def tweak_field(moose_wildcard, field, assignment_string):
"""Tweak a specified field of all objects that match the
moose_wildcard using assignment string. All identifiers in
assignment string must be fields of the target object.
Example:
tweak_field('/mycell/##[Class=Compartment]', 'Rm', '1.5 / (3.1416 * diameter * length')
will assign Rm to every compartment in mycell such that the
specific membrane resistance is 1.5 Ohm-m2.
"""
if not isinstance(moose_wildcard, str):
raise TypeError('moose_wildcard must be a string.')
id_list = _moose.getWildcardList(moose_wildcard, True)
expression = parser.expr(assignment_string)
expr_list = expression.tolist()
# This is a hack: I just tried out some possible syntax trees and
# hand coded the replacement such that any identifier is replaced
# by moose_obj.identifier
def replace_fields_with_value(x):
if len(x) > 1:
if x[0] == symbol.power and x[1][0] == symbol.atom and x[1][1][
0] == token.NAME:
field = x[1][1][1]
x[1] = [symbol.atom, [token.NAME, 'moose_obj']]
x.append(
[symbol.trailer, [token.DOT, '.'], [token.NAME, field]])
for item in x:
if isinstance(item, list):
replace_fields_with_value(item)
return x
tmp = replace_fields_with_value(expr_list)
new_expr = parser.sequence2st(tmp)
code = new_expr.compile()
for moose_id in id_list:
moose_obj = eval('_moose.%s(moose_id)' %
(_moose.Neutral(moose_id).className))
value = eval(code)
_moose.setField(moose_id, field, str(value))
def tweak_field(moose_wildcard, field, assignment_string):
"""Tweak a specified field of all objects that match the
moose_wildcard using assignment string. All identifiers in
assignment string must be fields of the target object.
Example:
tweak_field('/mycell/##[Class=Compartment]', 'Rm', '1.5 / (3.1416 * diameter * length')
will assign Rm to every compartment in mycell such that the
specific membrane resistance is 1.5 Ohm-m2.
"""
if not isinstance(moose_wildcard, str):
raise TypeError("moose_wildcard must be a string.")
id_list = _moose.getWildcardList(moose_wildcard, True)
expression = parser.expr(assignment_string)
expr_list = expression.tolist()
# This is a hack: I just tried out some possible syntax trees and
# hand coded the replacement such that any identifier is replaced
# by moose_obj.identifier
def replace_fields_with_value(x):
if len(x) > 1:
if x[0] == symbol.power and x[1][0] == symbol.atom and x[1][1][0] == token.NAME:
field = x[1][1][1]
x[1] = [symbol.atom, [token.NAME, "moose_obj"]]
x.append([symbol.trailer, [token.DOT, "."], [token.NAME, field]])
for item in x:
if isinstance(item, list):
replace_fields_with_value(item)
return x
tmp = replace_fields_with_value(expr_list)
new_expr = parser.sequence2st(tmp)
code = new_expr.compile()
for moose_id in id_list:
moose_obj = eval("_moose.%s(moose_id)" % (_moose.Neutral(moose_id).class_))
value = eval(code)
_moose.setField(moose_id, field, str(value))
def apply_to_tree(moose_wildcard, python_filter=None, value=None):
"""
Select objects by a moose/genesis wildcard, apply a python filter on them and apply a value on them.
moose_wildcard - this follows GENESIS convention.
{path}/#[{condition}] returns all elements directly under {path} that satisfy condition. For example:
'/mynetwork/mycell_0/#[TYPE=Compartment]'
will return all Compartment objects directly under mycell_0 in mynetwork.
'{path}/##[{condition}]' will recursively go through all the
objects that are under {path} (i.e. children, grandchildren,
great-grandchildren and so on up to the leaf level) and a list of
the ones meet {condition} will be obtained.
Thus, '/mynetwork/##[TYPE=Compartment]' will return all
compartments under mynetwork or its children, or children thereof
and so on.
python_filter - if a single string, it will be taken as a
fieldname, and value will be assigned to this field. It can also
be a lambda function returning True or False which will be applied
to each id in the id list returned by moose wildcard
search. Remember, the argument to the lambda will be an Id, so it
is up to you to wrap it into a moose object of appropriate type. An example is:
lambda moose_id: Compartment(moose_id).diameter < 2e-6
If your moose_wildcard selected objects of Compartment class, then
this lambda function will select only those with diameter less
than 2 um.
value - can be a lambda function to apply arbitrary operations on
the selected objects.
If python_filter is a string it, the return
value of applying the lambda for value() will assigned to the
field specified by python_filter.
But if it is value is a data object and {python_filter} is a
string, then {value} will be assigned to the field named
{python_filter}.
If you want to assign Rm = 1e6 for each compartment in mycell
whose name match 'axon_*':
apply_to_tree('/mycell/##[Class=Compartment]',
lambda x: 'axon_' in Neutral(x).name,
lambda x: setattr(Compartment(x), 'Rm', 1e6))
[you must use setattr to assign value to a field because lambda
functions don't allow assignments].
"""
if not isinstance(moose_wildcard, str):
raise TypeError('moose_wildcard must be a string.')
id_list = _moose.getWildcardList(moose_wildcard, True)
if isinstance(python_filter, types.LambdaType):
id_list = [moose_id for moose_id in id_list if python_filter(moose_id)]
elif isinstance(python_filter, str):
id_list = [moose_id for moose_id in id_list if hasattr(eval('_moose.%s(moose_id)' % (_moose.Neutral(moose_id).className)), python_filter)]
else:
pass
if isinstance(value, types.LambdaType):
if isinstance(python_filter, str):
for moose_id in id_list:
moose_obj = eval('_moose.%s(moose_id)' % (_moose.Neutral(moose_id).className))
setattr(moose_obj, python_filter, value(moose_id))
else:
for moose_id in id_list:
value(moose_id)
else:
if isinstance(python_filter, str):
for moose_id in id_list:
moose_obj = eval('_moose.%s(moose_id)' % (_moose.Neutral(moose_id).className))
setattr(moose_obj, python_filter, value)
else:
raise TypeError('Second argument must be a string specifying a field to assign to when third argument is a value')
def apply_to_tree(moose_wildcard, python_filter=None, value=None):
"""
Select objects by a moose/genesis wildcard, apply a python filter on them and apply a value on them.
moose_wildcard - this follows GENESIS convention.
{path}/#[{condition}] returns all elements directly under {path} that satisfy condition. For example:
'/mynetwork/mycell_0/#[TYPE=Compartment]'
will return all Compartment objects directly under mycell_0 in mynetwork.
'{path}/##[{condition}]' will recursively go through all the
objects that are under {path} (i.e. children, grandchildren,
great-grandchildren and so on up to the leaf level) and a list of
the ones meet {condition} will be obtained.
Thus, '/mynetwork/##[TYPE=Compartment]' will return all
compartments under mynetwork or its children, or children thereof
and so on.
python_filter - if a single string, it will be taken as a
fieldname, and value will be assigned to this field. It can also
be a lambda function returning True or False which will be applied
to each id in the id list returned by moose wildcard
search. Remember, the argument to the lambda will be an Id, so it
is up to you to wrap it into a moose object of appropriate type. An example is:
lambda moose_id: Compartment(moose_id).diameter < 2e-6
If your moose_wildcard selected objects of Compartment class, then
this lambda function will select only those with diameter less
than 2 um.
value - can be a lambda function to apply arbitrary operations on
the selected objects.
If python_filter is a string it, the return
value of applying the lambda for value() will assigned to the
field specified by python_filter.
But if it is value is a data object and {python_filter} is a
string, then {value} will be assigned to the field named
{python_filter}.
If you want to assign Rm = 1e6 for each compartment in mycell
whose name match 'axon_*':
apply_to_tree('/mycell/##[Class=Compartment]',
lambda x: 'axon_' in Neutral(x).name,
lambda x: setattr(Compartment(x), 'Rm', 1e6))
[you must use setattr to assign value to a field because lambda
functions don't allow assignments].
"""
if not isinstance(moose_wildcard, str):
raise TypeError('moose_wildcard must be a string.')
id_list = _moose.getWildcardList(moose_wildcard, True)
if isinstance(python_filter, types.LambdaType):
id_list = [moose_id for moose_id in id_list if python_filter(moose_id)]
elif isinstance(python_filter, str):
id_list = [
moose_id for moose_id in id_list if hasattr(
eval('_moose.%s(moose_id)' %
(_moose.Neutral(moose_id).className)), python_filter)
]
else:
pass
if isinstance(value, types.LambdaType):
if isinstance(python_filter, str):
for moose_id in id_list:
moose_obj = eval('_moose.%s(moose_id)' %
(_moose.Neutral(moose_id).className))
setattr(moose_obj, python_filter, value(moose_id))
else:
for moose_id in id_list:
value(moose_id)
else:
if isinstance(python_filter, str):
for moose_id in id_list:
moose_obj = eval('_moose.%s(moose_id)' %
(_moose.Neutral(moose_id).className))
setattr(moose_obj, python_filter, value)
else:
raise TypeError(
'Second argument must be a string specifying a field to assign to when third argument is a value'
)
