class Experiment(object):
"""
The Experiment object captures the state of a experiment
Properties:
actions
A list of Actions to be run sorted by priority.
config
A Config object storing the configuration for the experiment
data
A dict that can be used to store additional data. For example, see the
'type_count' value, which is used to store the counts of different cell
types (for cells that have different types) across the population.
This is faster than scanning the population whenever this information
is needed.
epoch
An integer storing the current epoch (unit of time)
plugin_manager
A PluginManager object which manages all Plugins for the experiment
population
A Population object that keeps information about the Cells (organisms)
and their interactions
proceed
Boolean value indicating whether or not the experiment should continue.
resources
A hash of available resources. The key is the name of the resource,
and the value is a Resource object.
uuid
A practically unique identifier for the experiment. (RFC 4122 ver 4)
label
A unique label identifying the configuration for this Experiment
config_section
The section of the config file in which to find settings for this
Experiment
"""
def __init__(self, configfile=None, seed=-1, label=None):
"""Initialize a Experiment object
Parameters:
*configfile*
Name of configuration file for the experiment. If none is
provided, the experiment will either use defaults for all
parameters or values provided to the Config object elsewhere (e.g.,
through the command-line or GUI program).
*seed*
Seed for pseudorandom number generator. If undefined, the current
time will be used.
*label*
A unique string identifying the configuration for this experiment.
By default, Experiment will look for settings in the [Experiment]
section of the config file. If a label is specified, it will look
in [Experiment:label].
"""
self.config = Config(experiment=self, filename=configfile)
self.epoch = 0
self.is_setup = False
self.proceed = True
self.seed = seed
self.uuid = uuid.uuid4()
self.data = {}
self.resources = {}
self.actions = []
self.label = label
if self.label:
self.config_section = "Experiment:{label}".format(label=self.label)
else:
self.config_section = "Experiment"
if not self.config.has_section(self.config_section):
raise ConfigurationError("Configuration section '{sec}' not defined".format(sec=self.config_section))
version_string = self.config.get(self.config_section, "seeds_version")
if version_string != None:
version = parse_version_string(version_string)
if not is_valid_version(ver=seeds.VERSION, target=version['version'], op=version['operator']):
raise SEEDSVersionError(version=version['version'], operator=version['operator'])
else:
self.config.set(self.config_section, 'seeds_version', seeds.__version__)
def setup(self):
"""Set up the Experiment including its Population, Resources, and Actions"""
if self.seed == -1:
configseed = self.config.getint(self.config_section, "seed", default=-1)
if configseed != -1:
self.seed = configseed
else:
self.seed = int(time.time()*10)
random.seed(self.seed)
self.config.set(self.config_section, 'seed', self.seed)
self.experiment_epochs = self.config.getint(self.config_section, 'epochs',
default=-1)
# Create the data directory. If the directory already exists, move it
# to a new directory named after the current name with a timestamp
# appended
data_dir = self.config.get(section=self.config_section,
name='data_dir',
default='data')
if os.path.exists(data_dir):
newname = data_dir + '-' + datetime.datetime.now().strftime("%Y%m%d%H%M%S")
shutil.move(data_dir, newname)
os.mkdir(data_dir)
# Create a plugin manager. Append the system-wide plugins
# to the list of plugin sources.
self.plugin_manager = PluginManager(self)
global_plugin_path = os.path.join(os.path.dirname(seeds.__file__), "plugins")
for d in ["cell", "topology", "action", "resource"]:
plugin_path = os.path.join(global_plugin_path, d)
self.plugin_manager.append_dir(plugin_path)
# Initialize all of the Resources
self.data['resources'] = {}
resourcestring = self.config.get(self.config_section, "resources")
if resourcestring:
reslist = [res.strip() for res in resourcestring.split(',')]
for res in reslist:
sec = "Resource:{resname}".format(resname=res)
if not self.config.has_section(sec):
raise ConfigurationError("No configuration for resource '{resname}'".format(resname=res))
r = Resource(experiment=self, label=res)
if r.name not in self.resources:
self.resources[r.name] = r
else:
warn("Resource '{resname}' listed twice. Skipping duplicates.".format(resname=res))
# Create the Population
self.data['population'] = {}
population_raw = self.config.get(self.config_section, "population", default="Population")
parsed = population_raw.split(':')
if parsed[0] != "Population":
raise ConfigurationError("Population configuration section name must begin with 'Population'")
if len(parsed) > 1:
poplabel = parsed[1]
else:
poplabel = None
self.population = Population(experiment=self, label=poplabel)
# Setup the list of Actions to be run
actionstring = self.config.get(section=self.config_section,
name="actions")
if actionstring:
actionlist = [action.strip() for action in actionstring.split(',')]
for item in actionlist:
parsed = item.split(':')
action = parsed[0]
if len(parsed) > 1:
label = parsed[1]
else:
label = None
oref = self.plugin_manager.get_action_plugin(action)
a = oref(self, label=label)
self.add_action(a)
self.is_setup = True
def update(self):
"""Update the Experiment and all of its objects"""
if not self.is_setup:
self.setup()
[a.update() for a in self.actions]
[self.resources[res].update() for res in self.resources]
self.population.update()
self.epoch += 1
# If we've surpassed the configured number of epochs to run for, set
# proceed to false
if self.experiment_epochs != -1 and self.epoch >= self.experiment_epochs:
self.proceed = False
def __iter__(self):
"""Experiment is an iterator, so it can be used with commands such as
e = Experiment(....)
for epoch in e:
print "Updated Experiment. Now at epoch %d" % (epoch)
"""
return self
def next(self):
"""Proceed with the experiment. Update the Experiment and return the
current epoch. Note: this is for Python 2 support and merely uses the
__next__ method from Python 3"""
return self.__next__()
def __next__(self):
"""Proceed with the experiment. Update the Experiment and return the current epoch"""
if not self.proceed:
raise StopIteration
else:
self.update()
return self.epoch
def end(self):
"""Set the experiment to end after this epoch"""
self.proceed = False
def teardown(self):
"""Perform any necessary cleanup at the end of a run"""
[a.teardown() for a in self.actions]
[self.resources[res].teardown() for res in self.resources]
self.population.teardown()
def is_resource_defined(self, name):
"""Helper function to determine whether a given resource has been
defined or not
"""
return self.resources.has_key(name)
def get_resource(self, name):
"""Helper function to get the Resource object with the given name. If
the resource is not defined, ResourceNotDefinedError is thrown.
"""
try:
r = self.resources[name]
return r
except KeyError:
raise ResourceNotDefinedError(name)
def add_action(self, action):
"""Add an Action to the list of actions to be scheduled.
Parameters:
*action*
An instantiated Action object
"""
loaded_actions = [a.config_section for a in self.actions]
if action.config_section in loaded_actions:
warn("Action '{aname}' listed twice. Skipping duplicates.".format(aname=action.config_section))
else:
self.actions.append(action)
self.actions = sorted(self.actions, reverse=True, key=lambda a: a.priority)
class Experiment(object):
"""
The Experiment object captures the state of a experiment
Properties:
actions
A list of Actions to be run sorted by priority.
config
A Config object storing the configuration for the experiment
data
A dict that can be used to store additional data. For example, see the
'type_count' value, which is used to store the counts of different cell
types (for cells that have different types) across the population.
This is faster than scanning the population whenever this information
is needed.
epoch
An integer storing the current epoch (unit of time)
plugin_manager
A PluginManager object which manages all Plugins for the experiment
population
A Population object that keeps information about the Cells (organisms)
and their interactions
proceed
Boolean value indicating whether or not the experiment should continue.
resources
A hash of available resources. The key is the name of the resource,
and the value is a Resource object.
uuid
A practically unique identifier for the experiment. (RFC 4122 ver 4)
label
A unique label identifying the configuration for this Experiment
config_section
The section of the config file in which to find settings for this
Experiment
"""
def __init__(self, configfile=None, seed=-1, label=None):
"""Initialize a Experiment object
Parameters:
*configfile*
Name of configuration file for the experiment. If none is
provided, the experiment will either use defaults for all
parameters or values provided to the Config object elsewhere (e.g.,
through the command-line or GUI program).
*seed*
Seed for pseudorandom number generator. If undefined, the current
time will be used.
*label*
A unique string identifying the configuration for this experiment.
By default, Experiment will look for settings in the [Experiment]
section of the config file. If a label is specified, it will look
in [Experiment:label].
"""
self.config = Config(experiment=self, filename=configfile)
self.epoch = 0
self.is_setup = False
self.proceed = True
self.seed = seed
self.uuid = uuid.uuid4()
self.data = {}
self.resources = {}
self.actions = []
self.label = label
if self.label:
self.config_section = "Experiment:{label}".format(label=self.label)
else:
self.config_section = "Experiment"
if not self.config.has_section(self.config_section):
raise ConfigurationError(
"Configuration section '{sec}' not defined".format(
sec=self.config_section))
version_string = self.config.get(self.config_section, "seeds_version")
if version_string != None:
version = parse_version_string(version_string)
if not is_valid_version(ver=seeds.VERSION,
target=version['version'],
op=version['operator']):
raise SEEDSVersionError(version=version['version'],
operator=version['operator'])
else:
self.config.set(self.config_section, 'seeds_version',
seeds.__version__)
def setup(self):
"""Set up the Experiment including its Population, Resources, and Actions"""
if self.seed == -1:
configseed = self.config.getint(self.config_section,
"seed",
default=-1)
if configseed != -1:
self.seed = configseed
else:
self.seed = int(time.time() * 10)
random.seed(self.seed)
self.config.set(self.config_section, 'seed', self.seed)
self.experiment_epochs = self.config.getint(self.config_section,
'epochs',
default=-1)
# Create the data directory. If the directory already exists, move it
# to a new directory named after the current name with a timestamp
# appended
data_dir = self.config.get(section=self.config_section,
name='data_dir',
default='data')
if os.path.exists(data_dir):
newname = data_dir + '-' + datetime.datetime.now().strftime(
"%Y%m%d%H%M%S")
shutil.move(data_dir, newname)
os.mkdir(data_dir)
# Create a plugin manager. Append the system-wide plugins
# to the list of plugin sources.
self.plugin_manager = PluginManager(self)
global_plugin_path = os.path.join(os.path.dirname(seeds.__file__),
"plugins")
for d in ["cell", "topology", "action", "resource"]:
plugin_path = os.path.join(global_plugin_path, d)
self.plugin_manager.append_dir(plugin_path)
# Initialize all of the Resources
self.data['resources'] = {}
resourcestring = self.config.get(self.config_section, "resources")
if resourcestring:
reslist = [res.strip() for res in resourcestring.split(',')]
for res in reslist:
sec = "Resource:{resname}".format(resname=res)
if not self.config.has_section(sec):
raise ConfigurationError(
"No configuration for resource '{resname}'".format(
resname=res))
r = Resource(experiment=self, label=res)
if r.name not in self.resources:
self.resources[r.name] = r
else:
warn(
"Resource '{resname}' listed twice. Skipping duplicates."
.format(resname=res))
# Create the Population
self.data['population'] = {}
population_raw = self.config.get(self.config_section,
"population",
default="Population")
parsed = population_raw.split(':')
if parsed[0] != "Population":
raise ConfigurationError(
"Population configuration section name must begin with 'Population'"
)
if len(parsed) > 1:
poplabel = parsed[1]
else:
poplabel = None
self.population = Population(experiment=self, label=poplabel)
# Setup the list of Actions to be run
actionstring = self.config.get(section=self.config_section,
name="actions")
if actionstring:
actionlist = [action.strip() for action in actionstring.split(',')]
for item in actionlist:
parsed = item.split(':')
action = parsed[0]
if len(parsed) > 1:
label = parsed[1]
else:
label = None
oref = self.plugin_manager.get_action_plugin(action)
a = oref(self, label=label)
self.add_action(a)
self.is_setup = True
def update(self):
"""Update the Experiment and all of its objects"""
if not self.is_setup:
self.setup()
[a.update() for a in self.actions]
[self.resources[res].update() for res in self.resources]
self.population.update()
self.epoch += 1
# If we've surpassed the configured number of epochs to run for, set
# proceed to false
if self.experiment_epochs != -1 and self.epoch >= self.experiment_epochs:
self.proceed = False
def __iter__(self):
"""Experiment is an iterator, so it can be used with commands such as
e = Experiment(....)
for epoch in e:
print "Updated Experiment. Now at epoch %d" % (epoch)
"""
return self
def next(self):
"""Proceed with the experiment. Update the Experiment and return the
current epoch. Note: this is for Python 2 support and merely uses the
__next__ method from Python 3"""
return self.__next__()
def __next__(self):
"""Proceed with the experiment. Update the Experiment and return the current epoch"""
if not self.proceed:
raise StopIteration
else:
self.update()
return self.epoch
def end(self):
"""Set the experiment to end after this epoch"""
self.proceed = False
def teardown(self):
"""Perform any necessary cleanup at the end of a run"""
[a.teardown() for a in self.actions]
[self.resources[res].teardown() for res in self.resources]
self.population.teardown()
def is_resource_defined(self, name):
"""Helper function to determine whether a given resource has been
defined or not
"""
return self.resources.has_key(name)
def get_resource(self, name):
"""Helper function to get the Resource object with the given name. If
the resource is not defined, ResourceNotDefinedError is thrown.
"""
try:
r = self.resources[name]
return r
except KeyError:
raise ResourceNotDefinedError(name)
def add_action(self, action):
"""Add an Action to the list of actions to be scheduled.
Parameters:
*action*
An instantiated Action object
"""
loaded_actions = [a.config_section for a in self.actions]
if action.config_section in loaded_actions:
warn("Action '{aname}' listed twice. Skipping duplicates.".format(
aname=action.config_section))
else:
self.actions.append(action)
self.actions = sorted(self.actions,
reverse=True,
key=lambda a: a.priority)
def setup(self):
"""Set up the Experiment including its Population, Resources, and Actions"""
if self.seed == -1:
configseed = self.config.getint(self.config_section, "seed", default=-1)
if configseed != -1:
self.seed = configseed
else:
self.seed = int(time.time()*10)
random.seed(self.seed)
self.config.set(self.config_section, 'seed', self.seed)
self.experiment_epochs = self.config.getint(self.config_section, 'epochs',
default=-1)
# Create the data directory. If the directory already exists, move it
# to a new directory named after the current name with a timestamp
# appended
data_dir = self.config.get(section=self.config_section,
name='data_dir',
default='data')
if os.path.exists(data_dir):
newname = data_dir + '-' + datetime.datetime.now().strftime("%Y%m%d%H%M%S")
shutil.move(data_dir, newname)
os.mkdir(data_dir)
# Create a plugin manager. Append the system-wide plugins
# to the list of plugin sources.
self.plugin_manager = PluginManager(self)
global_plugin_path = os.path.join(os.path.dirname(seeds.__file__), "plugins")
for d in ["cell", "topology", "action", "resource"]:
plugin_path = os.path.join(global_plugin_path, d)
self.plugin_manager.append_dir(plugin_path)
# Initialize all of the Resources
self.data['resources'] = {}
resourcestring = self.config.get(self.config_section, "resources")
if resourcestring:
reslist = [res.strip() for res in resourcestring.split(',')]
for res in reslist:
sec = "Resource:{resname}".format(resname=res)
if not self.config.has_section(sec):
raise ConfigurationError("No configuration for resource '{resname}'".format(resname=res))
r = Resource(experiment=self, label=res)
if r.name not in self.resources:
self.resources[r.name] = r
else:
warn("Resource '{resname}' listed twice. Skipping duplicates.".format(resname=res))
# Create the Population
self.data['population'] = {}
population_raw = self.config.get(self.config_section, "population", default="Population")
parsed = population_raw.split(':')
if parsed[0] != "Population":
raise ConfigurationError("Population configuration section name must begin with 'Population'")
if len(parsed) > 1:
poplabel = parsed[1]
else:
poplabel = None
self.population = Population(experiment=self, label=poplabel)
# Setup the list of Actions to be run
actionstring = self.config.get(section=self.config_section,
name="actions")
if actionstring:
actionlist = [action.strip() for action in actionstring.split(',')]
for item in actionlist:
parsed = item.split(':')
action = parsed[0]
if len(parsed) > 1:
label = parsed[1]
else:
label = None
oref = self.plugin_manager.get_action_plugin(action)
a = oref(self, label=label)
self.add_action(a)
self.is_setup = True
def setup(self):
"""Set up the Experiment including its Population, Resources, and Actions"""
if self.seed == -1:
configseed = self.config.getint(self.config_section,
"seed",
default=-1)
if configseed != -1:
self.seed = configseed
else:
self.seed = int(time.time() * 10)
random.seed(self.seed)
self.config.set(self.config_section, 'seed', self.seed)
self.experiment_epochs = self.config.getint(self.config_section,
'epochs',
default=-1)
# Create the data directory. If the directory already exists, move it
# to a new directory named after the current name with a timestamp
# appended
data_dir = self.config.get(section=self.config_section,
name='data_dir',
default='data')
if os.path.exists(data_dir):
newname = data_dir + '-' + datetime.datetime.now().strftime(
"%Y%m%d%H%M%S")
shutil.move(data_dir, newname)
os.mkdir(data_dir)
# Create a plugin manager. Append the system-wide plugins
# to the list of plugin sources.
self.plugin_manager = PluginManager(self)
global_plugin_path = os.path.join(os.path.dirname(seeds.__file__),
"plugins")
for d in ["cell", "topology", "action", "resource"]:
plugin_path = os.path.join(global_plugin_path, d)
self.plugin_manager.append_dir(plugin_path)
# Initialize all of the Resources
self.data['resources'] = {}
resourcestring = self.config.get(self.config_section, "resources")
if resourcestring:
reslist = [res.strip() for res in resourcestring.split(',')]
for res in reslist:
sec = "Resource:{resname}".format(resname=res)
if not self.config.has_section(sec):
raise ConfigurationError(
"No configuration for resource '{resname}'".format(
resname=res))
r = Resource(experiment=self, label=res)
if r.name not in self.resources:
self.resources[r.name] = r
else:
warn(
"Resource '{resname}' listed twice. Skipping duplicates."
.format(resname=res))
# Create the Population
self.data['population'] = {}
population_raw = self.config.get(self.config_section,
"population",
default="Population")
parsed = population_raw.split(':')
if parsed[0] != "Population":
raise ConfigurationError(
"Population configuration section name must begin with 'Population'"
)
if len(parsed) > 1:
poplabel = parsed[1]
else:
poplabel = None
self.population = Population(experiment=self, label=poplabel)
# Setup the list of Actions to be run
actionstring = self.config.get(section=self.config_section,
name="actions")
if actionstring:
actionlist = [action.strip() for action in actionstring.split(',')]
for item in actionlist:
parsed = item.split(':')
action = parsed[0]
if len(parsed) > 1:
label = parsed[1]
else:
label = None
oref = self.plugin_manager.get_action_plugin(action)
a = oref(self, label=label)
self.add_action(a)
self.is_setup = True