def __init__(self):
self.log_pa = init_log()
self._processes = {}
self._var_stack = {}
self._actions = []
self._seen = {}
self.systemeq = None
self.rate_parser = RateParser()
def __init__(self, rates):
self._visitstack= []
self.graph = ModelSSGraph()
self.log = init_log()
self.seq_components = {}
self.shared_actions = {}
self.operators = []
self.components = []
self.ss = StateSpace()
self.rates = rates
def __init__(self, **kwargs):
""" Create PEPA model instance and fill the fields """
self.args = kwargs
self.processes = {}
self.systemeq = None
self.rate_definitions = {}
self.components = {}
# from BU alg, get rid of it
self.tw = None
self.ss = None
self.log = init_log()
self._solver = None
self.log.info("Starting got args {}".format(kwargs))
self.name = os.path.basename(kwargs["file"])
self._parse_read_model(kwargs["file"])
def __init__(self, **kwargs):
""" Create PEPA model instance and fill the fields """
self.args = kwargs
self.processes = {}
self.systemeq = None
self.rate_definitions = {}
self.components = {}
# from BU alg, get rid of it
self.tw = None
self.ss = None
self.log = init_log()
self._solver = None
self.log.info("Starting got args {}".format(kwargs))
self.name = os.path.basename(kwargs["file"])
self._parse_read_model(kwargs["file"])
def __init__(self, **kwargs):
""" Create PEPA model instance and fill the fields """
self.args = kwargs
# Set up model_filename and model_string depending upon which is
# is set in the arguments.
self.model_filename = kwargs.get("file", None)
self.model_string = kwargs.get("modelstring", None)
self.name = os.path.basename(kwargs.get("name", self.model_filename))
# In case the name is still None, we set it to a default
if self.name == None:
self.name = "model"
self.processes = {}
self.systemeq = None
self.rate_definitions = {}
self.components = {}
# from BU alg, get rid of it
self.tw = None
self.ss = None
self.log = init_log()
self._solver = None
self.log.info("Starting got args {}".format(kwargs))
self._parse_model()
def __init__(self):
self.log_pa = init_log()
self._processes = {}
self._var_stack = {}
self._actions = []
self.systemeq = None
def main():
parser = argparse.ArgumentParser(
description="pypepa v{},"
" author {}, {}".format(__version__, __author__, __email__))
gen_args = parser.add_argument_group("General", "General arguments")
gen_args.add_argument("--log",
action="store",
dest="loglevel",
choices=["DEBUG", "INFO", "ERROR", "NONE"],
help="logging level",
default="NONE",
type=str)
sol_args = parser.add_argument_group("Solution",
"Solution related commands")
exp_args = parser.add_argument_group("Experimentations",
"Experimentations")
sol_args.add_argument("-s",
"--solver",
action="store",
dest="solver",
type=str,
choices=['direct', 'sparse'],
help="choose solver type DEFAULT: sparse",
default="sparse")
output_args = parser.add_argument_group("Output", "Output based options")
parser.add_argument("file", help="path to the model file")
output_args.add_argument("-gd",
"--generate_dots",
help="generate a Graphviz dot file for every"
"sequential component in a GENDOTS folder.",
action="store",
dest="gendots",
type=str)
output_args.add_argument("-st",
"--steady",
help="print steady state probability vector",
action="store_true")
output_args.add_argument("-th",
"--performance",
help="print throughoutput of actions",
action="store_true",
dest="top")
output_args.add_argument("-tr",
"--transient",
help="print throughoutput of actions",
action="store",
dest="trantime",
type=int)
# output_args.add_argument("-ut", "--utilization",
# help="print utilization of action",
# action="store_true", dest="util")
output_args.add_argument("-f",
"--format",
dest="format",
type=str,
choices=["graph", "console", "csv"],
help="format for -st -th -varrate",
default="console")
output_args.add_argument("-o",
"--output",
dest="output",
type=str,
action="store",
help="output file valid when format cvs")
exp_args.add_argument("-var",
"--variable",
help="more or one variables in format"
"rate:RATENAME:r:START,STOP,STEP"
"or rate:RATENAME:l:val1,val2,val3",
action="append",
dest="variables")
exp_args.add_argument("-val", "--value", action="store", dest="yvar")
exp_args.add_argument("--actionth",
help="throughoutput of action on the Y axis",
dest="actionth",
action="store",
metavar="action name")
args = parser.parse_args()
logger = init_log(log_level=args.loglevel)
pargs = {"file": args.file, "solver": args.solver}
if args.gendots:
pm = PEPAModel(**pargs)
import os
if os.path.isdir(args.gendots):
pass
else:
os.makedirs(args.gendots)
pm.generate_dots(args.gendots)
sys.exit(0)
if args.variables and args.yvar:
variables = decode_variables(args.variables)
if len(variables) == 1:
pm = PEPAModel(**pargs)
pm.derive()
result = experiment(variables, args.yvar, pm)
if args.format == "graph":
plot_2d(result[0],
result[1],
lw=2,
action="show",
xlab=args.yvar,
ylab=variables[0].varval)
elif args.format == "csv":
with open("{}.csv".format(args.output), "w") as f:
for i in range(0, len(result[0])):
f.write("{}, {}\n".format(result[0][i], result[1][i]))
elif len(variables) == 2:
pm = PEPAModel(**pargs)
pm.derive()
result = experiment(variables, args.yvar, pm)
plot_3d(result[0],
result[1],
result[2],
action="show",
xlab=args.yvar,
ylab=variables[0].varval)
else:
print("Wrong number of -var, either one or two")
sys.exit(1)
pm = PEPAModel(**pargs)
if args.steady or args.top:
pm.steady_state()
print("Statespace of {} has {} states \n".format(
args.file, len(pm.get_steady_state_vector())))
if args.trantime:
tr = pm.transient(0, int(args.trantime))
print("Transient analysis from time %d to %d" % (0, args.trantime))
args.output = "{}-transient.csv".format(pm.name)
pretty_print_vector(tr,
pm.get_state_names(),
fmt=args.format,
outfile=args.output)
if args.steady:
print("Steady state vector")
args.output = "{}-steady.csv".format(pm.name)
pretty_print_vector(pm.get_steady_state_vector(),
pm.get_state_names(),
fmt=args.format,
outfile=args.output)
if args.top:
print("Throuhoutput (successful action completion in one time unit)")
print("Output:{}".format(args.format))
args.output = "{}-throughput.csv".format(pm.name)
pretty_print_performance(pm.get_throughoutput(),
fmt=args.format,
outfile=args.output)
def __init__(self):
self.actionset = []
self.derivatives = []
self.log = init_log()
def __init__(self):
self.max_length = 0
self.log = init_log()
def main():
parser = argparse.ArgumentParser(description="pypepa v{},"
" author {}, {}".format(__version__,
__author__, __email__))
gen_args = parser.add_argument_group("General", "General arguments")
gen_args.add_argument("--log", action="store", dest="loglevel",
choices=["DEBUG", "INFO", "ERROR", "NONE"],
help="logging level",
default="ERROR", type=str)
sol_args = parser.add_argument_group("Solution",
"Solution related commands")
exp_args = parser.add_argument_group("Experimentations",
"Experimentations")
sol_args.add_argument("-s", "--solver", action="store",
dest="solver",type=str,
choices=['direct', 'sparse'],
help="choose solver type DEFAULT: sparse",
default="sparse")
output_args = parser.add_argument_group("Output", "Output based options")
parser.add_argument("file", help="path to the model file")
output_args.add_argument("-gd", "--generate_dots",
help="generate a graphviz dot file for every"
"sequential component in a GENDOTS folder and"
"for the whole state space",
action="store", dest="gendots", type=str)
output_args.add_argument("-st", "--steady",
help="print steady state probability vector",
action="store_true")
output_args.add_argument("-th", "--performance",
help="print throughoutput of actions",
action="store_true", dest="top")
output_args.add_argument("-tr", "--transient",
help="print throughoutput of actions",
action="store", dest="trantime", type=int)
# output_args.add_argument("-ut", "--utilization",
# help="print utilization of action",
# action="store_true", dest="util")
output_args.add_argument("-f", "--format", dest="format", type=str,
choices=["graph", "console", "csv"],
help="format for -st -th -varrate", default="console")
output_args.add_argument("-o", "--output", dest="output", type=str,
action="store",
help="output file valid when format cvs")
exp_args.add_argument("-var", "--variable",
help="one or more variables in format"
"rate:RATENAME:r:START,STOP,STEP"
"or rate:RATENAME:l:val1,val2,val3",
action="append", dest="variables")
exp_args.add_argument("-val", "--value", action="store", dest="yvar")
# exp_args.add_argument("--actionth",
# help="throughoutput of action on the Y axis",
# dest="actionth", action="store",
# metavar="action name")
args = parser.parse_args()
logger = init_log(log_level=args.loglevel)
pargs = {"file": args.file, "solver" : args.solver}
if args.gendots:
try:
pm = PEPAModel(**pargs)
except Exception as e:
print("Exception occured:", e)
sys.exit(1)
import os
if os.path.isdir(args.gendots):
pass
else:
os.makedirs(args.gendots)
pm.generate_dots(args.gendots)
sys.exit(0)
if args.variables and args.yvar:
variables = decode_variables(args.variables)
if len(variables) == 1:
pm = PEPAModel(**pargs)
pm.derive()
result = experiment(variables, args.yvar, pm)
if args.format == "graph":
plot_2d(result[0], result[1], lw=2, action="show",
xlab=args.yvar, ylab=variables[0].varval)
elif args.format == "csv":
with open("{}.csv".format(args.output), "w") as f:
for i in range(0, len(result[0])):
f.write("{}, {}\n".format(result[0][i], result[1][i]))
elif len(variables) == 2:
pm = PEPAModel(**pargs)
pm.derive()
result = experiment(variables, args.yvar, pm)
plot_3d(result[0], result[1], result[2], action="show",
xlab=args.yvar, ylab=variables[0].varval)
else:
print("Wrong number of -var, either one or two")
sys.exit(1)
try:
pm = PEPAModel(**pargs)
except Exception as e:
print("Exception occured: ", e)
sys.exit(1)
if args.steady or args.top:
pm.steady_state()
print("Statespace of {} has {} states \n".format(args.file,
len(pm.get_steady_state_vector() )))
if args.trantime:
tr = pm.transient(0, int(args.trantime))
print("Transient analysis from time %d to %d" % (0, args.trantime))
args.output = "{}-transient.csv".format(pm.name)
pretty_print_vector(tr,
pm.get_state_names(),
fmt=args.format,
outfile=args.output
)
if args.steady:
print("Steady state vector")
args.output = "{}-steady.csv".format(pm.name)
pretty_print_vector(pm.get_steady_state_vector(),
pm.get_state_names(),
fmt=args.format,
outfile=args.output
)
if args.top:
print("Throuhoutput (successful action completion in one time unit)")
print("Output:{}".format(args.format))
args.output = "{}-throughput.csv".format(pm.name)
pretty_print_performance(pm.get_throughoutput(), fmt=args.format,
outfile=args.output)