default color map

ampullaryexamplecell.py

@@ -94,7 +94,7 @@ def plot_chi2(ax, s, contrast, freqs, chi2, fcutoff, vmax):
     if vmax is None:
         vmax = np.quantile(1e-3*chi2, 0.99)
     pc = ax.pcolormesh(freqs, freqs, 1e-3*chi2, vmin=0, vmax=vmax,
-                       cmap='viridis', rasterized=True, zorder=10)
+                       rasterized=True, zorder=10)
     ax.set_xlim(0, fcutoff)
     ax.set_ylim(0, fcutoff)
     df = 100 if fcutoff == 300 else 50
@@ -220,3 +220,4 @@ if __name__ == '__main__':
     fig.tag(axs, xoffs=-3, yoffs=2)
     
     fig.savefig()
+    print()

dataoverview.py

@@ -274,3 +274,4 @@ if __name__ == '__main__':
     fig.common_yticks(axs[2, :])
     fig.tag(xoffs=-3.5, yoffs=2)
     fig.savefig()
+    print()

lifsuscept.py

@@ -0,0 +1,73 @@
+import matplotlib.pyplot as plt
+import numpy as np
+from matplotlib import rc
+
+from threefish.defaults import default_figsize, default_settings
+from threefish.load import save_visualization
+from threefish.plot.plotstyle import plot_style
+from threefish.plot.tags import tag2
+from threefish.RAM.calc_analytics import calc_nonlin_analytic_values
+from threefish.RAM.reformat_matrix import convert_csv_str_to_float
+
+rc('text', usetex=True)
+
+
+def plot_chi2():
+
+
+
+    default_settings()  # ts=13, ls=13, fs=13, lw = 0.7
+    plot_style()
+    default_figsize(column=2, length=2.5)
+    fig, ax = plt.subplots(1, 2)
+    plt.subplots_adjust(bottom=0.2, wspace=0.35, left=0.1, right=0.92)
+
+    ###################################################
+    transfer_values, suscept_values = calc_nonlin_analytic_values()
+
+    ###################################################
+    # plot transfer function, panel A
+    transfer_values = transfer_values.astype(complex)
+    ax[0].plot(transfer_values.index, np.abs(transfer_values['transfer']),
+               color='black')
+    ax[0].set_xlabel(r'$f$')
+    ax[0].set_ylabel(r'$|\chi_{1}(f)|$')
+    ax[0].set_xlim(0, transfer_values.index[-1])
+    ylim = ax[0].get_ylim()
+    ax[0].set_ylim(0, ylim[-1])
+
+    ###################################################
+    # plot matrix, panel B
+    suscept_values.columns = suscept_values.index
+    new_keys, stack_plot = convert_csv_str_to_float(suscept_values)
+    prss = np.abs(stack_plot)
+    vmax = np.quantile(prss, 0.994)
+    ten = 10**np.floor(np.log10(vmax))
+    for fac, delta in zip([1, 2, 3, 4, 6, 8, 10],
+                          [0.5, 1, 1, 2, 3, 4, 5]):
+        if fac*ten >= vmax:
+            vmax = fac*ten
+            ten *= delta
+            break
+    pc = ax[1].pcolormesh(new_keys, new_keys, prss, rasterized=True,
+                          cmap='viridis', vmin=0, vmax=vmax)
+    ax[1].set_aspect('equal')
+    cax = ax[1].inset_axes([1.04, 0, 0.05, 1])
+    cax.set_spines_outward('lrbt', 0)
+    fig.colorbar(pc, cax=cax, label=r'$|\chi_2(f_1, f_2)|$')
+    cax.set_yticks_delta(50)
+    ax[1].set_xlabel(r'$f_{1}$')
+    ax[1].set_ylabel(r'$f_{2}$')
+    ax[1].set_xlim(0, 1)
+    ax[1].set_ylim(0, 1)
+    ax[1].set_xticks_delta(0.2)
+    ax[1].set_xticks_delta(0.2)
+    tag2(axes=ax, xoffs=[-0.5, -5.5], yoffs=1.7)  # ax_ams[3],
+    save_visualization()
+
+
+if __name__ == '__main__':
+
+    plot_chi2()
+
+

modelsusceptcontrasts.py

@@ -47,7 +47,7 @@ def plot_chi2(ax, s, data_file):
             ten *= delta
             break
     pc = ax.pcolormesh(freqs, freqs, prss, vmin=0, vmax=vmax,
-                       cmap='viridis', rasterized=True)
+                       rasterized=True)
     if 'noise_frac' in data:
         ax.set_title('$c$=0\\,\\%', fontsize='medium')
     else:
@@ -182,3 +182,4 @@ if __name__ == '__main__':
     fig.common_yticks(axs[5, :])
     fig.tag(axs, xoffs=-4.5, yoffs=1.8)
     fig.savefig()
+    print()

modelsusceptlown.py

@@ -47,7 +47,7 @@ def plot_chi2(ax, s, data_file):
             ten *= delta
             break
     pc = ax.pcolormesh(freqs, freqs, prss, vmin=0, vmax=vmax,
-                       cmap='viridis', rasterized=True)
+                       rasterized=True)
     ns = f'$N={n}$' if n <= 100 else f'$N=10^{np.log10(n):.0f}$'
     if 'noise_frac' in data:
         ax.set_title(f'$c$=0\\,\\%, {ns}', fontsize='medium')
@@ -197,3 +197,4 @@ if __name__ == '__main__':
     fig.tag(axs, xoffs=-4.5, yoffs=1.8)
     axs[1, 0].set_visible(False)
     fig.savefig()
+    print()

modelsusceptovern.py

@@ -46,7 +46,7 @@ def plot_chi2(ax, s, data_file):
             ten *= delta
             break
     pc = ax.pcolormesh(freqs, freqs, prss, vmin=0, vmax=vmax,
-                       cmap='viridis', rasterized=True)
+                       rasterized=True)
     ax.set_title(f'$N=10^{np.log10(n):.0f}$', fontsize='medium')
     ax.set_xlim(0, 300)
     ax.set_ylim(0, 300)
@@ -164,3 +164,5 @@ if __name__ == '__main__':
     fig.common_yticks(axs[-1, :4])
     fig.tag(axs, xoffs=-2.5, yoffs=1.8)
     fig.savefig()
+    print()
+    

plotstyle.py

@@ -126,7 +126,7 @@ def plot_style():
     pt.colormap('YR', cmcolors, cmvalues)
     cycle_colors = ['blue', 'red', 'orange', 'lightgreen', 'magenta',
                     'yellow', 'cyan', 'pink']
-    pt.colors_params(palette, cycle_colors, 'RdYlBu')
+    pt.colors_params(palette, cycle_colors, 'viridis')
     pt.figure_params(palette['white'], format='pdf', compression=6,
                      fonttype=3, stripfonts=True)
     pt.labels_params('{label} [{unit}]', labelsize='medium', labelpad=6)

punitexamplecell.py

@@ -160,7 +160,7 @@ def plot_chi2(ax, s, contrast, freqs, chi2, fcutoff, vmax):
     if vmax is None:
         vmax = np.quantile(1e-3*chi2, 0.99)
     pc = ax.pcolormesh(freqs, freqs, 1e-3*chi2, vmin=0, vmax=vmax,
-                       cmap='viridis', rasterized=True, zorder=10)
+                       rasterized=True, zorder=10)
     ax.set_xlim(0, fcutoff)
     ax.set_ylim(0, fcutoff)
     df = 100 if fcutoff == 300 else 50
@@ -272,3 +272,4 @@ if __name__ == '__main__':
     fig.tag(axs, xoffs=-3, yoffs=2)
     
     fig.savefig()
+    print()