def __init__(self, paramtree=None, measuretree=None,
paramfile=PARAMFILE, measurefile=MEASUREFILE,
initial_plug='random', reduce_p=True,
verbose=False):
"""
Metaphase instanciation method
:param duration: The duration of the mitosis in seconds (defaults to 900)
:type duration: float
:param paramtree: The paramtree contains the parameters for the simulation
if paramtree is None, the parameters are read
from the file paramfile. Defaults to None.
:type paramtree: ParamTree instance or None
:param measuretree: The measuretree contains the observed characteristics
of the mitosis e.g. metaphase spindle elongation rate, etc.
if measuretree is None, the measures are read from the file
indicated by the measurefile argument. Defaults to None.
:type measuretree: ParamTree instance or None
:param paramfile: Path to a xml file to read the parameters from. Defaults to the
file params.xml in the module's default directory. Other parameter
files can be produced by editing and changing the default one.
If the paramtree argument is not None, paramfile is ignored
:type paramfile: string
:param measurefile: Path to a xml file to read the measures from. Defaults to the
file measures.xml in the module's default directory.
Other measure files can be produced by editing and changing
the default one. If the measuretree argument is not None, measurefile
is ignored
:type measurefile: string
:param initial_plug: Defines globally the initial attachment states.
This argument can have the following values:
* 'null': all kinetochores are detached
* 'amphitelic': all chromosmes are amphitelic
* 'random': all attachement site can be bound to
either pole or deteched with equal prob.
* 'monotelic': right kinetochores are attached to the same pole,
left ones are detached
* 'syntelic' : all kinetochores are attached to the same pole
:type initial_plug: string or None
:param reduce_p: If True, changes the parameters according to the measures
so that the simulation average behaviour complies with
the data in the measures dictionary
:type reduce_p: bool
"""
# Enable or disable log console
self.verbose = verbose
logger = logging.getLogger(__name__)
if not self.verbose:
logger.disabled = True
else:
logger.disabled = False
if paramtree is None:
self.paramtree = ParamTree(paramfile)
else:
self.paramtree = paramtree
if measuretree is None:
self.measuretree = ParamTree(measurefile, adimentionalized=False)
else:
self.measuretree = measuretree
if reduce_p:
parameters.reduce_params(self.paramtree, self.measuretree)
logger.info('Parameters loaded')
params = self.paramtree.relative_dic
# Reset explicitely the unit parameters to their
# dimentionalized value
params['Vk'] = self.paramtree.absolute_dic['Vk']
params['Fk'] = self.paramtree.absolute_dic['Fk']
params['dt'] = self.paramtree.absolute_dic['dt']
self.KD = KinetoDynamics(params, initial_plug=initial_plug)
dt = self.paramtree.absolute_dic['dt']
duration = self.paramtree.absolute_dic['span']
self.num_steps = int(duration / dt)
self.KD.anaphase = False
self.timelapse = np.arange(0, duration, dt)
self.report = []
self.delay = -1
self.observations = {}
logger.info('Simulation initialized')
logger.disabled = False
def __init__(self, results_path,
nsimu,
name="",
ncore=None,
paramtree=None,
measuretree=None,
paramfile=PARAMFILE,
measurefile=MEASUREFILE,
verbose=True,
name_without_date=False):
"""
:results_path: The path where simulation results are stored
:type results_path: string
:nsimu: Number of simulation to run
:type nsimu: int
:ncore: Number of process to launch at the same time
:type ncore: int
:param paramtree: The paramtree contains the parameters for the simulation
if paramtree is None, the parameters are read
from the file paramfile. Defaults to None.
:type paramtree: ParamTree instance or None
:param measuretree: The measuretree contains the observed characteristics
of the mitosis e.g. metaphase spindle elongation rate, etc.
if measuretree is None, the measures are read from the file
indicated by the measurefile argument. Defaults to None.
:type measuretree: ParamTree instance or None
:param paramfile: Path to a xml file to read the parameters from. Defaults to the
file params.xml in the module's default directory. Other parameter
files can be produced by editing and changing the default one.
If the paramtree argument is not None, paramfile is ignored
:type paramfile: string
:param measurefile: Path to a xml file to read the measures from. Defaults to the
file measures.xml in the module's default directory.
Other measure files can be produced by editing and changing
the default one. If the measuretree argument is not None, measurefile
is ignored
:type measurefile: string
"""
# Enable or disable log console
self.verbose = verbose
logger = logging.getLogger(__name__)
if not self.verbose:
logger.disabled = True
else:
logger.disabled = False
if paramtree is None:
self.paramtree = ParamTree(paramfile)
else:
self.paramtree = paramtree
if measuretree is None:
self.measuretree = ParamTree(measurefile, adimentionalized=False)
else:
self.measuretree = measuretree
# Reduce parameters
parameters.reduce_params(self.paramtree, self.measuretree)
self.results_path = results_path
self.nsimu = nsimu
if not ncore:
self.ncore = multiprocessing.cpu_count()
else:
self.ncore = ncore
self.last_progress = 0
self.name = name
# Make result directory
if not os.path.exists(self.results_path):
os.makedirs(self.results_path)
# Results directory according to date and time
if name_without_date and name:
dirname = name
else:
now = datetime.datetime.now()
if name:
dirname = now.strftime("%Y.%m.%d") + "_" + name
else:
dirname = now.strftime("%Y.%m.%d")
self.results_path = os.path.join(self.results_path, dirname)
# TODO: Ugly fix
if os.path.isdir(self.results_path):
self.results_path += "_2"
# Remove existing directory of it exist
if os.path.exists(self.results_path):
shutil.rmtree(self.results_path)
os.makedirs(self.results_path)
# Save params.xml and measures.xml in results dir
self.paramtree.save(os.path.join(self.results_path, "params.xml"))
self.measuretree.save(os.path.join(self.results_path, "measures.xml"))
self.raw_results_path = os.path.join(self.results_path, "raw")
os.makedirs(self.raw_results_path)
# Redirect log to run.log
logfile = os.path.join(self.results_path, "run.log")
handler = logging.FileHandler(logfile)
logging.getLogger(__name__).addHandler(handler)
def __init__(self, results_path,
nsimu,
name="",
ncore=None,
paramtree=None,
measuretree=None,
paramfile=PARAMFILE,
measurefile=MEASUREFILE,
verbose=True,
parameter_to_explore={},
pool_eval=False,
name_without_date=False):
"""
"""
if not parameter_to_explore:
raise Exception("No parameter to explore found !")
# Enable or disable log console
self.verbose = verbose
logger = logging.getLogger(__name__)
if not self.verbose:
logger.disabled = True
else:
logger.disabled = False
if paramtree is None:
self.paramtree = ParamTree(paramfile)
else:
self.paramtree = paramtree
if measuretree is None:
self.measuretree = ParamTree(measurefile, adimentionalized=False)
else:
self.measuretree = measuretree
# Reduce parameters
parameters.reduce_params(self.paramtree, self.measuretree)
self.parameter_to_explore = parameter_to_explore
self.results_path = results_path
self.nsimu = nsimu
self.nparam = len(self.parameter_to_explore['vector'])
self.total_simu = self.nsimu * self.nparam
self.last_progress = 0
self.name = name
self.ncore = ncore
self.pool_eval = pool_eval
# Make result directory
if not os.path.exists(self.results_path):
os.makedirs(self.results_path)
# Results directory according to date and time
if name_without_date and name:
dirname = name
else:
now = datetime.datetime.now()
if name:
dirname = now.strftime("%Y.%m.%d") + "_" + name
else:
dirname = now.strftime("%Y.%m.%d")
self.results_path = os.path.join(self.results_path, dirname)
# Remove existing directory of it exist
if os.path.exists(self.results_path):
shutil.rmtree(self.results_path)
os.makedirs(self.results_path)
# Redirect log to run.log
logfile = os.path.join(self.results_path, "run.log")
handler = logging.FileHandler(logfile)
logging.getLogger(__name__).addHandler(handler)
