cosmic-popsynth 3.4.17__cp310-cp310-macosx_14_0_arm64.whl

cosmic/plotting.py

@@ -0,0 +1,683 @@
+# -*- coding: utf-8 -*-
+# Copyright (C) Katelyn Breivik (2017 - 2021)
+#
+# This file is part of cosmic.
+#
+# cosmic is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# cosmic is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with cosmic.  If not, see <http://www.gnu.org/licenses/>.
+
+"""`plotting`
+"""
+
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+import matplotlib.gridspec as gridspec
+import matplotlib.patches as mpatches
+
+from matplotlib.lines import Line2D
+from .utils import a_from_p, calc_Roche_radius
+from .evolve import Evolve
+
+__author__ = "Jeff Andrews <andrews.jeff@gmail.com>"
+__all__ = [
+    "evolve_binary",
+    "plot_k_type",
+    "plot_radius",
+    "plot_mass",
+    "plot_Teff",
+    "plot_Mdot",
+    "plot_P_orb",
+    "plot_ecc",
+    "plot_HR_diagram",
+    "plot_binary_evol",
+    "evolve_and_plot",
+]
+
+rsun_in_au = 215.0954
+day_in_year = 365.242
+
+# Colors
+primary_color = "C0"
+secondary_color = "C1"
+
+
+def evolve_binary(initC, t_min=None, t_max=None, BSEDict={}):
+    """
+    Evolves a single binary with all timesteps written
+    to the bcm array for plotting
+
+    Parameters
+    ----------
+    initC : `pandas.DataFrame`
+        initial conditions for binary to evolve
+
+    t_min : `float`
+        starting time for plot in Myr
+
+    t_max : `float`
+        ending time for plot in Myr
+
+    BSEDict : `Dict`
+        Dictionary containing all BSE flags needed
+
+    Returns
+    -------
+    bcm : `pandas.DataFrame`
+        binary evolution data form BSE's bcm dict
+    """
+
+    # Disable chained warning for now which throws
+    # a warning for setting dtp and tphysf
+    pd.options.mode.chained_assignment = None
+
+    # Get highest BSE temporal resolution
+    BSEDict["dtp"] = 0.01
+
+    # To deal with the limited size of the bcm array, we need to reduce
+    # the time resolution if we are evolving a binary for more than 100 Myr
+    if t_max is not None:
+        if t_min is not None:
+            if t_max - t_min > 100:
+                BSEDict["dtp"] = (t_max - t_min) / 10000
+        else:
+            if t_max > 100:
+                BSEDict["dtp"] = t_max / 10000
+
+    # Set maximum time for evolution
+    if t_max is not None:
+        initC["tphysf"] = t_max
+
+    # Call evolution scripts
+    bpp, bcm, initC, kick_info = Evolve.evolve(
+        initialbinarytable=initC, BSEDict=BSEDict
+    )
+
+    # In case minimum and maximum times are not supplied by user
+    if t_min is None:
+        # BUG HERE - BSE sets first value to weird float
+        # HACKED FIX
+        t_phys = np.array(bcm.tphys)
+        t_phys[0] = 0.0
+        bcm.at[0, "tphys"] = t_phys
+        t_min = bcm.tphys.min()
+    if t_max is None:
+        t_max = bcm.tphys.max()
+
+    # Select for temporal range
+    bcm = bcm.loc[(bcm.tphys <= t_max) & (bcm.tphys >= t_min)]
+
+    return bcm
+
+
+def plot_k_type(ax_1, ax_2, ax_k_type_list, times, k1_out, k2_out,
+                k_type_colors=None, k_type_labels=None):
+    """Plots the stellar types as a function of time
+
+    Parameters
+    ----------
+    ax_1 : `matplotlib.Axes`
+        Axis instance for kstar 1
+
+    ax_2 : `matplotlib.Axes`
+        Axis instance for kstar 2
+
+    ax_k_type_list : `list`
+        List of ktypes for the legend of the ktype bar plots
+
+    times : `pandas.Series`
+        Series of times at each binary evolution time step in Myr
+
+    k1_out : `pandas.Series`
+        Series of kstar 1 type at each binary evolution time step in Myr
+
+    k2_out : `pandas.Series`
+        Series of kstar 2 type at each binary evolution time step in Myr
+
+    k_type_colors : `list`
+        List of colors for each ktype
+
+    k_type_labels : `list`
+        List of labels for each ktype
+
+    Returns
+    -------
+    Null
+    """
+
+    k_type_colors = [
+        "plum",
+        "sandybrown",
+        "lightseagreen",
+        "moccasin",
+        "chartreuse",
+        "deepskyblue",
+        "gold",
+        "rosybrown",
+        "m",
+        "darkgreen",
+        "grey",
+        "sienna",
+        "palevioletred",
+        "navy",
+        "tan",
+        "black",
+    ] if k_type_colors is None else k_type_colors
+    k_type = [
+        "MS conv",
+        "MS",
+        "HG",
+        "GB",
+        "CHeB",
+        "EAGB",
+        "TPAGB",
+        "HeMS",
+        "HeHG",
+        "HeGB",
+        "HeWD",
+        "COWD",
+        "ONeWD",
+        "NS",
+        "BH",
+        "no remnant",
+    ] if k_type_labels is None else k_type_labels
+
+    # k-type plots
+    for a in [ax_1, ax_2]:
+
+        a.axis("off")
+
+        for j, k in enumerate(np.unique(k1_out)):
+            a.fill_between(times[k1_out == k], 0.7, 0.9, color=k_type_colors[k])
+        for j, k in enumerate(np.unique(k2_out)):
+            a.fill_between(times[k2_out == k], 0.4, 0.6, color=k_type_colors[k])
+
+        a.set_title("Stellar Type")
+
+        a.set_xlim(np.min(times), np.max(times))
+
+    # Add legend
+    ax_k_type_list.axis("off")
+    k_type_all = np.unique(np.array([k1_out, k2_out]))
+    patches = [
+        mpatches.Patch(color=k_type_colors[k], label=k_type[k]) for k in k_type_all
+    ]
+    leg = ax_k_type_list.legend(handles=patches, mode="expand", ncol=len(k_type_all))
+    leg.get_frame().set_alpha(0.0)
+
+
+def plot_radius(
+    ax, times, R1_out, R2_out, M1_out, M2_out, P_orb_out, ecc_out, sys_obs, legend=True
+):
+    """Plots the stellar radii as a function of time
+
+    Parameters
+    ----------
+    ax : `matplotlib.Axes`
+        Axis instance for the plot
+
+    times : `pandas.Series`
+        Series of times at each binary evolution time step in Myr
+
+    R1_out : `pandas.Series`
+        Series of primary radius at each binary evolution time step in Rsun
+
+    R2_out : `pandas.Series`
+        Series of secondary radius at each binary evolution time step in Rsun
+
+    M1_out : `pandas.Series`
+        Series of primary mass at each binary evolution time step in Msun
+
+    M2_out : `pandas.Series`
+        Series of secondary mass at each binary evolution time step in Msun
+
+    P_orb_out : `pandas.Series`
+        Series of orbital periods at each binary evolution time step in days
+
+    ecc_out : `pandas.Series`
+        Series of eccentricities at each binary evolution time step
+
+    sys_obs : `Dict`
+        Dictionary containing keys for binary parameters with values to plot
+        as vertical lines for each stellar component
+
+    Returns
+    -------
+    Null
+    """
+    # Radius
+    ax.plot(times, R1_out, color=primary_color)
+    ax.plot(times, R2_out, color=secondary_color)
+
+    # Plot Roche radii - at periastron
+    A_out = a_from_p(M1_out, M2_out, P_orb_out)  # in Rsun
+    R1_Roche = calc_Roche_radius(M1_out, M2_out, A_out * (1.0 - ecc_out))  # in Rsun
+    R2_Roche = calc_Roche_radius(M2_out, M1_out, A_out * (1.0 - ecc_out))  # in Rsun
+    ax.plot(times, R1_Roche, color=primary_color, linestyle="--")
+    ax.plot(times, R2_Roche, color=secondary_color, linestyle="--")
+
+    for key, value in sys_obs.items():
+        if key == "R1":
+            ax.axhline(value, color=primary_color, linestyle="dashed")
+        if key == "R2":
+            ax.axhline(value, color=secondary_color, linestyle="dashed")
+
+    ax.set_yscale("log")
+    ax.set_ylim(0.5, ax.get_ylim()[1])
+
+    ax.set_ylabel(r"Radius ($R_{\odot}$)")
+
+    ax.set_xlim(np.min(times), np.max(times))
+
+    if legend:
+        custom_lines = [
+            Line2D([0], [0], color="k", linestyle="solid"),
+            Line2D([0], [0], color="k", linestyle="dashed"),
+        ]
+        ax.legend(custom_lines, ["Stellar Radius", "Roche Radius"], frameon=False)
+
+
+def plot_mass(ax, times, M1_out, M2_out, sys_obs):
+    """Plots the stellar mass as a function of time
+
+    Parameters
+    ----------
+    ax : `matplotlib.Axes`
+        Axis instance for the plot
+
+    times : `pandas.Series`
+        Series of times at each binary evolution time step in Myr
+
+    M1_out : `pandas.Series`
+        Series of primary mass at each binary evolution time step in Msun
+
+    M2_out : `pandas.Series`
+        Series of secondary mass at each binary evolution time step in Msun
+
+    sys_obs : `Dict`
+        Dictionary containing keys for binary parameters with values to plot
+        as vertical lines for each stellar component
+
+    Returns
+    -------
+    Null
+    """
+
+    # Mass
+    ax.plot(times, M1_out, color=primary_color)
+    ax.plot(times, M2_out, color=secondary_color)
+
+    for key, value in sys_obs.items():
+        if key == "M1":
+            ax.axhline(value, color=primary_color, linestyle="dashed")
+        if key == "M2":
+            ax.axhline(value, color=secondary_color, linestyle="dashed")
+
+    ax.set_ylabel(r"Mass ($M_{\odot}$)")
+    ax.set_xlim(np.min(times), np.max(times))
+
+
+def plot_Teff(ax, times, Teff1_out, Teff2_out, sys_obs):
+    """Plots the stellar effectvie temperature as a function of time
+
+    Parameters
+    ----------
+    ax : `matplotlib.Axes`
+        Axis instance for the plot
+
+    times : `pandas.Series`
+        Series of times at each binary evolution time step in Myr
+
+    Teff1_out : `pandas.Series`
+        Series of primary effective temperature at each binary evolution time step in K
+
+    Teff2_out : `pandas.Series`
+        Series of secondary effective temperature at each binary evolution time step in K
+
+    sys_obs : `Dict`
+        Dictionary containing keys for binary parameters with values to plot
+        as vertical lines for each stellar component
+
+    Returns
+    -------
+    Null
+    """
+
+    # Effective temperature
+    ax.plot(times, Teff1_out, color=primary_color)
+    ax.plot(times, Teff2_out, color=secondary_color)
+
+    for key, value in sys_obs.items():
+        if key == "T1":
+            ax.axhline(value, color=primary_color, linestyle="dashed")
+        if key == "T2":
+            ax.axhline(value, color=secondary_color, linestyle="dashed")
+
+    ax.set_yscale("log")
+    ax.set_ylabel(r"T$_{\rm eff}$ (K)")
+    ax.set_xlim(np.min(times), np.max(times))
+    ax.set_xlabel("Time (Myr)")
+
+
+def plot_Mdot(ax, times, Mdot1_out, Mdot2_out, legend=True):
+    """Plots the stellar effectvie temperature as a function of time
+
+    Parameters
+    ----------
+    ax : `matplotlib.Axes`
+        Axis instance for the plot
+
+    times : `pandas.Series`
+        Series of times at each binary evolution time step in Myr
+
+    Mdot1_out : `pandas.Series`
+        Series of primary mass transfer rate at each binary evolution time step in Msun/yr
+
+    Mdot2_out : `pandas.Series`
+        Series of secondary mass transfer rate at each binary evolution time step in Msun/yr
+
+    sys_obs : `Dict`
+        Dictionary containing keys for binary parameters with values to plot
+        as vertical lines for each stellar component
+
+    Returns
+    -------
+    Null
+    """
+
+    # Mass accretion rate
+    ax.plot(times, np.log10(np.clip(Mdot1_out, 1.0e-16, None)), color=primary_color)
+    ax.plot(times, np.log10(np.clip(Mdot2_out, 1.0e-16, None)), color=secondary_color)
+    ax.set_ylabel(r"Mass Accretion Rate ($M_{\odot}$ yr$^{-1}$)")
+
+    ax.set_ylim(-14, ax.get_ylim()[1])
+    ax.set_xlim(np.min(times), np.max(times))
+
+    if legend:
+        custom_lines = [
+            Line2D([0], [0], color="C0", linestyle="solid"),
+            Line2D([0], [0], color="C1", linestyle="solid"),
+        ]
+        ax.legend(custom_lines, ["Primary", "Secondary"], loc=2, frameon=False)
+
+
+def plot_P_orb(ax, times, P_orb_out, t_max, sys_obs):
+    """Plots the orbital period as a function of time
+
+    Parameters
+    ----------
+    ax : `matplotlib.Axes`
+        Axis instance for the plot
+
+    times : `pandas.Series`
+        Series of times at each binary evolution time step in Myr
+
+    P_orb_out : `pandas.Series`
+        Series of orbital periods at each binary evolution time step in days
+
+    t_max : `float`
+        ending time for plot in Myr
+
+    sys_obs : `Dict`
+        Dictionary containing keys for binary parameters with values to plot
+        as vertical lines for each stellar component
+
+    Returns
+    -------
+    Null
+    """
+
+    ax.plot(times, P_orb_out, color="k")
+
+    for key, value in sys_obs.items():
+        if key == "P_orb":
+            ax.axhline(value, color="k", linestyle="dashed")
+
+    ax.set_xlim(np.min(times), t_max)
+
+    ax.set_ylabel(r"P$_{\rm orb}$ (days)")
+    ax.set_yscale("log")
+
+
+def plot_ecc(ax, times, ecc_out, t_max, sys_obs):
+    """Plots the eccentricity as a function of time
+
+    Parameters
+    ----------
+    ax : `matplotlib.Axes`
+        Axis instance for the plot
+
+    times : `pandas.Series`
+        Series of times at each binary evolution time step in Myr
+
+    ecc_out : `pandas.Series`
+        Series of eccentricities at each binary evolution time step
+
+    t_max : `float`
+        ending time for plot in Myr
+
+    sys_obs : `Dict`
+        Dictionary containing keys for binary parameters with values to plot
+        as vertical lines for each stellar component
+
+    Returns
+    -------
+    Null
+    """
+
+    ax.plot(times, ecc_out, color="k")
+
+    for key, value in sys_obs.items():
+        if key == "ecc":
+            ax.axhline(value, color="k", linestyle="dashed")
+
+    ax.set_xlim(np.min(times), t_max)
+
+    ax.set_ylabel("Eccentricity")
+    ax.set_xlabel("Time (Myr)")
+
+
+def plot_HR_diagram(ax, L1_out, L2_out, Teff1_out, Teff2_out):
+    """Plots the eccentricity as a function of time
+
+    Parameters
+    ----------
+    ax : `matplotlib.Axes`
+        Axis instance for the plot
+
+    times : `pandas.Series`
+        Series of times at each binary evolution time step in Myr
+
+    L1_out : `pandas.Series`
+        Series of primary luminosities at each binary evolution time step in Lsun
+
+    L2_out : `pandas.Series`
+        Series of secondary luminosities at each binary evolution time step in Lsun
+
+    Teff1_out : `pandas.Series`
+        Series of primary effective temperature at each binary evolution time step in K
+
+    Teff2_out : `pandas.Series`
+        Series of secondary effective temperature at each binary evolution time step in K
+
+    sys_obs : `Dict`
+        Dictionary containing keys for binary parameters with values to plot
+        as vertical lines for each stellar component
+
+    Returns
+    -------
+    Null
+    """
+
+    ax.plot(Teff1_out, L1_out, color=primary_color)
+    ax.plot(Teff2_out, L2_out, color=secondary_color)
+
+    ax.set_xscale("log")
+    ax.set_yscale("log")
+    ax.set_xlim(40000, 2000)
+
+    ax.set_xlabel(r"log T$_{\rm eff}$ (K)")
+    ax.set_ylabel("log L (erg/s)")
+
+    ax.set_xticks([2000, 5000, 10000, 20000, 40000])
+
+
+def plot_binary_evol(bcm, sys_obs={}, ktype_kwargs={}, t_min=None, t_max=None):
+    """Plots the full set of plots and kstar bar plots
+
+    Parameters
+    ----------
+    bcm : `pandas.DataFrame`
+        binary evolution data form BSE's bcm dict
+
+    sys_obs : `Dict`
+        Dictionary containing keys for binary parameters with values to plot
+        as vertical lines for each stellar component
+
+    Returns
+    -------
+    fig : `matplotlib.figure`
+        Figure containing all the plots!
+    """
+
+    fig = plt.figure(figsize=(10, 10), layout="tight")
+
+    gs = fig.add_gridspec(2, 1, height_ratios=[1.3, 6], hspace=0.0)
+    gs_top = gs[0].subgridspec(2, 2, width_ratios=[1, 1], height_ratios=[1, 1.3], hspace=0.15)
+    gs_bottom = gs[1].subgridspec(3, 2, width_ratios=[1, 1], height_ratios=[2, 2, 2], hspace=0.15)
+
+    if t_min is not None:
+        bcm = bcm.loc[bcm.tphys >= t_min]
+    if t_max is not None:
+        bcm = bcm.loc[bcm.tphys <= t_max]
+
+    # k-type panels
+    plot_k_type(
+        fig.add_subplot(gs_top[0, 0]),
+        fig.add_subplot(gs_top[0, 1]),
+        fig.add_subplot(gs_top[1, :]),
+        bcm.tphys,
+        bcm.kstar_1.astype(int),
+        bcm.kstar_2.astype(int),
+        **ktype_kwargs
+    )
+
+    # Radius panel
+    plot_radius(
+        fig.add_subplot(gs_bottom[0, 0]),
+        bcm.tphys,
+        bcm.rad_1,
+        bcm.rad_2,
+        bcm.mass_1,
+        bcm.mass_2,
+        bcm.porb,
+        bcm.ecc,
+        sys_obs,
+    )
+
+    # Mass panel
+    plot_mass(fig.add_subplot(gs_bottom[1, 0]), bcm.tphys, bcm.mass_1, bcm.mass_2, sys_obs)
+
+    # Teff panel
+    plot_Teff(fig.add_subplot(gs_bottom[2, 0]), bcm.tphys, bcm.teff_1, bcm.teff_2, sys_obs)
+
+    # Mass accretion rate panel
+    plot_Mdot(fig.add_subplot(gs_bottom[0, 1]), bcm.tphys, bcm.deltam_1, bcm.deltam_2)
+
+    # Orbital period panel
+    plot_P_orb(
+        fig.add_subplot(gs_bottom[1, 1]),
+        bcm.loc[bcm.kstar_2 < 15].tphys,
+        bcm.loc[bcm.kstar_2 < 15].porb,
+        np.max(bcm.tphys),
+        sys_obs,
+    )
+
+    # Plot eccentricity panel
+    plot_ecc(
+        fig.add_subplot(gs_bottom[2, 1]),
+        bcm.loc[bcm.kstar_2 < 15].tphys,
+        bcm.loc[bcm.kstar_2 < 15].ecc,
+        np.max(bcm.tphys),
+        sys_obs,
+    )
+
+    # Plot HR diagram
+    # idx_1 = np.where(k1_out < 10)[0]
+    # idx_2 = np.where(k2_out < 10)[0]
+    # plot_HR_diagram(ax[7], L1_out[k1_out<10], L2_out[k2_out<10], Teff1_out[k1_out<10], Teff2_out[k2_out<10])
+
+    return fig
+
+
+def evolve_and_plot(initC, t_min=None, t_max=None, BSEDict=None, sys_obs={}):
+    """
+    Evolve and plot binaries as a function of time
+
+    Parameters
+    ----------
+    initC : `pandas.DataFrame`
+        initial conditions for binary to evolve
+
+    t_min : `float or list`
+        starting time for plot in Myr
+
+    t_max : `float or list`
+        ending time for plot in Myr
+
+    BSEDict : `Dict`
+        Dictionary containing all BSE flags needed
+
+    sys_obs : `Dict`
+        Dictionary containing keys for binary parameters with values to plot
+        as vertical lines for each stellar component
+
+    Returns
+    -------
+    all_figs : `list`
+        list of all figures created
+    """
+
+    # Throw an error if user is plotting more than 10 binaries
+    if len(initC) > 10:
+        raise ValueError(
+            "You have asked to plot more than 10 separate binaries. This could cause problems..."
+        )
+
+    # Iterate over all binaries in initC
+    all_figs = []
+    for i in range(len(initC)):
+
+        # Check if t_min and t_max are lists
+        if isinstance(t_min, list):
+            t_min_tmp = t_min[i]
+        else:
+            t_min_tmp = t_min
+        if isinstance(t_max, list):
+            t_max_tmp = t_max[i]
+        else:
+            t_max_tmp = t_max
+
+        # Evolve binary
+        bcm = evolve_binary(
+            initC.iloc[i: i + 1], t_min=t_min_tmp, t_max=t_max_tmp, BSEDict=BSEDict
+        )
+
+        # Plot binary
+        fig = plot_binary_evol(bcm, sys_obs=sys_obs)
+
+        # Add to list of figs
+        all_figs.append(fig)
+
+    # Return list of figs
+    return all_figs

cosmic/sample/__init__.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# Copyright (C) Katie Breivik (2017 - 2020)
+#
+# This file is part of COSMIC
+#
+# COSMIC is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# COSMIC is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with COSMIC.  If not, see <http://www.gnu.org/licenses/>
+
+# load tables
+from astropy.table import Column, Table
+from .initialbinarytable import InitialBinaryTable
+from .initialcmctable import InitialCMCTable
+
+# attach unified I/O
+from . import sampler