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def f_remove_child(self, name, recursive=False, predicate=None):
"""Removes a child of the group.
Note that groups and leaves are only removed from the current trajectory in RAM.
If the trajectory is stored to disk, this data is not affected. Thus, removing children
can be only be used ... |
def f_contains(self, item, with_links=True, shortcuts=False, max_depth=None):
"""Checks if the node contains a specific parameter or result.
It is checked if the item can be found via the
:func:`~pypet.naturalnaming.NNGroupNode.f_get` method.
:param item: Parameter/Result name or insta... |
def f_iter_nodes(self, recursive=True, with_links=True, max_depth=None, predicate=None):
"""Iterates recursively (default) over nodes hanging below this group.
:param recursive: Whether to iterate the whole sub tree or only immediate children.
:param with_links: If links should be considered
... |
def f_iter_leaves(self, with_links=True):
"""Iterates (recursively) over all leaves hanging below the current group.
:param with_links:
If links should be ignored, leaves hanging below linked nodes are not listed.
:returns:
Iterator over all leaf nodes
"""
... |
def f_get_all(self, name, max_depth=None, shortcuts=True):
""" Searches for all occurrences of `name` under `node`.
Links are NOT considered since nodes are searched bottom up in the tree.
:param node:
Start node
:param name:
Name of what to look for, can be ... |
def f_get_default(self, name, default=None, fast_access=True, with_links=True,
shortcuts=True, max_depth=None, auto_load=False):
""" Similar to `f_get`, but returns the default value if `name` is not found in the
trajectory.
This function uses the `f_get` method and will return th... |
def f_get(self, name, fast_access=False, with_links=True,
shortcuts=True, max_depth=None, auto_load=False):
"""Searches and returns an item (parameter/result/group node) with the given `name`.
:param name: Name of the item (full name or parts of the full name)
:param fast_access:... |
def f_get_children(self, copy=True):
"""Returns a children dictionary.
:param copy:
Whether the group's original dictionary or a shallow copy is returned.
If you want the real dictionary please do not modify it at all!
:returns: Dictionary of nodes
"""
... |
def f_get_groups(self, copy=True):
"""Returns a dictionary of groups hanging immediately below this group.
:param copy:
Whether the group's original dictionary or a shallow copy is returned.
If you want the real dictionary please do not modify it at all!
:returns: Dict... |
def f_get_leaves(self, copy=True):
"""Returns a dictionary of all leaves hanging immediately below this group.
:param copy:
Whether the group's original dictionary or a shallow copy is returned.
If you want the real dictionary please do not modify it at all!
:returns: ... |
def f_get_links(self, copy=True):
"""Returns a link dictionary.
:param copy:
Whether the group's original dictionary or a shallow copy is returned.
If you want the real dictionary please do not modify it at all!
:returns: Dictionary of nodes
"""
if cop... |
def f_store_child(self, name, recursive=False, store_data=pypetconstants.STORE_DATA,
max_depth=None):
"""Stores a child or recursively a subtree to disk.
:param name:
Name of child to store. If grouped ('groupA.groupB.childC') the path along the way
to las... |
def f_store(self, recursive=True, store_data=pypetconstants.STORE_DATA,
max_depth=None):
"""Stores a group node to disk
:param recursive:
Whether recursively all children should be stored too. Default is ``True``.
:param store_data:
For how to choose '... |
def f_load_child(self, name, recursive=False, load_data=pypetconstants.LOAD_DATA,
max_depth=None):
"""Loads a child or recursively a subtree from disk.
:param name:
Name of child to load. If grouped ('groupA.groupB.childC') the path along the way
to last no... |
def f_load(self, recursive=True, load_data=pypetconstants.LOAD_DATA,
max_depth=None):
"""Loads a group from disk.
:param recursive:
Default is ``True``.
Whether recursively all nodes below the current node should be loaded, too.
Note that links are ne... |
def f_add_parameter_group(self, *args, **kwargs):
"""Adds an empty parameter group under the current node.
Can be called with ``f_add_parameter_group('MyName', 'this is an informative comment')``
or ``f_add_parameter_group(name='MyName', comment='This is an informative comment')``
or wi... |
def f_add_parameter(self, *args, **kwargs):
""" Adds a parameter under the current node.
There are two ways to add a new parameter either by adding a parameter instance:
>>> new_parameter = Parameter('group1.group2.myparam', data=42, comment='Example!')
>>> traj.f_add_parameter(new_par... |
def f_add_result_group(self, *args, **kwargs):
"""Adds an empty result group under the current node.
Adds the full name of the current node as prefix to the name of the group.
If current node is a single run (root) adds the prefix `'results.runs.run_08%d%'` to the
full name where `'08%d... |
def f_add_result(self, *args, **kwargs):
"""Adds a result under the current node.
There are two ways to add a new result either by adding a result instance:
>>> new_result = Result('group1.group2.myresult', 1666, x=3, y=4, comment='Example!')
>>> traj.f_add_result(new_result)
... |
def f_add_derived_parameter_group(self, *args, **kwargs):
"""Adds an empty derived parameter group under the current node.
Adds the full name of the current node as prefix to the name of the group.
If current node is a single run (root) adds the prefix `'derived_parameters.runs.run_08%d%'`
... |
def f_add_derived_parameter(self, *args, **kwargs):
"""Adds a derived parameter under the current group.
Similar to
:func:`~pypet.naturalnaming.ParameterGroup.f_add_parameter`
Naming prefixes are added as in
:func:`~pypet.naturalnaming.DerivedParameterGroup.f_add_derived_parame... |
def f_add_config_group(self, *args, **kwargs):
"""Adds an empty config group under the current node.
Adds the full name of the current node as prefix to the name of the group.
If current node is the trajectory (root), the prefix `'config'` is added to the full name.
The `name` can also... |
def f_add_config(self, *args, **kwargs):
"""Adds a config parameter under the current group.
Similar to
:func:`~pypet.naturalnaming.ParameterGroup.f_add_parameter`.
If current group is the trajectory the prefix `'config'` is added to the name.
"""
return self._nn_inter... |
def eval_one_max(traj, individual):
"""The fitness function"""
traj.f_add_result('$set.$.individual', list(individual))
fitness = sum(individual)
traj.f_add_result('$set.$.fitness', fitness)
traj.f_store()
return (fitness,) |
def unit_from_expression(expr):
"""Takes a unit string like ``'1. * volt'`` and returns the BRIAN2 unit."""
if expr == '1':
return get_unit_fast(1)
elif isinstance(expr, str):
mod = ast.parse(expr, mode='eval')
expr = mod.body
return unit_from_expression(expr)
elif expr._... |
def f_supports(self, data):
""" Simply checks if data is supported """
if isinstance(data, Quantity):
return True
elif super(Brian2Parameter, self).f_supports(data):
return True
return False |
def _supports(self, data):
""" Simply checks if data is supported """
if isinstance(data, Quantity):
return True
elif super(Brian2Result, self)._supports(data):
return True
return False |
def f_set_single(self, name, item):
""" To add a monitor use `f_set_single('monitor', brian_monitor)`.
Otherwise `f_set_single` works similar to :func:`~pypet.parameter.Result.f_set_single`.
"""
if type(item) in [SpikeMonitor, StateMonitor, PopulationRateMonitor]:
if self.v_... |
def add_commit_variables(traj, commit):
"""Adds commit information to the trajectory."""
git_time_value = time.strftime('%Y_%m_%d_%Hh%Mm%Ss', time.localtime(commit.committed_date))
git_short_name = str(commit.hexsha[0:7])
git_commit_name = 'commit_%s_' % git_short_name
git_commit_name = 'git.' + g... |
def make_git_commit(environment, git_repository, user_message, git_fail):
""" Makes a commit and returns if a new commit was triggered and the SHA_1 code of the commit.
If `git_fail` is `True` program fails instead of triggering a new commit given
not committed changes. Then a `GitDiffError` is raised.
... |
def flatten_dictionary(nested_dict, separator):
"""Flattens a nested dictionary.
New keys are concatenations of nested keys with the `separator` in between.
"""
flat_dict = {}
for key, val in nested_dict.items():
if isinstance(val, dict):
new_flat_dict = flatten_dictionary(val,... |
def nest_dictionary(flat_dict, separator):
""" Nests a given flat dictionary.
Nested keys are created by splitting given keys around the `separator`.
"""
nested_dict = {}
for key, val in flat_dict.items():
split_key = key.split(separator)
act_dict = nested_dict
final_key = ... |
def progressbar(index, total, percentage_step=10, logger='print', log_level=logging.INFO,
reprint=True, time=True, length=20, fmt_string=None, reset=False):
"""Plots a progress bar to the given `logger` for large for loops.
To be used inside a for-loop at the end of the loop:
.. code-bloc... |
def _get_argspec(func):
"""Helper function to support both Python versions"""
if inspect.isclass(func):
func = func.__init__
if not inspect.isfunction(func):
# Init function not existing
return [], False
parameters = inspect.signature(func).parameters
args = []
uses_stars... |
def get_matching_kwargs(func, kwargs):
"""Takes a function and keyword arguments and returns the ones that can be passed."""
args, uses_startstar = _get_argspec(func)
if uses_startstar:
return kwargs.copy()
else:
matching_kwargs = dict((k, kwargs[k]) for k in args if k in kwargs)
... |
def result_sort(result_list, start_index=0):
"""Sorts a list of results in O(n) in place (since every run is unique)
:param result_list: List of tuples [(run_idx, res), ...]
:param start_index: Index with which to start, every entry before `start_index` is ignored
"""
if len(result_list) < 2:
... |
def format_time(timestamp):
"""Formats timestamp to human readable format"""
format_string = '%Y_%m_%d_%Hh%Mm%Ss'
formatted_time = datetime.datetime.fromtimestamp(timestamp).strftime(format_string)
return formatted_time |
def port_to_tcp(port=None):
"""Returns local tcp address for a given `port`, automatic port if `None`"""
#address = 'tcp://' + socket.gethostbyname(socket.getfqdn())
domain_name = socket.getfqdn()
try:
addr_list = socket.getaddrinfo(domain_name, None)
except Exception:
addr_list = so... |
def racedirs(path):
"""Like os.makedirs but takes care about race conditions"""
if os.path.isfile(path):
raise IOError('Path `%s` is already a file not a directory')
while True:
try:
if os.path.isdir(path):
# only break if full path has been created or exists
... |
def _reset(self, index, total, percentage_step, length):
"""Resets to the progressbar to start a new one"""
self._start_time = datetime.datetime.now()
self._start_index = index
self._current_index = index
self._percentage_step = percentage_step
self._total = float(total)
... |
def _get_remaining(self, index):
"""Calculates remaining time as a string"""
try:
current_time = datetime.datetime.now()
time_delta = current_time - self._start_time
try:
total_seconds = time_delta.total_seconds()
except AttributeError:
... |
def f_to_dict(self, copy=True):
"""Returns annotations as dictionary.
:param copy: Whether to return a shallow copy or the real thing (aka _dict).
"""
if copy:
return self._dict.copy()
else:
return self._dict |
def f_get(self, *args):
"""Returns annotations
If len(args)>1, then returns a list of annotations.
`f_get(X)` with *X* integer will return the annotation with name `annotation_X`.
If the annotation contains only a single entry you can call `f_get()` without arguments.
If you c... |
def f_set(self, *args, **kwargs):
"""Sets annotations
Items in args are added as `annotation` and `annotation_X` where
'X' is the position in args for following arguments.
"""
for idx, arg in enumerate(args):
valstr = self._translate_key(idx)
self.f_set_... |
def f_remove(self, key):
"""Removes `key` from annotations"""
key = self._translate_key(key)
try:
del self._dict[key]
except KeyError:
raise AttributeError('Your annotations do not contain %s' % key) |
def f_ann_to_str(self):
"""Returns all annotations lexicographically sorted as a concatenated string."""
resstr = ''
for key in sorted(self._dict.keys()):
resstr += '%s=%s; ' % (key, str(self._dict[key]))
return resstr[:-2] |
def make_ordinary_result(result, key, trajectory=None, reload=True):
"""Turns a given shared data item into a an ordinary one.
:param result: Result container with shared data
:param key: The name of the shared data
:param trajectory:
The trajectory, only needed if shared data has
no a... |
def make_shared_result(result, key, trajectory, new_class=None):
"""Turns an ordinary data item into a shared one.
Removes the old result from the trajectory and replaces it.
Empties the given result.
:param result: The result containing ordinary data
:param key: Name of ordinary data item
:pa... |
def create_shared_data(self, **kwargs):
"""Creates shared data on disk with a StorageService on disk.
Needs to be called before shared data can be used later on.
Actual arguments of ``kwargs`` depend on the type of data to be
created. For instance, creating an array one can use the key... |
def _request_data(self, request, args=None, kwargs=None):
"""Interface with the underlying storage.
Passes request to the StorageService that performs the appropriate action.
For example, given a shared table ``t``.
``t.remove_row(4)`` is parsed into ``request='remove_row', args=(4,)`` ... |
def get_data_node(self):
"""Returns the actula node of the underlying data.
In case one uses HDF5 this will be the HDF5 leaf node.
"""
if not self._storage_service.is_open:
warnings.warn('You requesting the data item but your store is not open, '
'... |
def _supports(self, item):
"""Checks if outer data structure is supported."""
result = super(SharedResult, self)._supports(item)
result = result or type(item) in SharedResult.SUPPORTED_DATA
return result |
def create_shared_data(self, name=None, **kwargs):
"""Calls the corresponding function of the shared data item"""
if name is None:
item = self.f_get()
else:
item = self.f_get(name)
return item.create_shared_data(**kwargs) |
def manipulate_multiproc_safe(traj):
""" Target function that manipulates the trajectory.
Stores the current name of the process into the trajectory and
**overwrites** previous settings.
:param traj:
Trajectory container with multiprocessing safe storage service
"""
# Manipulate the... |
def multiply(traj, result_list):
"""Example of a sophisticated simulation that involves multiplying two values.
This time we will store tha value in a shared list and only in the end add the result.
:param traj:
Trajectory containing
the parameters in a particular combination,
it ... |
def _lock(self, name, client_id, request_id):
"""Hanldes locking of locks
If a lock is already locked sends a WAIT command,
else LOCKs it and sends GO.
Complains if a given client re-locks a lock without releasing it before.
"""
if name in self._locks:
othe... |
def _unlock(self, name, client_id, request_id):
"""Handles unlocking
Complains if a non-existent lock should be released or
if a lock should be released that was acquired by
another client before.
"""
if name in self._locks:
other_client_id, other_request_id... |
def run(self):
"""Runs server"""
try:
self._start()
running = True
while running:
msg = ''
name = ''
client_id = ''
request_id = ''
request = self._socket.recv_string()
s... |
def _lock(self, name, client_id, request_id):
"""Handles locking
Locking time is stored to determine time out.
If a lock is timed out it can be acquired by a different client.
"""
if name in self._locks:
other_client_id, other_request_id, lock_time = self._locks[nam... |
def _unlock(self, name, client_id, request_id):
"""Handles unlocking"""
if name in self._locks:
other_client_id, other_request_id, lock_time = self._locks[name]
if other_client_id != client_id:
response = (self.RELEASE_ERROR + self.DELIMITER +
... |
def send_done(self):
"""Notifies the Server to shutdown"""
self.start(test_connection=False)
self._logger.debug('Sending shutdown signal')
self._req_rep(ZMQServer.DONE) |
def finalize(self):
"""Closes socket and terminates context
NO-OP if already closed.
"""
if self._context is not None:
if self._socket is not None:
self._close_socket(confused=False)
self._context.term()
self._context = None
... |
def start(self, test_connection=True):
"""Starts connection to server if not existent.
NO-OP if connection is already established.
Makes ping-pong test as well if desired.
"""
if self._context is None:
self._logger.debug('Starting Client')
self._context ... |
def _req_rep_retry(self, request):
"""Returns response and number of retries"""
retries_left = self.RETRIES
while retries_left:
self._logger.log(1, 'Sending REQ `%s`', request)
self._send_request(request)
socks = dict(self._poll.poll(self.TIMEOUT))
... |
def acquire(self):
"""Acquires lock and returns `True`
Blocks until lock is available.
"""
self.start(test_connection=False)
while True:
str_response, retries = self._req_rep_retry(LockerServer.LOCK)
response = str_response.split(LockerServer.DELIMITER)
... |
def release(self):
"""Releases lock"""
# self.start(test_connection=False)
str_response, retries = self._req_rep_retry(LockerServer.UNLOCK)
response = str_response.split(LockerServer.DELIMITER)
if response[0] == LockerServer.RELEASED:
pass # Everything is fine
... |
def listen(self):
""" Handles listening requests from the client.
There are 4 types of requests:
1- Check space in the queue
2- Tests the socket
3- If there is a space, it sends data
4- after data is sent, puts it to queue for storing
"""
count = 0
... |
def put(self, data, block=True):
""" If there is space it sends data to server
If no space in the queue
It returns the request in every 10 millisecond
until there will be space in the queue.
"""
self.start(test_connection=False)
while True:
respon... |
def _detect_fork(self):
"""Detects if lock client was forked.
Forking is detected by comparing the PID of the current
process with the stored PID.
"""
if self._pid is None:
self._pid = os.getpid()
if self._context is not None:
current_pid = os.ge... |
def start(self, test_connection=True):
"""Checks for forking and starts/restarts if desired"""
self._detect_fork()
super(ForkAwareLockerClient, self).start(test_connection) |
def _put_on_queue(self, to_put):
"""Puts data on queue"""
old = self.pickle_queue
self.pickle_queue = False
try:
self.queue.put(to_put, block=True)
finally:
self.pickle_queue = old |
def _put_on_pipe(self, to_put):
"""Puts data on queue"""
self.acquire_lock()
self._send_chunks(to_put)
self.release_lock() |
def _handle_data(self, msg, args, kwargs):
"""Handles data and returns `True` or `False` if everything is done."""
stop = False
try:
if msg == 'DONE':
stop = True
elif msg == 'STORE':
if 'msg' in kwargs:
store_msg = kwar... |
def run(self):
"""Starts listening to the queue."""
try:
while True:
msg, args, kwargs = self._receive_data()
stop = self._handle_data(msg, args, kwargs)
if stop:
break
finally:
if self._storage_service.i... |
def _receive_data(self):
"""Gets data from queue"""
result = self.queue.get(block=True)
if hasattr(self.queue, 'task_done'):
self.queue.task_done()
return result |
def _receive_data(self):
"""Gets data from pipe"""
while True:
while len(self._buffer) < self.max_size and self.conn.poll():
data = self._read_chunks()
if data is not None:
self._buffer.append(data)
if len(self._buffer) > 0:
... |
def store(self, *args, **kwargs):
"""Acquires a lock before storage and releases it afterwards."""
try:
self.acquire_lock()
return self._storage_service.store(*args, **kwargs)
finally:
if self.lock is not None:
try:
self.rel... |
def store(self, msg, stuff_to_store, *args, **kwargs):
"""Simply keeps a reference to the stored data """
trajectory_name = kwargs['trajectory_name']
if trajectory_name not in self.references:
self.references[trajectory_name] = []
self.references[trajectory_name].append((msg,... |
def store_references(self, references):
"""Stores references to disk and may collect garbage."""
for trajectory_name in references:
self._storage_service.store(pypetconstants.LIST, references[trajectory_name], trajectory_name=trajectory_name)
self._check_and_collect_garbage() |
def parse_config(init_func):
"""Decorator wrapping the environment to use a config file"""
@functools.wraps(init_func)
def new_func(env, *args, **kwargs):
config_interpreter = ConfigInterpreter(kwargs)
# Pass the config data to the kwargs
new_kwargs = config_interpreter.interpret()
... |
def _collect_section(self, section):
"""Collects all settings within a section"""
kwargs = {}
try:
if self.parser.has_section(section):
options = self.parser.options(section)
for option in options:
str_val = self.parser.get(section,... |
def _collect_config(self):
"""Collects all info from three sections"""
kwargs = {}
sections = ('storage_service', 'trajectory', 'environment')
for section in sections:
kwargs.update(self._collect_section(section))
return kwargs |
def interpret(self):
"""Copies parsed arguments into the kwargs passed to the environment"""
if self.config_file:
new_kwargs = self._collect_config()
for key in new_kwargs:
# Already specified kwargs take precedence over the ini file
if key not in ... |
def add_parameters(self, traj):
"""Adds parameters and config from the `.ini` file to the trajectory"""
if self.config_file:
parameters = self._collect_section('parameters')
for name in parameters:
value = parameters[name]
if not isinstance(value, ... |
def convert_rule(rule_number):
""" Converts a rule given as an integer into a binary list representation.
It reads from left to right (contrary to the Wikipedia article given below),
i.e. the 2**0 is found on the left hand side and 2**7 on the right.
For example:
``convert_rule(30)`` returns ... |
def make_initial_state(name, ncells, seed=42):
""" Creates an initial state for the automaton.
:param name:
Either ``'single'`` for a single live cell in the middle of the cell ring,
or ``'random'`` for uniformly distributed random pattern of zeros and ones.
:param ncells: Number of cells... |
def plot_pattern(pattern, rule_number, filename):
""" Plots an automaton ``pattern`` and stores the image under a given ``filename``.
For axes labels the ``rule_number`` is also required.
"""
plt.figure()
plt.imshow(pattern)
plt.xlabel('Cell No.')
plt.ylabel('Time Step')
plt.title('CA ... |
def cellular_automaton_1D(initial_state, rule_number, steps):
""" Simulates a 1 dimensional cellular automaton.
:param initial_state:
The initial state of *dead* and *alive* cells as a 1D numpy array.
It's length determines the size of the simulation.
:param rule_number:
The upda... |
def main():
""" Main simulation function """
rules_to_test = [10, 30, 90, 110, 184] # rules we want to explore:
steps = 250 # cell iterations
ncells = 400 # number of cells
seed = 100042 # RNG seed
initial_states = ['single', 'random'] # Initial states we want to explore
# create a fol... |
def get_all_slots(cls):
"""Iterates through a class' (`cls`) mro to get all slots as a set."""
slots_iterator = (getattr(c, '__slots__', ()) for c in cls.__mro__)
# `__slots__` might only be a single string,
# so we need to put the strings into a tuple.
slots_converted = ((slots,) if isinstance(slot... |
def signal_update(self):
"""Signals the process timer.
If more time than the display time has passed a message is emitted.
"""
if not self.active:
return
self._updates += 1
current_time = time.time()
dt = current_time - self._last_time
if dt... |
def _overview_group(self):
"""Direct link to the overview group"""
if self._overview_group_ is None:
self._overview_group_ = self._all_create_or_get_groups('overview')[0]
return self._overview_group_ |
def _all_get_filters(self, kwargs=None):
"""Makes filters
Pops filter arguments from `kwargs` such that they are not passed
on to other functions also using kwargs.
"""
if kwargs is None:
kwargs = {}
complib = kwargs.pop('complib', None)
complevel = ... |
def _srvc_set_config(self, trajectory):
"""Sets a config value to the Trajectory or changes it if the trajectory was loaded
a the settings no longer match"""
def _set_config(name, value, comment):
if not trajectory.f_contains('config.'+name, shortcuts=False):
trajecto... |
def load(self, msg, stuff_to_load, *args, **kwargs):
"""Loads a particular item from disk.
The storage service always accepts these parameters:
:param trajectory_name: Name of current trajectory and name of top node in hdf5 file.
:param trajectory_index:
If no `trajectory... |
def store(self, msg, stuff_to_store, *args, **kwargs):
""" Stores a particular item to disk.
The storage service always accepts these parameters:
:param trajectory_name: Name or current trajectory and name of top node in hdf5 file
:param filename: Name of the hdf5 file
:param... |
def _srvc_load_several_items(self, iterable, *args, **kwargs):
"""Loads several items from an iterable
Iterables are supposed to be of a format like `[(msg, item, args, kwarg),...]`
If `args` and `kwargs` are not part of a tuple, they are taken from the
current `args` and `kwargs` provi... |
def _srvc_check_hdf_properties(self, traj):
"""Reads out the properties for storing new data into the hdf5file
:param traj:
The trajectory
"""
for attr_name in HDF5StorageService.ATTR_LIST:
try:
config = traj.f_get('config.hdf5.' + attr_name).f... |
def _srvc_store_several_items(self, iterable, *args, **kwargs):
"""Stores several items from an iterable
Iterables are supposed to be of a format like `[(msg, item, args, kwarg),...]`
If `args` and `kwargs` are not part of a tuple, they are taken from the
current `args` and `kwargs` pro... |
def _srvc_opening_routine(self, mode, msg=None, kwargs=()):
"""Opens an hdf5 file for reading or writing
The file is only opened if it has not been opened before (i.e. `self._hdf5file is None`).
:param mode:
'a' for appending
'r' for reading
Unfortuna... |
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