possibility to defined grid of configuration files

build/lib/py21cmcast/core.py

@@ -360,8 +360,9 @@ def plot_power_spectrum(self, std = None, figname = None, plot=True, ps_modeling
                 figname = self._dir_path + "/power_spectra/power_spectrum.pdf"
 
             fig.savefig(figname, bbox_layout='tight')
+            p21c_tools.close_figure(fig)
 
-        return fig
+        return
 
     @property
     def power_spectrum(self):
@@ -703,6 +704,7 @@ def chi2_UV_luminosity_functions(self, data_set = 'Bouwens21', plot = True):
 
             fig.gca().legend()
             fig.savefig(self._dir_path + '/global_quantities/UV_lum_func_FIDUCIAL.pdf', bbox_inches='tight')
+            p21c_tools.close_figure(fig)
 
         ## The chi2 is given by a sum on the elements where z > 6 (as we cannot trust 21cmFAST below)
 
@@ -730,21 +732,23 @@ def plot_xH_box(self):
                                     xlabel=r'$z$',
                                     ylabel=r'$x_{\rm H_{I}}$')
         fig.savefig(self._dir_path + '/global_quantities/xH_FIDUCIAL.pdf', bbox_inches='tight')
+        p21c_tools.close_figure(fig)
 
 
     def plot_global_signal(self):
         fig = p21c_tools.plot_func(self.z_glob, self.global_signal, ylim=[-150, 50],
                                     xlabel=r'$z$',
                                     ylabel=r'$\overline{T_{\rm b}}~\rm [mK]$')
         fig.savefig(self._dir_path + '/global_quantities/global_signal_FIDUCIAL.pdf', bbox_inches='tight')
+        p21c_tools.close_figure(fig)
 
 
 
 
 
 class Parameter:
 
-    def __init__(self, fiducial, name, plot = True, verbose = True, **kwargs):
+    def __init__(self, fiducial, name, plot = True, verbose = True, values = None, **kwargs):
 
         self._fiducial       = fiducial
         self._name           = name
@@ -761,7 +765,7 @@ def __init__(self, fiducial, name, plot = True, verbose = True, **kwargs):
         self._verbose        = verbose
 
         # Additional parameters to specify the value of the parameter
-        self._values         =  kwargs.get('values', None)
+        self._values         =  values
         self._add_name       =  kwargs.get('add_name', '')
 
         if self._add_name != '':
@@ -890,9 +894,19 @@ def __init__(self, fiducial, name, plot = True, verbose = True, **kwargs):
 
         # Plotting the derivatives
         if self._plot is True:
-            self.plot_ps_derivative()
-            self.plot_weighted_ps_derivative()
-            self.plot_power_spectra()
+
+            fig_der = self.plot_ps_derivative()
+            fig_w_der = self.plot_weighted_ps_derivative()
+            fig_ps = self.plot_power_spectra()
+
+            fig_der.savefig(self._dir_path + "/derivatives/derivatives_" + self._name + self._add_name + ".pdf")
+            fig_w_der.savefig(self._dir_path + "/derivatives/weighted_derivatives_" + self._name + self._add_name + ".pdf")
+            fig_ps.savefig(self._dir_path + "/power_spectra/power_spectra_" + self._name + self._add_name + ".pdf")
+
+            p21c_tools.close_figure(fig_der)
+            p21c_tools.close_figure(fig_w_der)
+            p21c_tools.close_figure(fig_ps)
+
 
     @property
     def ps_derivative(self):
@@ -1039,7 +1053,6 @@ def plot_ps_derivative(self):
         fig = p21c_tools.plot_func_vs_z_and_k(self._z_array, self._k_array, der_array, marker='.', markersize=2, 
                                                 title=r'$\frac{\partial \Delta_{21}^2}{\partial ' + self._tex_name + r'}$', 
                                                 xlim = [0.1, 1], xlog=self._logk, ylog=False)
-        fig.savefig(self._dir_path + "/derivatives/derivatives_" + self._name + self._add_name + ".pdf")
         return fig
 
 
@@ -1063,7 +1076,6 @@ def plot_power_spectra(self, **kwargs):
                                                 title=r'$\Delta_{21}^2 ~ {\rm [mK^2]}$', 
                                                 xlog=self._logk, ylog=True, istd = _order[0], **kwargs)
 
-        fig.savefig(self._dir_path + "/power_spectra/power_spectra_" + self._name + self._add_name + ".pdf")
         return fig
 
 
@@ -1078,7 +1090,7 @@ def plot_weighted_ps_derivative(self):
         fig = p21c_tools.plot_func_vs_z_and_k(self._z_array, self._k_array, der_array, marker='.', markersize=2, 
                                                 title=r'$\frac{1}{\sigma}\frac{\partial \Delta_{21}^2}{\partial ' + self._tex_name + r'}$', 
                                                 xlim = [0.1, 1], xlog=self._logk, ylog=False)
-        fig.savefig(self._dir_path + "/derivatives/weighted_derivatives_" + self._name + self._add_name + ".pdf")
+
         return fig
 
 

build/lib/py21cmcast/tools.py

@@ -45,9 +45,11 @@
 
 
 
-from matplotlib.pyplot import *
-
+from matplotlib.gridspec import GridSpec
+from matplotlib.lines import Line2D
 from matplotlib.patches import Ellipse
+import matplotlib.cm as mplt_cm
+import matplotlib.pyplot as plt
 import matplotlib.transforms as transforms
 
 import numpy as np
@@ -560,7 +562,7 @@ def plot_func_vs_z_and_k(z, k, func, func_err = None, std = None, istd  : float
 
     if len(func) > 1:
 
-        cmap = matplotlib.cm.get_cmap('Spectral')
+        cmap = mplt_cm.get_cmap('Spectral')
         a_lin = (0.99-0.2)/(len(func)-1) if len(func) > 1 else 1
         b_lin = 0.2 if len(func) > 1 else 0.5
 

examples/run_lightcone.py

@@ -1,18 +1,27 @@
 import argparse
 import py21cmcast as p21c
+from astropy import units
 
 parser = argparse.ArgumentParser()
 parser.add_argument("config_file", type = str, help="Path to config file")
 parser.add_argument("-nomp", "--n_omp", type = int, help="number of OMP threads available")
 parser.add_argument("-nruns", "--n_runs", type = int, help="number of times to run the code < 25")
 parser.add_argument("-rs", "--random_seed", type = int, help="the first random seed of the runs")
+parser.add_argument("-pp", "--pre_process", help = "pre-process the lightcone and only extract part of the data in the cache", action = 'store_false')
 args = parser.parse_args()
 
 config_file   = args.config_file
 n_omp         = args.n_omp       if (args.n_omp       is not None) else 1
 n_runs        = args.n_runs      if (args.n_runs      is not None) else 1
 random_seed   = args.random_seed if (args.random_seed is not None) else None
+preprocess    = args.pre_process
 
 # Run the lightcone with the given seed
 lightcone, run_id, output_dir = p21c.run_lightcone_from_config(config_file, n_omp, random_seed)
-lightcone.save(fname = "Lightcone_rs" + str(lightcone.random_seed) + "_" + run_id + ".h5", direc = output_dir)
+
+if preprocess is True:
+    z_bins, z_centers, k_bins = p21c.define_grid_modes_redshifts(6., 8 * units.MHz, z_max = 22, k_min = 0.1 / units.Mpc, k_max = 1 / units.Mpc)
+    p21c.Run(output_dir, "Lightcone_rs" + str(lightcone.random_seed) + "_" + run_id + ".h5", z_bins, z_centers, k_bins, False, lightcone = lightcone, verbose = False)
+else:
+    lightcone.save(fname = "Lightcone_rs" + str(lightcone.random_seed) + "_" + run_id + ".h5", direc = output_dir)
+

src/py21cmcast/__init__.py

@@ -7,6 +7,7 @@
 
 from .runs import (
     init_runs,
+    init_grid_runs,
     make_config_one_varying_param,
     run_lightcone_from_config,
 )