len(str(spec)) for spec in specs)
for spec in sorted(specs):
modified = [str(el) for el in sorted(spec.modified_parameters)]
lines.append("%s : [%s]" % (str(spec).ljust(padding), ", ".join(modified)))
lines.append('')
print "\n".join(lines)