Source code for pysb.simulator.kappa

from pysb.simulator.base import Simulator, SimulationResult, SimulatorException
from pysb.generator.kappa import KappaGenerator
from pysb.kappa import KasimInterfaceError, _parse_kasim_outfile
import numpy as np
import os
import tempfile
import shutil
import pysb.pathfinder as pf
import subprocess

[docs]class KappaSimulator(Simulator): """ Simulate a model using Kappa """ _supports = { 'multi_initials': True, 'multi_param_values': True } def __init__(self, model, tspan=None, cleanup=True, verbose=False): super(KappaSimulator, self).__init__(model, tspan=tspan, verbose=verbose) self.cleanup = cleanup self._outdir = None
[docs] def run(self, tspan=None, initials=None, param_values=None, n_runs=1, output_dir=None, output_file_basename=None, cleanup=None, **additional_args): """ Simulate a model using Kappa Parameters ---------- tspan: vector-like time span of simulation initials: vector-like, optional initial conditions of model param_values : vector-like or dictionary, optional Values to use for every parameter in the model. Ordering is determined by the order of model.parameters. If not specified, parameter values will be taken directly from model.parameters. n_runs: int number of simulations to run output_dir : string, optional Location for temporary files generated by Kappa. If None (the default), uses a temporary directory provided by the system. A temporary directory with a random name is created within the supplied location. output_file_basename : string, optional This argument is used as a prefix for the temporary Kappa output directory, rather than the individual files. cleanup : bool, optional If True (default), delete the temporary files after the simulation is finished. If False, leave them in place (Useful for debugging). The default value, None, means to use the value specified in :py:func:`__init__`. additional_args: kwargs, optional Additional arguments to pass to Kappa * seed : int, optional Random number seed for Kappa simulation * perturbation : string, optional Optional perturbation language syntax to be appended to the Kappa file. See KaSim manual for more details. Examples -------- >>> import numpy as np >>> from pysb.examples import michment >>> from pysb.simulator import KappaSimulator >>> sim = KappaSimulator(michment.model, tspan=np.linspace(0, 1)) >>> x = """ super(KappaSimulator, self).run(tspan=tspan, initials=initials, param_values=param_values, _run_kwargs=locals() ) if cleanup is None: cleanup = self.cleanup tspan_lin_spaced = np.allclose( self.tspan, np.linspace(self.tspan[0], self.tspan[-1], len(self.tspan)) ) if not tspan_lin_spaced or self.tspan[0] != 0.0: raise SimulatorException('Kappa requires tspan to be linearly ' 'spaced starting at t=0') points = len(self.tspan) time = self.tspan[-1] plot_period = time / (len(self.tspan) - 1) if output_file_basename is None: output_file_basename = 'tmpKappa_%s_' % base_directory = tempfile.mkdtemp(prefix=output_file_basename, dir=output_dir) base_filename = os.path.join(base_directory, kappa_filename_pattern = base_filename + '_{}.ka' out_filename_pattern = base_filename + '_{}_run{}.out' base_args = ['-u', 'time', '-l', str(time), '-p', '%.5f' % plot_period] if 'seed' in additional_args: seed = additional_args.pop('seed') base_args.extend(['-seed', str(seed)]) kasim_path = pf.get_path('kasim') n_param_sets = self.initials_length gen = KappaGenerator(self.model, _exclude_ic_param=True) file_data_base = gen.get_content() # Check if a perturbation has been set try: perturbation = additional_args.pop('perturbation') except KeyError: perturbation = None # Check no unknown arguments have been set if additional_args: raise ValueError('Unknown argument(s): {}'.format( ', '.join(additional_args.keys()) )) # Kappa column names, for sanity check kappa_col_names = tuple(['time'] + [ for o in self.model.observables]) tout = [] observable_traj = [] try: for pset_idx in range(n_param_sets): file_data = file_data_base + '' for param, param_value in zip(self.model.parameters, self.param_values[pset_idx]): file_data += "%var: '{}' {:e}\n".format(, param_value) file_data += '\n' for cp, values in self.initials_dict.items(): file_data += "%init: {} {}\n".format( values[pset_idx], gen.format_complexpattern(cp) ) # If any perturbation language code has been passed in, add it # to the Kappa file: if perturbation: file_data += '%s\n' % perturbation # Generate the Kappa model code from the PySB model and write # it to the Kappa file: kappa_filename = kappa_filename_pattern.format(pset_idx) with open(kappa_filename, 'w') as kappa_file: self._logger.debug('Kappa file contents:\n\n' + file_data) kappa_file.write(file_data) for sim_rpt in range(n_runs): # Run Kappa out_filename = out_filename_pattern.format(pset_idx, sim_rpt) args = [kasim_path] + base_args + [ '-i', kappa_filename, '-o', out_filename] # Run KaSim self._logger.debug('Running: {}'.format(' '.join(args))) p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=base_directory) for line in p.stdout: self._logger.debug('@@' + line.decode('utf8')[:-1]) (p_out, p_err) = p.communicate() if p.returncode: raise KasimInterfaceError( p_out.decode('utf8') + '\n' + p_err.decode('utf8')) # The simulation data, as a numpy array data = _parse_kasim_outfile(out_filename) # Sanity check that observables are in correct order assert data.dtype.names == kappa_col_names data = data.view('<f8') # Handle case with single row output if data.ndim == 1: data.shape = (1, data.shape[0]) # Parse into format tout.append(data[:, 0]) observable_traj.append(data[:, 1:]) finally: if cleanup: shutil.rmtree(base_directory) return SimulationResult(self, tout=tout, observables_and_expressions=observable_traj, simulations_per_param_set=n_runs)