Source code for sbmlsim.simulation.scan

"""Scan simulation.

Allows scans over other simulations.
from copy import deepcopy
from typing import Dict, List

import numpy as np
from sbmlutils import log

from sbmlsim.simulation import AbstractSim, Dimension
from sbmlsim.units import UnitsInformation

[docs]logger = log.get_logger(__name__)
[docs]class ScanSim(AbstractSim): """A scan simulation over another AbstractSim. FIXME: probably not necessary to make this a simulation. """ def __init__( self, simulation: AbstractSim, dimensions: List[Dimension] = None, mapping: Dict[str, int] = None, ): """Scan a simulation. Parameters or initial conditions can be scanned. Multiple parameters will result in a multi-dimensional scan. If the changes should be applied to a later timecourse in the timecourse simulation the mapping dictionary can be used to map the changes of a given dimension on the respective timecourse index (starting from index 0). E.g., mapping = {dim_1: 1} will apply the changes of 'dim_1' on the second timecouse in the timecourse simulation. :param simulation: simulation to scan over the given parameters :param scan: dictionary of parameters or conditions to scan :param mapping: map of changes to parts of simulations """ self.simulation = simulation if dimensions is None: # handling the simple simulation case dimensions = [Dimension("dim0", index=np.arange(1))] self.dimensions = dimensions dimension_keys = [dim.dimension for dim in self.dimensions] if len(dimension_keys) > len(set(dimension_keys)): raise ValueError(f"duplicate dimension keys in scan: {dimension_keys}") if mapping is None: # if no mapping is provided than the changes map on the # initial part of the simulation mapping = {dim.dimension: 0 for dim in self.dimensions} if len(mapping) != len(dimensions): raise ValueError( f"mapping '{mapping}' incompatible with dimensions " f"'{dimensions}'." ) self.mapping = mapping
[docs] def __repr__(self) -> str: """Get representation.""" return ( f"Scan({self.simulation.__class__.__name__}: "
f"[{', '.join([str(d) for d in self.dimensions])}])" )
[docs] def dimensions(self) -> List[Dimension]: """Get dimensions.""" return self.dimensions
[docs] def get_dimension(self, key: str) -> Dimension: """Get dimension by key.""" for dim in self.dimensions: if dim.dimension == dim: return dim raise KeyError(f"Dimension with key '{key}' does not exist.")
[docs] def indices(self): """Get indices of all combinations.""" return Dimension.indices_from_dimensions(self.dimensions)
[docs] def add_model_changes(self, model_changes: Dict) -> None: """Add model changes to first timecourse.""" # import here to avoid circular import from sbmlsim.simulation import TimecourseSim if self.simulation and isinstance(self.simulation, TimecourseSim): self.simulation.add_model_changes(model_changes)
[docs] def normalize(self, uinfo: UnitsInformation): """Normalize units in scan. Requires normalization of timecourse simulation as well as all dimensions in the scan. """ # normalize simulation # logger.error("NORMALIZING SCAN") self.simulation.normalize(uinfo=uinfo) # normalize changes in all dimensions for scan_dim in self.dimensions: scan_dim.changes = UnitsInformation.normalize_changes( scan_dim.changes, uinfo=uinfo
[docs] def to_simulations(self): """Flatten the scan to individual simulations. Here the changes are appended. Scan should be normalized before calling this function. Necessary to track the results. """ # create all combinations of the scan indices = self.indices() # create respective simulations simulations = [] for index_list in indices: sim_new = deepcopy(self.simulation) # TODO: support additional simulation types (currently # only Timecourses assumed. for k_dim, k_index in enumerate(index_list): # add all changes for the given dimension and index dim = self.dimensions[k_dim] changes = dim.changes map_index = self.mapping[dim.dimension] # changes have to be applied to correct part of simulation tc = sim_new.timecourses[map_index] for key in changes.keys(): value = changes[key][k_index] tc.add_change(key, value) simulations.append(sim_new) return indices, simulations
if __name__ == "__main__": from sbmlsim.simulation import Timecourse, TimecourseSim from sbmlsim.units import UnitRegistry
[docs] ureg = UnitRegistry()
Q_ = ureg.Quantity uinfo = UnitsInformation( udict={k: "dimensionless" for k in ["X", "[X]", "n", "Y"]}, ureg=ureg ) scan2d = ScanSim( simulation=TimecourseSim( [ Timecourse( start=0, end=100, steps=100, changes={"X": Q_(10, "dimensionless")} ), Timecourse( start=0, end=60, steps=100, changes={"[X]": Q_(10, "dimensionless")} ), Timecourse( start=0, end=60, steps=100, changes={"X": Q_(10, "dimensionless")} ), ] ), dimensions=[ Dimension( "dim1", index=range(8), changes={ "n": Q_(np.linspace(start=2, stop=10, num=8), "dimensionless"), }, ), Dimension( "dim2", index=range(4), changes={ "Y": Q_(np.linspace(start=10, stop=20, num=4), "dimensionless"), }, ), ], ) indices, sims = scan2d.to_simulations() scan2d.normalize(uinfo=uinfo)