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15,900 | wmayner/pyphi | pyphi/actual.py | nice_true_ces | def nice_true_ces(tc):
"""Format a true |CauseEffectStructure|."""
cause_list = []
next_list = []
cause = '<--'
effect = '-->'
for event in tc:
if event.direction == Direction.CAUSE:
cause_list.append(["{0:.4f}".format(round(event.alpha, 4)),
ev... | python | def nice_true_ces(tc):
"""Format a true |CauseEffectStructure|."""
cause_list = []
next_list = []
cause = '<--'
effect = '-->'
for event in tc:
if event.direction == Direction.CAUSE:
cause_list.append(["{0:.4f}".format(round(event.alpha, 4)),
ev... | [
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15,901 | wmayner/pyphi | pyphi/actual.py | true_ces | def true_ces(subsystem, previous_state, next_state):
"""Set of all sets of elements that have true causes and true effects.
.. note::
Since the true |CauseEffectStructure| is always about the full system,
the background conditions don't matter and the subsystem should be
conditioned on ... | python | def true_ces(subsystem, previous_state, next_state):
"""Set of all sets of elements that have true causes and true effects.
.. note::
Since the true |CauseEffectStructure| is always about the full system,
the background conditions don't matter and the subsystem should be
conditioned on ... | [
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15,902 | wmayner/pyphi | pyphi/actual.py | true_events | def true_events(network, previous_state, current_state, next_state,
indices=None, major_complex=None):
"""Return all mechanisms that have true causes and true effects within the
complex.
Args:
network (Network): The network to analyze.
previous_state (tuple[int]): The state ... | python | def true_events(network, previous_state, current_state, next_state,
indices=None, major_complex=None):
"""Return all mechanisms that have true causes and true effects within the
complex.
Args:
network (Network): The network to analyze.
previous_state (tuple[int]): The state ... | [
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15,903 | wmayner/pyphi | pyphi/actual.py | extrinsic_events | def extrinsic_events(network, previous_state, current_state, next_state,
indices=None, major_complex=None):
"""Set of all mechanisms that are in the major complex but which have true
causes and effects within the entire network.
Args:
network (Network): The network to analyze.
... | python | def extrinsic_events(network, previous_state, current_state, next_state,
indices=None, major_complex=None):
"""Set of all mechanisms that are in the major complex but which have true
causes and effects within the entire network.
Args:
network (Network): The network to analyze.
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15,904 | wmayner/pyphi | pyphi/actual.py | Transition.apply_cut | def apply_cut(self, cut):
"""Return a cut version of this transition."""
return Transition(self.network, self.before_state, self.after_state,
self.cause_indices, self.effect_indices, cut) | python | def apply_cut(self, cut):
"""Return a cut version of this transition."""
return Transition(self.network, self.before_state, self.after_state,
self.cause_indices, self.effect_indices, cut) | [
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15,905 | wmayner/pyphi | pyphi/actual.py | Transition.cause_repertoire | def cause_repertoire(self, mechanism, purview):
"""Return the cause repertoire."""
return self.repertoire(Direction.CAUSE, mechanism, purview) | python | def cause_repertoire(self, mechanism, purview):
"""Return the cause repertoire."""
return self.repertoire(Direction.CAUSE, mechanism, purview) | [
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15,906 | wmayner/pyphi | pyphi/actual.py | Transition.effect_repertoire | def effect_repertoire(self, mechanism, purview):
"""Return the effect repertoire."""
return self.repertoire(Direction.EFFECT, mechanism, purview) | python | def effect_repertoire(self, mechanism, purview):
"""Return the effect repertoire."""
return self.repertoire(Direction.EFFECT, mechanism, purview) | [
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15,907 | wmayner/pyphi | pyphi/actual.py | Transition.repertoire | def repertoire(self, direction, mechanism, purview):
"""Return the cause or effect repertoire function based on a direction.
Args:
direction (str): The temporal direction, specifiying the cause or
effect repertoire.
"""
system = self.system[direction]
... | python | def repertoire(self, direction, mechanism, purview):
"""Return the cause or effect repertoire function based on a direction.
Args:
direction (str): The temporal direction, specifiying the cause or
effect repertoire.
"""
system = self.system[direction]
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15,908 | wmayner/pyphi | pyphi/actual.py | Transition.state_probability | def state_probability(self, direction, repertoire, purview,):
"""Compute the probability of the purview in its current state given
the repertoire.
Collapses the dimensions of the repertoire that correspond to the
purview nodes onto their state. All other dimension are already
si... | python | def state_probability(self, direction, repertoire, purview,):
"""Compute the probability of the purview in its current state given
the repertoire.
Collapses the dimensions of the repertoire that correspond to the
purview nodes onto their state. All other dimension are already
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Collapses the dimensions of the repertoire that correspond to the
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15,909 | wmayner/pyphi | pyphi/actual.py | Transition.probability | def probability(self, direction, mechanism, purview):
"""Probability that the purview is in it's current state given the
state of the mechanism.
"""
repertoire = self.repertoire(direction, mechanism, purview)
return self.state_probability(direction, repertoire, purview) | python | def probability(self, direction, mechanism, purview):
"""Probability that the purview is in it's current state given the
state of the mechanism.
"""
repertoire = self.repertoire(direction, mechanism, purview)
return self.state_probability(direction, repertoire, purview) | [
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15,910 | wmayner/pyphi | pyphi/actual.py | Transition.purview_state | def purview_state(self, direction):
"""The state of the purview when we are computing coefficients in
``direction``.
For example, if we are computing the cause coefficient of a mechanism
in ``after_state``, the direction is``CAUSE`` and the ``purview_state``
is ``before_state``.... | python | def purview_state(self, direction):
"""The state of the purview when we are computing coefficients in
``direction``.
For example, if we are computing the cause coefficient of a mechanism
in ``after_state``, the direction is``CAUSE`` and the ``purview_state``
is ``before_state``.... | [
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15,911 | wmayner/pyphi | pyphi/actual.py | Transition.mechanism_indices | def mechanism_indices(self, direction):
"""The indices of nodes in the mechanism system."""
return {
Direction.CAUSE: self.effect_indices,
Direction.EFFECT: self.cause_indices
}[direction] | python | def mechanism_indices(self, direction):
"""The indices of nodes in the mechanism system."""
return {
Direction.CAUSE: self.effect_indices,
Direction.EFFECT: self.cause_indices
}[direction] | [
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15,912 | wmayner/pyphi | pyphi/actual.py | Transition.purview_indices | def purview_indices(self, direction):
"""The indices of nodes in the purview system."""
return {
Direction.CAUSE: self.cause_indices,
Direction.EFFECT: self.effect_indices
}[direction] | python | def purview_indices(self, direction):
"""The indices of nodes in the purview system."""
return {
Direction.CAUSE: self.cause_indices,
Direction.EFFECT: self.effect_indices
}[direction] | [
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15,913 | wmayner/pyphi | pyphi/actual.py | Transition.cause_ratio | def cause_ratio(self, mechanism, purview):
"""The cause ratio of the ``purview`` given ``mechanism``."""
return self._ratio(Direction.CAUSE, mechanism, purview) | python | def cause_ratio(self, mechanism, purview):
"""The cause ratio of the ``purview`` given ``mechanism``."""
return self._ratio(Direction.CAUSE, mechanism, purview) | [
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15,914 | wmayner/pyphi | pyphi/actual.py | Transition.effect_ratio | def effect_ratio(self, mechanism, purview):
"""The effect ratio of the ``purview`` given ``mechanism``."""
return self._ratio(Direction.EFFECT, mechanism, purview) | python | def effect_ratio(self, mechanism, purview):
"""The effect ratio of the ``purview`` given ``mechanism``."""
return self._ratio(Direction.EFFECT, mechanism, purview) | [
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15,915 | wmayner/pyphi | pyphi/actual.py | Transition.partitioned_repertoire | def partitioned_repertoire(self, direction, partition):
"""Compute the repertoire over the partition in the given direction."""
system = self.system[direction]
return system.partitioned_repertoire(direction, partition) | python | def partitioned_repertoire(self, direction, partition):
"""Compute the repertoire over the partition in the given direction."""
system = self.system[direction]
return system.partitioned_repertoire(direction, partition) | [
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15,916 | wmayner/pyphi | pyphi/actual.py | Transition.partitioned_probability | def partitioned_probability(self, direction, partition):
"""Compute the probability of the mechanism over the purview in
the partition.
"""
repertoire = self.partitioned_repertoire(direction, partition)
return self.state_probability(direction, repertoire, partition.purview) | python | def partitioned_probability(self, direction, partition):
"""Compute the probability of the mechanism over the purview in
the partition.
"""
repertoire = self.partitioned_repertoire(direction, partition)
return self.state_probability(direction, repertoire, partition.purview) | [
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15,917 | wmayner/pyphi | pyphi/actual.py | Transition.find_mip | def find_mip(self, direction, mechanism, purview, allow_neg=False):
"""Find the ratio minimum information partition for a mechanism
over a purview.
Args:
direction (str): |CAUSE| or |EFFECT|
mechanism (tuple[int]): A mechanism.
purview (tuple[int]): A purview... | python | def find_mip(self, direction, mechanism, purview, allow_neg=False):
"""Find the ratio minimum information partition for a mechanism
over a purview.
Args:
direction (str): |CAUSE| or |EFFECT|
mechanism (tuple[int]): A mechanism.
purview (tuple[int]): A purview... | [
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15,918 | wmayner/pyphi | pyphi/actual.py | Transition.find_causal_link | def find_causal_link(self, direction, mechanism, purviews=False,
allow_neg=False):
"""Return the maximally irreducible cause or effect ratio for a
mechanism.
Args:
direction (str): The temporal direction, specifying cause or
effect.
... | python | def find_causal_link(self, direction, mechanism, purviews=False,
allow_neg=False):
"""Return the maximally irreducible cause or effect ratio for a
mechanism.
Args:
direction (str): The temporal direction, specifying cause or
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15,919 | wmayner/pyphi | pyphi/actual.py | Transition.find_actual_cause | def find_actual_cause(self, mechanism, purviews=False):
"""Return the actual cause of a mechanism."""
return self.find_causal_link(Direction.CAUSE, mechanism, purviews) | python | def find_actual_cause(self, mechanism, purviews=False):
"""Return the actual cause of a mechanism."""
return self.find_causal_link(Direction.CAUSE, mechanism, purviews) | [
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15,920 | wmayner/pyphi | pyphi/actual.py | Transition.find_actual_effect | def find_actual_effect(self, mechanism, purviews=False):
"""Return the actual effect of a mechanism."""
return self.find_causal_link(Direction.EFFECT, mechanism, purviews) | python | def find_actual_effect(self, mechanism, purviews=False):
"""Return the actual effect of a mechanism."""
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15,921 | wmayner/pyphi | pyphi/db.py | find | def find(key):
"""Return the value associated with a key.
If there is no value with the given key, returns ``None``.
"""
docs = list(collection.find({KEY_FIELD: key}))
# Return None if we didn't find anything.
if not docs:
return None
pickled_value = docs[0][VALUE_FIELD]
# Unpic... | python | def find(key):
"""Return the value associated with a key.
If there is no value with the given key, returns ``None``.
"""
docs = list(collection.find({KEY_FIELD: key}))
# Return None if we didn't find anything.
if not docs:
return None
pickled_value = docs[0][VALUE_FIELD]
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15,922 | wmayner/pyphi | pyphi/db.py | insert | def insert(key, value):
"""Store a value with a key.
If the key is already present in the database, this does nothing.
"""
# Pickle the value.
value = pickle.dumps(value, protocol=constants.PICKLE_PROTOCOL)
# Store the value as binary data in a document.
doc = {
KEY_FIELD: key,
... | python | def insert(key, value):
"""Store a value with a key.
If the key is already present in the database, this does nothing.
"""
# Pickle the value.
value = pickle.dumps(value, protocol=constants.PICKLE_PROTOCOL)
# Store the value as binary data in a document.
doc = {
KEY_FIELD: key,
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15,923 | wmayner/pyphi | pyphi/db.py | generate_key | def generate_key(filtered_args):
"""Get a key from some input.
This function should be used whenever a key is needed, to keep keys
consistent.
"""
# Convert the value to a (potentially singleton) tuple to be consistent
# with joblib.filtered_args.
if isinstance(filtered_args, Iterable):
... | python | def generate_key(filtered_args):
"""Get a key from some input.
This function should be used whenever a key is needed, to keep keys
consistent.
"""
# Convert the value to a (potentially singleton) tuple to be consistent
# with joblib.filtered_args.
if isinstance(filtered_args, Iterable):
... | [
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15,924 | wmayner/pyphi | pyphi/memory.py | cache | def cache(ignore=None):
"""Decorator for memoizing a function using either the filesystem or a
database.
"""
def decorator(func):
# Initialize both cached versions
joblib_cached = constants.joblib_memory.cache(func, ignore=ignore)
db_cached = DbMemoizedFunc(func, ignore)
... | python | def cache(ignore=None):
"""Decorator for memoizing a function using either the filesystem or a
database.
"""
def decorator(func):
# Initialize both cached versions
joblib_cached = constants.joblib_memory.cache(func, ignore=ignore)
db_cached = DbMemoizedFunc(func, ignore)
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15,925 | wmayner/pyphi | pyphi/memory.py | DbMemoizedFunc.get_output_key | def get_output_key(self, args, kwargs):
"""Return the key that the output should be cached with, given
arguments, keyword arguments, and a list of arguments to ignore.
"""
# Get a dictionary mapping argument names to argument values where
# ignored arguments are omitted.
... | python | def get_output_key(self, args, kwargs):
"""Return the key that the output should be cached with, given
arguments, keyword arguments, and a list of arguments to ignore.
"""
# Get a dictionary mapping argument names to argument values where
# ignored arguments are omitted.
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15,926 | wmayner/pyphi | pyphi/memory.py | DbMemoizedFunc.load_output | def load_output(self, args, kwargs):
"""Return cached output."""
return db.find(self.get_output_key(args, kwargs)) | python | def load_output(self, args, kwargs):
"""Return cached output."""
return db.find(self.get_output_key(args, kwargs)) | [
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15,927 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.cache_info | def cache_info(self):
"""Report repertoire cache statistics."""
return {
'single_node_repertoire':
self._single_node_repertoire_cache.info(),
'repertoire': self._repertoire_cache.info(),
'mice': self._mice_cache.info()
} | python | def cache_info(self):
"""Report repertoire cache statistics."""
return {
'single_node_repertoire':
self._single_node_repertoire_cache.info(),
'repertoire': self._repertoire_cache.info(),
'mice': self._mice_cache.info()
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15,928 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.clear_caches | def clear_caches(self):
"""Clear the mice and repertoire caches."""
self._single_node_repertoire_cache.clear()
self._repertoire_cache.clear()
self._mice_cache.clear() | python | def clear_caches(self):
"""Clear the mice and repertoire caches."""
self._single_node_repertoire_cache.clear()
self._repertoire_cache.clear()
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15,929 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.apply_cut | def apply_cut(self, cut):
"""Return a cut version of this |Subsystem|.
Args:
cut (Cut): The cut to apply to this |Subsystem|.
Returns:
Subsystem: The cut subsystem.
"""
return Subsystem(self.network, self.state, self.node_indices,
... | python | def apply_cut(self, cut):
"""Return a cut version of this |Subsystem|.
Args:
cut (Cut): The cut to apply to this |Subsystem|.
Returns:
Subsystem: The cut subsystem.
"""
return Subsystem(self.network, self.state, self.node_indices,
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15,930 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.indices2nodes | def indices2nodes(self, indices):
"""Return |Nodes| for these indices.
Args:
indices (tuple[int]): The indices in question.
Returns:
tuple[Node]: The |Node| objects corresponding to these indices.
Raises:
ValueError: If requested indices are not in ... | python | def indices2nodes(self, indices):
"""Return |Nodes| for these indices.
Args:
indices (tuple[int]): The indices in question.
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tuple[Node]: The |Node| objects corresponding to these indices.
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15,931 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.cause_repertoire | def cause_repertoire(self, mechanism, purview):
"""Return the cause repertoire of a mechanism over a purview.
Args:
mechanism (tuple[int]): The mechanism for which to calculate the
cause repertoire.
purview (tuple[int]): The purview over which to calculate the
... | python | def cause_repertoire(self, mechanism, purview):
"""Return the cause repertoire of a mechanism over a purview.
Args:
mechanism (tuple[int]): The mechanism for which to calculate the
cause repertoire.
purview (tuple[int]): The purview over which to calculate the
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15,932 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.effect_repertoire | def effect_repertoire(self, mechanism, purview):
"""Return the effect repertoire of a mechanism over a purview.
Args:
mechanism (tuple[int]): The mechanism for which to calculate the
effect repertoire.
purview (tuple[int]): The purview over which to calculate the... | python | def effect_repertoire(self, mechanism, purview):
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mechanism (tuple[int]): The mechanism for which to calculate the
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15,933 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.repertoire | def repertoire(self, direction, mechanism, purview):
"""Return the cause or effect repertoire based on a direction.
Args:
direction (Direction): |CAUSE| or |EFFECT|.
mechanism (tuple[int]): The mechanism for which to calculate the
repertoire.
purview ... | python | def repertoire(self, direction, mechanism, purview):
"""Return the cause or effect repertoire based on a direction.
Args:
direction (Direction): |CAUSE| or |EFFECT|.
mechanism (tuple[int]): The mechanism for which to calculate the
repertoire.
purview ... | [
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Args:
direction (Direction): |CAUSE| or |EFFECT|.
mechanism (tuple[int]): The mechanism for which to calculate the
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purview (tuple[int]): The purview over which to calculate the
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15,934 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.partitioned_repertoire | def partitioned_repertoire(self, direction, partition):
"""Compute the repertoire of a partitioned mechanism and purview."""
repertoires = [
self.repertoire(direction, part.mechanism, part.purview)
for part in partition
]
return functools.reduce(np.multiply, reper... | python | def partitioned_repertoire(self, direction, partition):
"""Compute the repertoire of a partitioned mechanism and purview."""
repertoires = [
self.repertoire(direction, part.mechanism, part.purview)
for part in partition
]
return functools.reduce(np.multiply, reper... | [
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15,935 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.expand_repertoire | def expand_repertoire(self, direction, repertoire, new_purview=None):
"""Distribute an effect repertoire over a larger purview.
Args:
direction (Direction): |CAUSE| or |EFFECT|.
repertoire (np.ndarray): The repertoire to expand.
Keyword Args:
new_purview (tu... | python | def expand_repertoire(self, direction, repertoire, new_purview=None):
"""Distribute an effect repertoire over a larger purview.
Args:
direction (Direction): |CAUSE| or |EFFECT|.
repertoire (np.ndarray): The repertoire to expand.
Keyword Args:
new_purview (tu... | [
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15,936 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.cause_info | def cause_info(self, mechanism, purview):
"""Return the cause information for a mechanism over a purview."""
return repertoire_distance(
Direction.CAUSE,
self.cause_repertoire(mechanism, purview),
self.unconstrained_cause_repertoire(purview)
) | python | def cause_info(self, mechanism, purview):
"""Return the cause information for a mechanism over a purview."""
return repertoire_distance(
Direction.CAUSE,
self.cause_repertoire(mechanism, purview),
self.unconstrained_cause_repertoire(purview)
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15,937 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.effect_info | def effect_info(self, mechanism, purview):
"""Return the effect information for a mechanism over a purview."""
return repertoire_distance(
Direction.EFFECT,
self.effect_repertoire(mechanism, purview),
self.unconstrained_effect_repertoire(purview)
) | python | def effect_info(self, mechanism, purview):
"""Return the effect information for a mechanism over a purview."""
return repertoire_distance(
Direction.EFFECT,
self.effect_repertoire(mechanism, purview),
self.unconstrained_effect_repertoire(purview)
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15,938 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.cause_effect_info | def cause_effect_info(self, mechanism, purview):
"""Return the cause-effect information for a mechanism over a purview.
This is the minimum of the cause and effect information.
"""
return min(self.cause_info(mechanism, purview),
self.effect_info(mechanism, purview)) | python | def cause_effect_info(self, mechanism, purview):
"""Return the cause-effect information for a mechanism over a purview.
This is the minimum of the cause and effect information.
"""
return min(self.cause_info(mechanism, purview),
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15,939 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.evaluate_partition | def evaluate_partition(self, direction, mechanism, purview, partition,
repertoire=None):
"""Return the |small_phi| of a mechanism over a purview for the given
partition.
Args:
direction (Direction): |CAUSE| or |EFFECT|.
mechanism (tuple[int]): ... | python | def evaluate_partition(self, direction, mechanism, purview, partition,
repertoire=None):
"""Return the |small_phi| of a mechanism over a purview for the given
partition.
Args:
direction (Direction): |CAUSE| or |EFFECT|.
mechanism (tuple[int]): ... | [
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15,940 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.find_mip | def find_mip(self, direction, mechanism, purview):
"""Return the minimum information partition for a mechanism over a
purview.
Args:
direction (Direction): |CAUSE| or |EFFECT|.
mechanism (tuple[int]): The nodes in the mechanism.
purview (tuple[int]): The node... | python | def find_mip(self, direction, mechanism, purview):
"""Return the minimum information partition for a mechanism over a
purview.
Args:
direction (Direction): |CAUSE| or |EFFECT|.
mechanism (tuple[int]): The nodes in the mechanism.
purview (tuple[int]): The node... | [
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15,941 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.cause_mip | def cause_mip(self, mechanism, purview):
"""Return the irreducibility analysis for the cause MIP.
Alias for |find_mip()| with ``direction`` set to |CAUSE|.
"""
return self.find_mip(Direction.CAUSE, mechanism, purview) | python | def cause_mip(self, mechanism, purview):
"""Return the irreducibility analysis for the cause MIP.
Alias for |find_mip()| with ``direction`` set to |CAUSE|.
"""
return self.find_mip(Direction.CAUSE, mechanism, purview) | [
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15,942 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.effect_mip | def effect_mip(self, mechanism, purview):
"""Return the irreducibility analysis for the effect MIP.
Alias for |find_mip()| with ``direction`` set to |EFFECT|.
"""
return self.find_mip(Direction.EFFECT, mechanism, purview) | python | def effect_mip(self, mechanism, purview):
"""Return the irreducibility analysis for the effect MIP.
Alias for |find_mip()| with ``direction`` set to |EFFECT|.
"""
return self.find_mip(Direction.EFFECT, mechanism, purview) | [
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15,943 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.phi_cause_mip | def phi_cause_mip(self, mechanism, purview):
"""Return the |small_phi| of the cause MIP.
This is the distance between the unpartitioned cause repertoire and the
MIP cause repertoire.
"""
mip = self.cause_mip(mechanism, purview)
return mip.phi if mip else 0 | python | def phi_cause_mip(self, mechanism, purview):
"""Return the |small_phi| of the cause MIP.
This is the distance between the unpartitioned cause repertoire and the
MIP cause repertoire.
"""
mip = self.cause_mip(mechanism, purview)
return mip.phi if mip else 0 | [
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15,944 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.phi_effect_mip | def phi_effect_mip(self, mechanism, purview):
"""Return the |small_phi| of the effect MIP.
This is the distance between the unpartitioned effect repertoire and
the MIP cause repertoire.
"""
mip = self.effect_mip(mechanism, purview)
return mip.phi if mip else 0 | python | def phi_effect_mip(self, mechanism, purview):
"""Return the |small_phi| of the effect MIP.
This is the distance between the unpartitioned effect repertoire and
the MIP cause repertoire.
"""
mip = self.effect_mip(mechanism, purview)
return mip.phi if mip else 0 | [
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15,945 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.phi | def phi(self, mechanism, purview):
"""Return the |small_phi| of a mechanism over a purview."""
return min(self.phi_cause_mip(mechanism, purview),
self.phi_effect_mip(mechanism, purview)) | python | def phi(self, mechanism, purview):
"""Return the |small_phi| of a mechanism over a purview."""
return min(self.phi_cause_mip(mechanism, purview),
self.phi_effect_mip(mechanism, purview)) | [
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15,946 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.find_mice | def find_mice(self, direction, mechanism, purviews=False):
"""Return the |MIC| or |MIE| for a mechanism.
Args:
direction (Direction): :|CAUSE| or |EFFECT|.
mechanism (tuple[int]): The mechanism to be tested for
irreducibility.
Keyword Args:
p... | python | def find_mice(self, direction, mechanism, purviews=False):
"""Return the |MIC| or |MIE| for a mechanism.
Args:
direction (Direction): :|CAUSE| or |EFFECT|.
mechanism (tuple[int]): The mechanism to be tested for
irreducibility.
Keyword Args:
p... | [
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15,947 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.phi_max | def phi_max(self, mechanism):
"""Return the |small_phi_max| of a mechanism.
This is the maximum of |small_phi| taken over all possible purviews.
"""
return min(self.mic(mechanism).phi, self.mie(mechanism).phi) | python | def phi_max(self, mechanism):
"""Return the |small_phi_max| of a mechanism.
This is the maximum of |small_phi| taken over all possible purviews.
"""
return min(self.mic(mechanism).phi, self.mie(mechanism).phi) | [
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15,948 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.null_concept | def null_concept(self):
"""Return the null concept of this subsystem.
The null concept is a point in concept space identified with
the unconstrained cause and effect repertoire of this subsystem.
"""
# Unconstrained cause repertoire.
cause_repertoire = self.cause_reperto... | python | def null_concept(self):
"""Return the null concept of this subsystem.
The null concept is a point in concept space identified with
the unconstrained cause and effect repertoire of this subsystem.
"""
# Unconstrained cause repertoire.
cause_repertoire = self.cause_reperto... | [
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15,949 | wmayner/pyphi | pyphi/subsystem.py | Subsystem.concept | def concept(self, mechanism, purviews=False, cause_purviews=False,
effect_purviews=False):
"""Return the concept specified by a mechanism within this subsytem.
Args:
mechanism (tuple[int]): The candidate set of nodes.
Keyword Args:
purviews (tuple[tuple[... | python | def concept(self, mechanism, purviews=False, cause_purviews=False,
effect_purviews=False):
"""Return the concept specified by a mechanism within this subsytem.
Args:
mechanism (tuple[int]): The candidate set of nodes.
Keyword Args:
purviews (tuple[tuple[... | [
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15,950 | wmayner/pyphi | pyphi/models/actual_causation.py | _null_ac_sia | def _null_ac_sia(transition, direction, alpha=0.0):
"""Return an |AcSystemIrreducibilityAnalysis| with zero |big_alpha| and
empty accounts.
"""
return AcSystemIrreducibilityAnalysis(
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account=(),
partitioned_... | python | def _null_ac_sia(transition, direction, alpha=0.0):
"""Return an |AcSystemIrreducibilityAnalysis| with zero |big_alpha| and
empty accounts.
"""
return AcSystemIrreducibilityAnalysis(
transition=transition,
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15,951 | wmayner/pyphi | pyphi/models/actual_causation.py | Event.mechanism | def mechanism(self):
"""The mechanism of the event."""
assert self.actual_cause.mechanism == self.actual_effect.mechanism
return self.actual_cause.mechanism | python | def mechanism(self):
"""The mechanism of the event."""
assert self.actual_cause.mechanism == self.actual_effect.mechanism
return self.actual_cause.mechanism | [
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15,952 | wmayner/pyphi | pyphi/models/actual_causation.py | Account.irreducible_causes | def irreducible_causes(self):
"""The set of irreducible causes in this |Account|."""
return tuple(link for link in self
if link.direction is Direction.CAUSE) | python | def irreducible_causes(self):
"""The set of irreducible causes in this |Account|."""
return tuple(link for link in self
if link.direction is Direction.CAUSE) | [
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15,953 | wmayner/pyphi | pyphi/models/actual_causation.py | Account.irreducible_effects | def irreducible_effects(self):
"""The set of irreducible effects in this |Account|."""
return tuple(link for link in self
if link.direction is Direction.EFFECT) | python | def irreducible_effects(self):
"""The set of irreducible effects in this |Account|."""
return tuple(link for link in self
if link.direction is Direction.EFFECT) | [
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15,954 | wmayner/pyphi | pyphi/models/fmt.py | make_repr | def make_repr(self, attrs):
"""Construct a repr string.
If `config.REPR_VERBOSITY` is ``1`` or ``2``, this function calls the
object's __str__ method. Although this breaks the convention that __repr__
should return a string which can reconstruct the object, readable reprs are
invaluable since the P... | python | def make_repr(self, attrs):
"""Construct a repr string.
If `config.REPR_VERBOSITY` is ``1`` or ``2``, this function calls the
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15,955 | wmayner/pyphi | pyphi/models/fmt.py | indent | def indent(lines, amount=2, char=' '):
r"""Indent a string.
Prepends whitespace to every line in the passed string. (Lines are
separated by newline characters.)
Args:
lines (str): The string to indent.
Keyword Args:
amount (int): The number of columns to indent by.
char (s... | python | def indent(lines, amount=2, char=' '):
r"""Indent a string.
Prepends whitespace to every line in the passed string. (Lines are
separated by newline characters.)
Args:
lines (str): The string to indent.
Keyword Args:
amount (int): The number of columns to indent by.
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Prepends whitespace to every line in the passed string. (Lines are
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Args:
lines (str): The string to indent.
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15,956 | wmayner/pyphi | pyphi/models/fmt.py | margin | def margin(text):
r"""Add a margin to both ends of each line in the string.
Example:
>>> margin('line1\nline2')
' line1 \n line2 '
"""
lines = str(text).split('\n')
return '\n'.join(' {} '.format(l) for l in lines) | python | def margin(text):
r"""Add a margin to both ends of each line in the string.
Example:
>>> margin('line1\nline2')
' line1 \n line2 '
"""
lines = str(text).split('\n')
return '\n'.join(' {} '.format(l) for l in lines) | [
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15,957 | wmayner/pyphi | pyphi/models/fmt.py | box | def box(text):
r"""Wrap a chunk of text in a box.
Example:
>>> print(box('line1\nline2'))
┌───────┐
│ line1 │
│ line2 │
└───────┘
"""
lines = text.split('\n')
width = max(len(l) for l in lines)
top_bar = (TOP_LEFT_CORNER + HORIZONTAL_BAR * (2 + width) +
... | python | def box(text):
r"""Wrap a chunk of text in a box.
Example:
>>> print(box('line1\nline2'))
┌───────┐
│ line1 │
│ line2 │
└───────┘
"""
lines = text.split('\n')
width = max(len(l) for l in lines)
top_bar = (TOP_LEFT_CORNER + HORIZONTAL_BAR * (2 + width) +
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15,958 | wmayner/pyphi | pyphi/models/fmt.py | side_by_side | def side_by_side(left, right):
r"""Put two boxes next to each other.
Assumes that all lines in the boxes are the same width.
Example:
>>> left = 'A \nC '
>>> right = 'B\nD'
>>> print(side_by_side(left, right))
A B
C D
<BLANKLINE>
"""
left_lines = lis... | python | def side_by_side(left, right):
r"""Put two boxes next to each other.
Assumes that all lines in the boxes are the same width.
Example:
>>> left = 'A \nC '
>>> right = 'B\nD'
>>> print(side_by_side(left, right))
A B
C D
<BLANKLINE>
"""
left_lines = lis... | [
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15,959 | wmayner/pyphi | pyphi/models/fmt.py | header | def header(head, text, over_char=None, under_char=None, center=True):
"""Center a head over a block of text.
The width of the text is the width of the longest line of the text.
"""
lines = list(text.split('\n'))
width = max(len(l) for l in lines)
# Center or left-justify
if center:
... | python | def header(head, text, over_char=None, under_char=None, center=True):
"""Center a head over a block of text.
The width of the text is the width of the longest line of the text.
"""
lines = list(text.split('\n'))
width = max(len(l) for l in lines)
# Center or left-justify
if center:
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15,960 | wmayner/pyphi | pyphi/models/fmt.py | labels | def labels(indices, node_labels=None):
"""Get the labels for a tuple of mechanism indices."""
if node_labels is None:
return tuple(map(str, indices))
return node_labels.indices2labels(indices) | python | def labels(indices, node_labels=None):
"""Get the labels for a tuple of mechanism indices."""
if node_labels is None:
return tuple(map(str, indices))
return node_labels.indices2labels(indices) | [
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15,961 | wmayner/pyphi | pyphi/models/fmt.py | fmt_number | def fmt_number(p):
"""Format a number.
It will be printed as a fraction if the denominator isn't too big and as a
decimal otherwise.
"""
formatted = '{:n}'.format(p)
if not config.PRINT_FRACTIONS:
return formatted
fraction = Fraction(p)
nice = fraction.limit_denominator(128)
... | python | def fmt_number(p):
"""Format a number.
It will be printed as a fraction if the denominator isn't too big and as a
decimal otherwise.
"""
formatted = '{:n}'.format(p)
if not config.PRINT_FRACTIONS:
return formatted
fraction = Fraction(p)
nice = fraction.limit_denominator(128)
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15,962 | wmayner/pyphi | pyphi/models/fmt.py | fmt_part | def fmt_part(part, node_labels=None):
"""Format a |Part|.
The returned string looks like::
0,1
───
∅
"""
def nodes(x): # pylint: disable=missing-docstring
return ','.join(labels(x, node_labels)) if x else EMPTY_SET
numer = nodes(part.mechanism)
denom = nodes(... | python | def fmt_part(part, node_labels=None):
"""Format a |Part|.
The returned string looks like::
0,1
───
∅
"""
def nodes(x): # pylint: disable=missing-docstring
return ','.join(labels(x, node_labels)) if x else EMPTY_SET
numer = nodes(part.mechanism)
denom = nodes(... | [
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15,963 | wmayner/pyphi | pyphi/models/fmt.py | fmt_partition | def fmt_partition(partition):
"""Format a |Bipartition|.
The returned string looks like::
0,1 ∅
─── ✕ ───
2 0,1
Args:
partition (Bipartition): The partition in question.
Returns:
str: A human-readable string representation of the partition.
"""
... | python | def fmt_partition(partition):
"""Format a |Bipartition|.
The returned string looks like::
0,1 ∅
─── ✕ ───
2 0,1
Args:
partition (Bipartition): The partition in question.
Returns:
str: A human-readable string representation of the partition.
"""
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15,964 | wmayner/pyphi | pyphi/models/fmt.py | fmt_ces | def fmt_ces(c, title=None):
"""Format a |CauseEffectStructure|."""
if not c:
return '()\n'
if title is None:
title = 'Cause-effect structure'
concepts = '\n'.join(margin(x) for x in c) + '\n'
title = '{} ({} concept{})'.format(
title, len(c), '' if len(c) == 1 else 's')
... | python | def fmt_ces(c, title=None):
"""Format a |CauseEffectStructure|."""
if not c:
return '()\n'
if title is None:
title = 'Cause-effect structure'
concepts = '\n'.join(margin(x) for x in c) + '\n'
title = '{} ({} concept{})'.format(
title, len(c), '' if len(c) == 1 else 's')
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15,965 | wmayner/pyphi | pyphi/models/fmt.py | fmt_concept | def fmt_concept(concept):
"""Format a |Concept|."""
def fmt_cause_or_effect(x): # pylint: disable=missing-docstring
return box(indent(fmt_ria(x.ria, verbose=False, mip=True), amount=1))
cause = header('MIC', fmt_cause_or_effect(concept.cause))
effect = header('MIE', fmt_cause_or_effect(concep... | python | def fmt_concept(concept):
"""Format a |Concept|."""
def fmt_cause_or_effect(x): # pylint: disable=missing-docstring
return box(indent(fmt_ria(x.ria, verbose=False, mip=True), amount=1))
cause = header('MIC', fmt_cause_or_effect(concept.cause))
effect = header('MIE', fmt_cause_or_effect(concep... | [
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15,966 | wmayner/pyphi | pyphi/models/fmt.py | fmt_ria | def fmt_ria(ria, verbose=True, mip=False):
"""Format a |RepertoireIrreducibilityAnalysis|."""
if verbose:
mechanism = 'Mechanism: {}\n'.format(
fmt_mechanism(ria.mechanism, ria.node_labels))
direction = '\nDirection: {}'.format(ria.direction)
else:
mechanism = ''
... | python | def fmt_ria(ria, verbose=True, mip=False):
"""Format a |RepertoireIrreducibilityAnalysis|."""
if verbose:
mechanism = 'Mechanism: {}\n'.format(
fmt_mechanism(ria.mechanism, ria.node_labels))
direction = '\nDirection: {}'.format(ria.direction)
else:
mechanism = ''
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15,967 | wmayner/pyphi | pyphi/models/fmt.py | fmt_cut | def fmt_cut(cut):
"""Format a |Cut|."""
return 'Cut {from_nodes} {symbol} {to_nodes}'.format(
from_nodes=fmt_mechanism(cut.from_nodes, cut.node_labels),
symbol=CUT_SYMBOL,
to_nodes=fmt_mechanism(cut.to_nodes, cut.node_labels)) | python | def fmt_cut(cut):
"""Format a |Cut|."""
return 'Cut {from_nodes} {symbol} {to_nodes}'.format(
from_nodes=fmt_mechanism(cut.from_nodes, cut.node_labels),
symbol=CUT_SYMBOL,
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15,968 | wmayner/pyphi | pyphi/models/fmt.py | fmt_sia | def fmt_sia(sia, ces=True):
"""Format a |SystemIrreducibilityAnalysis|."""
if ces:
body = (
'{ces}'
'{partitioned_ces}'.format(
ces=fmt_ces(
sia.ces,
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partitioned_ces=fmt_ces(
... | python | def fmt_sia(sia, ces=True):
"""Format a |SystemIrreducibilityAnalysis|."""
if ces:
body = (
'{ces}'
'{partitioned_ces}'.format(
ces=fmt_ces(
sia.ces,
'Cause-effect structure'),
partitioned_ces=fmt_ces(
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15,969 | wmayner/pyphi | pyphi/models/fmt.py | fmt_repertoire | def fmt_repertoire(r):
"""Format a repertoire."""
# TODO: will this get unwieldy with large repertoires?
if r is None:
return ''
r = r.squeeze()
lines = []
# Header: 'S P(S)'
space = ' ' * 4
head = '{S:^{s_width}}{space}Pr({S})'.format(
S='S', s_width=r.ndim, spac... | python | def fmt_repertoire(r):
"""Format a repertoire."""
# TODO: will this get unwieldy with large repertoires?
if r is None:
return ''
r = r.squeeze()
lines = []
# Header: 'S P(S)'
space = ' ' * 4
head = '{S:^{s_width}}{space}Pr({S})'.format(
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15,970 | wmayner/pyphi | pyphi/models/fmt.py | fmt_ac_ria | def fmt_ac_ria(ria):
"""Format an AcRepertoireIrreducibilityAnalysis."""
causality = {
Direction.CAUSE: (fmt_mechanism(ria.purview, ria.node_labels),
ARROW_LEFT,
fmt_mechanism(ria.mechanism, ria.node_labels)),
Direction.EFFECT: (fmt_mechanism(r... | python | def fmt_ac_ria(ria):
"""Format an AcRepertoireIrreducibilityAnalysis."""
causality = {
Direction.CAUSE: (fmt_mechanism(ria.purview, ria.node_labels),
ARROW_LEFT,
fmt_mechanism(ria.mechanism, ria.node_labels)),
Direction.EFFECT: (fmt_mechanism(r... | [
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15,971 | wmayner/pyphi | pyphi/models/fmt.py | fmt_account | def fmt_account(account, title=None):
"""Format an Account or a DirectedAccount."""
if title is None:
title = account.__class__.__name__ # `Account` or `DirectedAccount`
title = '{} ({} causal link{})'.format(
title, len(account), '' if len(account) == 1 else 's')
body = ''
body +... | python | def fmt_account(account, title=None):
"""Format an Account or a DirectedAccount."""
if title is None:
title = account.__class__.__name__ # `Account` or `DirectedAccount`
title = '{} ({} causal link{})'.format(
title, len(account), '' if len(account) == 1 else 's')
body = ''
body +... | [
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15,972 | wmayner/pyphi | pyphi/models/fmt.py | fmt_ac_sia | def fmt_ac_sia(ac_sia):
"""Format a AcSystemIrreducibilityAnalysis."""
body = (
'{ALPHA} = {alpha}\n'
'direction: {ac_sia.direction}\n'
'transition: {ac_sia.transition}\n'
'before state: {ac_sia.before_state}\n'
'after state: {ac_sia.after_state}\n'
'cut:\n{ac_sia... | python | def fmt_ac_sia(ac_sia):
"""Format a AcSystemIrreducibilityAnalysis."""
body = (
'{ALPHA} = {alpha}\n'
'direction: {ac_sia.direction}\n'
'transition: {ac_sia.transition}\n'
'before state: {ac_sia.before_state}\n'
'after state: {ac_sia.after_state}\n'
'cut:\n{ac_sia... | [
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15,973 | wmayner/pyphi | pyphi/models/fmt.py | fmt_transition | def fmt_transition(t):
"""Format a |Transition|."""
return "Transition({} {} {})".format(
fmt_mechanism(t.cause_indices, t.node_labels),
ARROW_RIGHT,
fmt_mechanism(t.effect_indices, t.node_labels)) | python | def fmt_transition(t):
"""Format a |Transition|."""
return "Transition({} {} {})".format(
fmt_mechanism(t.cause_indices, t.node_labels),
ARROW_RIGHT,
fmt_mechanism(t.effect_indices, t.node_labels)) | [
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15,974 | wmayner/pyphi | pyphi/validate.py | direction | def direction(direction, allow_bi=False):
"""Validate that the given direction is one of the allowed constants.
If ``allow_bi`` is ``True`` then ``Direction.BIDIRECTIONAL`` is
acceptable.
"""
valid = [Direction.CAUSE, Direction.EFFECT]
if allow_bi:
valid.append(Direction.BIDIRECTIONAL)
... | python | def direction(direction, allow_bi=False):
"""Validate that the given direction is one of the allowed constants.
If ``allow_bi`` is ``True`` then ``Direction.BIDIRECTIONAL`` is
acceptable.
"""
valid = [Direction.CAUSE, Direction.EFFECT]
if allow_bi:
valid.append(Direction.BIDIRECTIONAL)
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15,975 | wmayner/pyphi | pyphi/validate.py | tpm | def tpm(tpm, check_independence=True):
"""Validate a TPM.
The TPM can be in
* 2-dimensional state-by-state form,
* 2-dimensional state-by-node form, or
* multidimensional state-by-node form.
"""
see_tpm_docs = (
'See the documentation on TPM conventions and the `pyphi.N... | python | def tpm(tpm, check_independence=True):
"""Validate a TPM.
The TPM can be in
* 2-dimensional state-by-state form,
* 2-dimensional state-by-node form, or
* multidimensional state-by-node form.
"""
see_tpm_docs = (
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15,976 | wmayner/pyphi | pyphi/validate.py | conditionally_independent | def conditionally_independent(tpm):
"""Validate that the TPM is conditionally independent."""
if not config.VALIDATE_CONDITIONAL_INDEPENDENCE:
return True
tpm = np.array(tpm)
if is_state_by_state(tpm):
there_and_back_again = convert.state_by_node2state_by_state(
convert.state... | python | def conditionally_independent(tpm):
"""Validate that the TPM is conditionally independent."""
if not config.VALIDATE_CONDITIONAL_INDEPENDENCE:
return True
tpm = np.array(tpm)
if is_state_by_state(tpm):
there_and_back_again = convert.state_by_node2state_by_state(
convert.state... | [
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15,977 | wmayner/pyphi | pyphi/validate.py | connectivity_matrix | def connectivity_matrix(cm):
"""Validate the given connectivity matrix."""
# Special case for empty matrices.
if cm.size == 0:
return True
if cm.ndim != 2:
raise ValueError("Connectivity matrix must be 2-dimensional.")
if cm.shape[0] != cm.shape[1]:
raise ValueError("Connecti... | python | def connectivity_matrix(cm):
"""Validate the given connectivity matrix."""
# Special case for empty matrices.
if cm.size == 0:
return True
if cm.ndim != 2:
raise ValueError("Connectivity matrix must be 2-dimensional.")
if cm.shape[0] != cm.shape[1]:
raise ValueError("Connecti... | [
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15,978 | wmayner/pyphi | pyphi/validate.py | node_labels | def node_labels(node_labels, node_indices):
"""Validate that there is a label for each node."""
if len(node_labels) != len(node_indices):
raise ValueError("Labels {0} must label every node {1}.".format(
node_labels, node_indices))
if len(node_labels) != len(set(node_labels)):
ra... | python | def node_labels(node_labels, node_indices):
"""Validate that there is a label for each node."""
if len(node_labels) != len(node_indices):
raise ValueError("Labels {0} must label every node {1}.".format(
node_labels, node_indices))
if len(node_labels) != len(set(node_labels)):
ra... | [
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15,979 | wmayner/pyphi | pyphi/validate.py | network | def network(n):
"""Validate a |Network|.
Checks the TPM and connectivity matrix.
"""
tpm(n.tpm)
connectivity_matrix(n.cm)
if n.cm.shape[0] != n.size:
raise ValueError("Connectivity matrix must be NxN, where N is the "
"number of nodes in the network.")
retur... | python | def network(n):
"""Validate a |Network|.
Checks the TPM and connectivity matrix.
"""
tpm(n.tpm)
connectivity_matrix(n.cm)
if n.cm.shape[0] != n.size:
raise ValueError("Connectivity matrix must be NxN, where N is the "
"number of nodes in the network.")
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15,980 | wmayner/pyphi | pyphi/validate.py | state_length | def state_length(state, size):
"""Check that the state is the given size."""
if len(state) != size:
raise ValueError('Invalid state: there must be one entry per '
'node in the network; this state has {} entries, but '
'there are {} nodes.'.format(len(sta... | python | def state_length(state, size):
"""Check that the state is the given size."""
if len(state) != size:
raise ValueError('Invalid state: there must be one entry per '
'node in the network; this state has {} entries, but '
'there are {} nodes.'.format(len(sta... | [
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15,981 | wmayner/pyphi | pyphi/validate.py | state_reachable | def state_reachable(subsystem):
"""Return whether a state can be reached according to the network's TPM."""
# If there is a row `r` in the TPM such that all entries of `r - state` are
# between -1 and 1, then the given state has a nonzero probability of being
# reached from some state.
# First we ta... | python | def state_reachable(subsystem):
"""Return whether a state can be reached according to the network's TPM."""
# If there is a row `r` in the TPM such that all entries of `r - state` are
# between -1 and 1, then the given state has a nonzero probability of being
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15,982 | wmayner/pyphi | pyphi/validate.py | cut | def cut(cut, node_indices):
"""Check that the cut is for only the given nodes."""
if cut.indices != node_indices:
raise ValueError('{} nodes are not equal to subsystem nodes '
'{}'.format(cut, node_indices)) | python | def cut(cut, node_indices):
"""Check that the cut is for only the given nodes."""
if cut.indices != node_indices:
raise ValueError('{} nodes are not equal to subsystem nodes '
'{}'.format(cut, node_indices)) | [
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15,983 | wmayner/pyphi | pyphi/validate.py | subsystem | def subsystem(s):
"""Validate a |Subsystem|.
Checks its state and cut.
"""
node_states(s.state)
cut(s.cut, s.cut_indices)
if config.VALIDATE_SUBSYSTEM_STATES:
state_reachable(s)
return True | python | def subsystem(s):
"""Validate a |Subsystem|.
Checks its state and cut.
"""
node_states(s.state)
cut(s.cut, s.cut_indices)
if config.VALIDATE_SUBSYSTEM_STATES:
state_reachable(s)
return True | [
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15,984 | wmayner/pyphi | pyphi/validate.py | partition | def partition(partition):
"""Validate a partition - used by blackboxes and coarse grains."""
nodes = set()
for part in partition:
for node in part:
if node in nodes:
raise ValueError(
'Micro-element {} may not be partitioned into multiple '
... | python | def partition(partition):
"""Validate a partition - used by blackboxes and coarse grains."""
nodes = set()
for part in partition:
for node in part:
if node in nodes:
raise ValueError(
'Micro-element {} may not be partitioned into multiple '
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15,985 | wmayner/pyphi | pyphi/validate.py | coarse_grain | def coarse_grain(coarse_grain):
"""Validate a macro coarse-graining."""
partition(coarse_grain.partition)
if len(coarse_grain.partition) != len(coarse_grain.grouping):
raise ValueError('output and state groupings must be the same size')
for part, group in zip(coarse_grain.partition, coarse_gra... | python | def coarse_grain(coarse_grain):
"""Validate a macro coarse-graining."""
partition(coarse_grain.partition)
if len(coarse_grain.partition) != len(coarse_grain.grouping):
raise ValueError('output and state groupings must be the same size')
for part, group in zip(coarse_grain.partition, coarse_gra... | [
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15,986 | wmayner/pyphi | pyphi/validate.py | blackbox | def blackbox(blackbox):
"""Validate a macro blackboxing."""
if tuple(sorted(blackbox.output_indices)) != blackbox.output_indices:
raise ValueError('Output indices {} must be ordered'.format(
blackbox.output_indices))
partition(blackbox.partition)
for part in blackbox.partition:
... | python | def blackbox(blackbox):
"""Validate a macro blackboxing."""
if tuple(sorted(blackbox.output_indices)) != blackbox.output_indices:
raise ValueError('Output indices {} must be ordered'.format(
blackbox.output_indices))
partition(blackbox.partition)
for part in blackbox.partition:
... | [
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15,987 | wmayner/pyphi | pyphi/validate.py | blackbox_and_coarse_grain | def blackbox_and_coarse_grain(blackbox, coarse_grain):
"""Validate that a coarse-graining properly combines the outputs of a
blackboxing.
"""
if blackbox is None:
return
for box in blackbox.partition:
# Outputs of the box
outputs = set(box) & set(blackbox.output_indices)
... | python | def blackbox_and_coarse_grain(blackbox, coarse_grain):
"""Validate that a coarse-graining properly combines the outputs of a
blackboxing.
"""
if blackbox is None:
return
for box in blackbox.partition:
# Outputs of the box
outputs = set(box) & set(blackbox.output_indices)
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15,988 | wmayner/pyphi | pyphi/registry.py | Registry.register | def register(self, name):
"""Decorator for registering a function with PyPhi.
Args:
name (string): The name of the function
"""
def register_func(func):
self.store[name] = func
return func
return register_func | python | def register(self, name):
"""Decorator for registering a function with PyPhi.
Args:
name (string): The name of the function
"""
def register_func(func):
self.store[name] = func
return func
return register_func | [
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15,989 | wmayner/pyphi | pyphi/compute/subsystem.py | ces | def ces(subsystem, mechanisms=False, purviews=False, cause_purviews=False,
effect_purviews=False, parallel=False):
"""Return the conceptual structure of this subsystem, optionally restricted
to concepts with the mechanisms and purviews given in keyword arguments.
If you don't need the full |CauseEf... | python | def ces(subsystem, mechanisms=False, purviews=False, cause_purviews=False,
effect_purviews=False, parallel=False):
"""Return the conceptual structure of this subsystem, optionally restricted
to concepts with the mechanisms and purviews given in keyword arguments.
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15,990 | wmayner/pyphi | pyphi/compute/subsystem.py | conceptual_info | def conceptual_info(subsystem):
"""Return the conceptual information for a |Subsystem|.
This is the distance from the subsystem's |CauseEffectStructure| to the
null concept.
"""
ci = ces_distance(ces(subsystem),
CauseEffectStructure((), subsystem=subsystem))
return round(c... | python | def conceptual_info(subsystem):
"""Return the conceptual information for a |Subsystem|.
This is the distance from the subsystem's |CauseEffectStructure| to the
null concept.
"""
ci = ces_distance(ces(subsystem),
CauseEffectStructure((), subsystem=subsystem))
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15,991 | wmayner/pyphi | pyphi/compute/subsystem.py | evaluate_cut | def evaluate_cut(uncut_subsystem, cut, unpartitioned_ces):
"""Compute the system irreducibility for a given cut.
Args:
uncut_subsystem (Subsystem): The subsystem without the cut applied.
cut (Cut): The cut to evaluate.
unpartitioned_ces (CauseEffectStructure): The cause-effect structure... | python | def evaluate_cut(uncut_subsystem, cut, unpartitioned_ces):
"""Compute the system irreducibility for a given cut.
Args:
uncut_subsystem (Subsystem): The subsystem without the cut applied.
cut (Cut): The cut to evaluate.
unpartitioned_ces (CauseEffectStructure): The cause-effect structure... | [
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15,992 | wmayner/pyphi | pyphi/compute/subsystem.py | sia_bipartitions | def sia_bipartitions(nodes, node_labels=None):
"""Return all |big_phi| cuts for the given nodes.
This value changes based on :const:`config.CUT_ONE_APPROXIMATION`.
Args:
nodes (tuple[int]): The node indices to partition.
Returns:
list[Cut]: All unidirectional partitions.
"""
if... | python | def sia_bipartitions(nodes, node_labels=None):
"""Return all |big_phi| cuts for the given nodes.
This value changes based on :const:`config.CUT_ONE_APPROXIMATION`.
Args:
nodes (tuple[int]): The node indices to partition.
Returns:
list[Cut]: All unidirectional partitions.
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15,993 | wmayner/pyphi | pyphi/compute/subsystem.py | _sia | def _sia(cache_key, subsystem):
"""Return the minimal information partition of a subsystem.
Args:
subsystem (Subsystem): The candidate set of nodes.
Returns:
SystemIrreducibilityAnalysis: A nested structure containing all the
data from the intermediate calculations. The top level c... | python | def _sia(cache_key, subsystem):
"""Return the minimal information partition of a subsystem.
Args:
subsystem (Subsystem): The candidate set of nodes.
Returns:
SystemIrreducibilityAnalysis: A nested structure containing all the
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15,994 | wmayner/pyphi | pyphi/compute/subsystem.py | _sia_cache_key | def _sia_cache_key(subsystem):
"""The cache key of the subsystem.
This includes the native hash of the subsystem and all configuration values
which change the results of ``sia``.
"""
return (
hash(subsystem),
config.ASSUME_CUTS_CANNOT_CREATE_NEW_CONCEPTS,
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"""The cache key of the subsystem.
This includes the native hash of the subsystem and all configuration values
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"""
return (
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15,995 | wmayner/pyphi | pyphi/compute/subsystem.py | concept_cuts | def concept_cuts(direction, node_indices, node_labels=None):
"""Generator over all concept-syle cuts for these nodes."""
for partition in mip_partitions(node_indices, node_indices):
yield KCut(direction, partition, node_labels) | python | def concept_cuts(direction, node_indices, node_labels=None):
"""Generator over all concept-syle cuts for these nodes."""
for partition in mip_partitions(node_indices, node_indices):
yield KCut(direction, partition, node_labels) | [
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] | deeca69a084d782a6fde7bf26f59e93b593c5d77 | https://github.com/wmayner/pyphi/blob/deeca69a084d782a6fde7bf26f59e93b593c5d77/pyphi/compute/subsystem.py#L390-L393 |
15,996 | wmayner/pyphi | pyphi/compute/subsystem.py | directional_sia | def directional_sia(subsystem, direction, unpartitioned_ces=None):
"""Calculate a concept-style SystemIrreducibilityAnalysisCause or
SystemIrreducibilityAnalysisEffect.
"""
if unpartitioned_ces is None:
unpartitioned_ces = _ces(subsystem)
c_system = ConceptStyleSystem(subsystem, direction)
... | python | def directional_sia(subsystem, direction, unpartitioned_ces=None):
"""Calculate a concept-style SystemIrreducibilityAnalysisCause or
SystemIrreducibilityAnalysisEffect.
"""
if unpartitioned_ces is None:
unpartitioned_ces = _ces(subsystem)
c_system = ConceptStyleSystem(subsystem, direction)
... | [
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15,997 | wmayner/pyphi | pyphi/compute/subsystem.py | sia_concept_style | def sia_concept_style(subsystem):
"""Compute a concept-style SystemIrreducibilityAnalysis"""
unpartitioned_ces = _ces(subsystem)
sia_cause = directional_sia(subsystem, Direction.CAUSE,
unpartitioned_ces)
sia_effect = directional_sia(subsystem, Direction.EFFECT,
... | python | def sia_concept_style(subsystem):
"""Compute a concept-style SystemIrreducibilityAnalysis"""
unpartitioned_ces = _ces(subsystem)
sia_cause = directional_sia(subsystem, Direction.CAUSE,
unpartitioned_ces)
sia_effect = directional_sia(subsystem, Direction.EFFECT,
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] | deeca69a084d782a6fde7bf26f59e93b593c5d77 | https://github.com/wmayner/pyphi/blob/deeca69a084d782a6fde7bf26f59e93b593c5d77/pyphi/compute/subsystem.py#L447-L456 |
15,998 | wmayner/pyphi | pyphi/compute/subsystem.py | ComputeCauseEffectStructure.compute | def compute(mechanism, subsystem, purviews, cause_purviews,
effect_purviews):
"""Compute a |Concept| for a mechanism, in this |Subsystem| with the
provided purviews.
"""
concept = subsystem.concept(mechanism,
purviews=purviews,
... | python | def compute(mechanism, subsystem, purviews, cause_purviews,
effect_purviews):
"""Compute a |Concept| for a mechanism, in this |Subsystem| with the
provided purviews.
"""
concept = subsystem.concept(mechanism,
purviews=purviews,
... | [
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15,999 | wmayner/pyphi | pyphi/compute/subsystem.py | ComputeCauseEffectStructure.process_result | def process_result(self, new_concept, concepts):
"""Save all concepts with non-zero |small_phi| to the
|CauseEffectStructure|.
"""
if new_concept.phi > 0:
# Replace the subsystem
new_concept.subsystem = self.subsystem
concepts.append(new_concept)
... | python | def process_result(self, new_concept, concepts):
"""Save all concepts with non-zero |small_phi| to the
|CauseEffectStructure|.
"""
if new_concept.phi > 0:
# Replace the subsystem
new_concept.subsystem = self.subsystem
concepts.append(new_concept)
... | [
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] | deeca69a084d782a6fde7bf26f59e93b593c5d77 | https://github.com/wmayner/pyphi/blob/deeca69a084d782a6fde7bf26f59e93b593c5d77/pyphi/compute/subsystem.py#L54-L62 |
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