modelbase2 0.1.79__py3-none-any.whl → 0.3.0__py3-none-any.whl

modelbase2/ode/mca.py

@@ -1,270 +0,0 @@
-from __future__ import annotations
-
-import copy
-import math
-import matplotlib.pyplot as plt
-import numpy as np
-import pandas as pd
-from ..types import Array, DataFrame, Series
-from ..utils.plotting import get_norm as _get_norm
-from ..utils.plotting import heatmap_from_dataframe as _heatmap_from_dataframe
-from .integrator import Assimulo
-from .model import Model
-from .simulator import Simulator
-from matplotlib import cm
-from matplotlib.axes import Axes
-from matplotlib.collections import QuadMesh
-from matplotlib.figure import Figure
-from typing import Optional, cast
-
-_DISPLACEMENT = 1e-4
-_DEFAULT_TOLERANCE = 1e-8
-
-
-def get_variable_elasticity(
-    m: Model,
-    variable: str,
-    y: dict[str, float],
-    displacement: float = _DISPLACEMENT,
-) -> Array:
-    """Get sensitivity of all rates to a change of the concentration of a variable.
-
-    Also called epsilon-elasticities. Not in steady state!
-    """
-    y_full = y | m.get_derived_variables(y)
-    old_concentration = y_full[variable]
-    fluxes: list[Array] = []
-    for new_concentration in (
-        old_concentration * (1 + displacement),
-        old_concentration * (1 - displacement),
-    ):
-        y_full[variable] = new_concentration
-        fluxes.append(m.get_fluxes(y_full, "array"))
-    elasticity_coef = (fluxes[0] - fluxes[1]) / (2 * displacement * old_concentration)
-    # normalise
-    y_full[variable] = old_concentration
-    flux_array = m.get_fluxes(y_full, "array")
-    elasticity_coef *= old_concentration / flux_array
-    return np.atleast_1d(np.squeeze(elasticity_coef))
-
-
-def get_variable_elasticities(
-    m: Model,
-    variables: list[str],
-    y: dict[str, float],
-    displacement: float = _DISPLACEMENT,
-) -> DataFrame:
-    """Get sensitivity of all rates to a change of the concentration of multiple variables.
-
-    Also called epsilon-elasticities. Not in steady state!
-    """
-    stoichiometries = m.get_stoichiometries().columns
-    elasticities = np.full(
-        shape=(len(variables), len(stoichiometries)), fill_value=np.nan
-    )
-    for i, variable in enumerate(variables):
-        elasticities[i] = get_variable_elasticity(
-            m=m,
-            variable=variable,
-            y=y,
-            displacement=displacement,
-        )
-    return pd.DataFrame(elasticities, index=variables, columns=stoichiometries)
-
-
-def get_constant_elasticity(
-    m: Model,
-    constant: str,
-    y: dict[str, float],
-    displacement: float = _DISPLACEMENT,
-) -> Array:
-    """Get sensitivity of all rates to a change of a constant value.
-
-    Also called pi-elasticities. Not in steady state!
-    """
-    m = copy.deepcopy(m)
-    old_value = m.constant_values[constant]
-    fluxes = []
-    for new_value in [old_value * (1 + displacement), old_value * (1 - displacement)]:
-        m.update_constant(constant, new_value)
-        fluxes.append(m.get_fluxes(y, "array"))
-    elasticity_coef = (fluxes[0] - fluxes[1]) / (2 * displacement * old_value)
-    # normalise
-    m.update_constant(constant, old_value)
-    fluxes_array = m.get_fluxes(y, "array")
-    elasticity_coef *= old_value / fluxes_array
-    return np.atleast_1d(np.squeeze(elasticity_coef))
-
-
-def get_constant_elasticities(
-    m: Model,
-    constants: list[str],
-    y: dict[str, float],
-    displacement: float = _DISPLACEMENT,
-) -> DataFrame:
-    """Get sensitivity of all rates to a change of multiple constant values.
-
-    Also called pi-elasticities. Not in steady state!
-    """
-    stoichiometries = m.get_stoichiometries().columns
-    elasticities = np.full(
-        shape=(len(constants), len(stoichiometries)), fill_value=np.nan
-    )
-    for i, constant in enumerate(constants):
-        elasticities[i] = get_constant_elasticity(
-            m=m,
-            constant=constant,
-            y=y,
-            displacement=displacement,
-        )
-    return pd.DataFrame(elasticities, index=constants, columns=stoichiometries)
-
-
-def _get_response_coefficients_single_constant(
-    m: Model,
-    constant: str,
-    y0: dict[str, float],
-    displacement: float = _DISPLACEMENT,
-    tolerance: float = _DEFAULT_TOLERANCE,
-) -> tuple[Optional[Series], Optional[Series]]:
-    """Get response of the steady state concentrations and fluxes to a change of the given constant."""
-    old_value = m.constant_values[constant]
-    m = copy.deepcopy(m)
-
-    # normalise
-    y_ss = Simulator(m, Assimulo, y0).simulate_to_steady_state(tolerance=tolerance)
-    if y_ss is None:
-        return None, None
-    y_full = y0 | m.get_derived_variables(y_ss)
-    y_ss_norm = old_value / np.fromiter(y_full.values(), dtype="float")
-    fluxes_norm = old_value / m.get_fluxes(y_full, return_type="array")
-
-    # scan
-    ss: list[Array] = []
-    fluxes: list[Array] = []
-    for new_value in [
-        old_value * (1 + displacement),
-        old_value * (1 - displacement),
-    ]:
-        m.update_constant(constant, new_value)
-        y_ss = Simulator(m, Assimulo, y_ss).simulate_to_steady_state(tolerance=tolerance)
-        if y_ss is None:
-            return None, None
-        y_full = y_ss | m.get_derived_variables(y_ss)
-        ss.append(np.fromiter(y_full.values(), dtype="float"))
-        fluxes.append(m.get_fluxes(y_full, return_type="array"))
-
-    conc_resp_coef = (ss[0] - ss[1]) / (2 * displacement * old_value)
-    flux_resp_coef = (fluxes[0] - fluxes[1]) / (2 * displacement * old_value)
-
-    return (
-        pd.Series(conc_resp_coef * y_ss_norm, index=list(y_full.keys())).replace(
-            [np.inf, -np.inf], np.nan
-        ),
-        pd.Series(flux_resp_coef * fluxes_norm, index=list(m.reactions)).replace(
-            [np.inf, -np.inf], np.nan
-        ),
-    )
-
-
-def get_response_coefficients(
-    m: Model,
-    constants: list[str],
-    y0: dict[str, float],
-    displacement: float = _DISPLACEMENT,
-    tolerance: float = _DEFAULT_TOLERANCE,
-) -> tuple[DataFrame, DataFrame]:
-    crcs: dict[str, pd.Series] = {}
-    frcs: dict[str, pd.Series] = {}
-    for constant in constants:
-        crc, frc = _get_response_coefficients_single_constant(
-            m=m,
-            constant=constant,
-            y0=y0,
-            displacement=displacement,
-            tolerance=tolerance,
-        )
-        if crc is not None and frc is not None:
-            crcs[constant] = crc
-            frcs[constant] = frc
-    return pd.DataFrame(crcs).T, pd.DataFrame(frcs).T
-
-
-def plot_coefficient_heatmap(
-    df: pd.DataFrame,
-    title: str,
-    cmap: str = "RdBu_r",
-    norm: plt.Normalize | None = None,
-    annotate: bool = True,
-    colorbar: bool = True,
-    xlabel: str | None = None,
-    ylabel: str | None = None,
-    ax: Optional[Axes] = None,
-    cax: Optional[Axes] = None,
-    figsize: tuple[float, float] = (8, 6),
-) -> tuple[Figure, Axes, QuadMesh]:
-    df = df.T.round(2)
-    if norm is None:
-        end = abs(df.abs().max().max())
-        norm = _get_norm(vmin=-end, vmax=end)
-
-    fig, ax, hm = _heatmap_from_dataframe(
-        df=df,
-        title=title,
-        xlabel=xlabel,
-        ylabel=ylabel,
-        annotate=annotate,
-        colorbar=colorbar,
-        cmap=cmap,
-        norm=norm,
-        ax=ax,
-        cax=cax,
-        figsize=figsize,
-    )
-    ax.set_xticklabels(ax.get_xticklabels(), **{"rotation": 45, "ha": "right"})
-    return fig, ax, hm
-
-
-def plot_multiple(
-    dfs: list[pd.DataFrame],
-    titles: list[str],
-    cmap: str = "RdBu_r",
-    annotate: bool = True,
-    colorbar: bool = True,
-    figsize: tuple[float, float] = (20, 10),
-    norm: plt.Normalize | None = None,
-) -> tuple[Figure, Axes]:
-    if norm is None:
-        vmin = min(i.values.min() for i in dfs)
-        vmax = max(i.values.max() for i in dfs)
-        end = max(abs(vmin), abs(vmax))
-        norm = _get_norm(vmin=-end, vmax=end)
-
-    n_cols = 2
-    n_rows = math.ceil(len(dfs) / n_cols)
-
-    if figsize is None:
-        figsize = (n_cols * 4, n_rows * 4)
-
-    fig, axs = plt.subplots(nrows=n_rows, ncols=n_cols, figsize=figsize, squeeze=False)
-    axs = cast(Axes, axs)
-    for ax, df, title in zip(axs.ravel(), dfs, titles):
-        plot_coefficient_heatmap(
-            df=df,
-            title=title,
-            cmap=cmap,
-            annotate=annotate,
-            colorbar=False,
-            norm=norm,
-            ax=ax,
-        )
-
-    # Add a colorbar
-    if colorbar:
-        cb = fig.colorbar(
-            cm.ScalarMappable(norm=norm, cmap=cmap),
-            ax=axs.ravel()[-1],
-        )
-        cb.outline.set_linewidth(0)
-    fig.tight_layout()
-    return fig, axs