Merge pull request #151 from Neuroinflab/figs2023

figure for submission

Author: m-kowalska

figures/kCSD_properties/L_curve_simulation.py

@@ -112,7 +112,7 @@ def main_loop(src_width, total_ele, inpos, lpos, nm, noise=0, srcs=1):
     t_csd_x, t_csd_y, true_csd = generate_csd_1D(src_width, nm, srcs=srcs,
                                                  start_x=0, end_x=1.,
                                                  start_y=0, end_y=1,
-                                                 res_x=100, res_y=100)
+                                                 res_x=101, res_y=101)
     if type(noise) ==  float: n_spec = [noise]
     else: n_spec = noise
     for i, noise in enumerate(n_spec):
@@ -142,6 +142,7 @@ def main_loop(src_width, total_ele, inpos, lpos, nm, noise=0, srcs=1):
                         'pots':pots, 'estm_x':k.estm_x, 'est_pot':est_pot, 
                         'est_csd':est_csd, 'noreg_csd':noreg_csd, 'errsy':errsy}
         np.savez('data_fig4_and_fig13_'+save_as, **vals_to_save)
+        print(true_csd.shape, est_csd[:,0].shape)
         RMS_wek[0, i] = np.linalg.norm(true_csd/np.linalg.norm(true_csd) - est_csd[:,0]/np.linalg.norm(est_csd[:,0]))
         RMS_wek[1, i] = np.linalg.norm(true_csd/np.linalg.norm(true_csd) - est_csd_cv[:,0]/np.linalg.norm(est_csd_cv[:,0]))
 

figures/kCSD_properties/figure_LC.py

@@ -103,11 +103,11 @@ def make_plots(title, m_norm, m_resi, true_csd, curveseq, ele_y,
 #    os.chdir("./LCurve/LC2")
     noises = 3
     noise_lvl = np.linspace(0, 0.5, noises)
-#    df = np.load('data_fig4_and_fig13_lc_noise25.0.npz')
+    #df = np.load('data_fig4_and_fig13_lc_noise25.0.npz')
     Rs = np.linspace(0.025, 8*0.025, 8)
     title = ['nazwa_pliku']
     save_as = 'noise'
-#    make_plots(title, df['m_norm'], df['m_resi'], df['true_csd'], 
-#               df['curve_surf'], df['ele_y'], df['pots_n'],
-#               df['pots'], df['estm_x'], df['est_pot'], df['est_csd'], 
-#               df['noreg_csd'], save_as)
+    make_plots(title, df['m_norm'], df['m_resi'], df['true_csd'], 
+               df['curve_surf'], df['ele_y'], df['pots_n'],
+               df['pots'], df['estm_x'], df['est_pot'], df['est_csd'], 
+               df['noreg_csd'], save_as)

figures/kCSD_properties/figure_LCandCV.py

@@ -23,51 +23,58 @@ def set_axis(ax, x, y, letter=None):
 def plot_surface(curve_surf, errsy, save_as):
     fsize = 18
     lambdas = np.logspace(-7, -3, 50)
-    fig = plt.figure(figsize = (20,9), dpi = 300)
-    gs = gridspec.GridSpec(16, 12, hspace=2, wspace=2)
+    fig = plt.figure(figsize = (15, 6), dpi = 300)
+    gs = gridspec.GridSpec(16, 12, hspace=1, wspace=1)
     ax = plt.subplot(gs[0:16, 0:6])
     set_axis(ax, -0.05, 1.05, letter='A')
-    plt.pcolormesh(lambdas, np.arange(9), curve_surf, 
-                   cmap = 'BrBG', vmin = -2, vmax=2)
+
+    plt.pcolormesh(lambdas, np.arange(8), curve_surf, 
+                   cmap = 'BrBG', vmin = -3, vmax=3)
     plt.colorbar()
     for i,m in enumerate(curve_surf.argmax(axis=1)):
-        plt.scatter([lambdas[m]], [i+0.5], s=50, color='red', alpha = 0.7)
+        plt.scatter([lambdas[m]], [i], s=50, color='red', alpha = 0.7)
         if i==7:
-            plt.scatter([lambdas[m]], [i+0.5], s=50, color='red', 
-                        label = 'Maximum Curvature', alpha = 0.7)
+            plt.scatter([lambdas[m]], [i], s=50, color='red', 
+                        label = 'Maximum \nCurvature', alpha = 0.7)
     plt.xlim(lambdas[1],lambdas[-1])
     plt.title('L-curve regularization', fontsize = fsize)
-    plt.legend(loc='center', bbox_to_anchor=(0.5, -0.12), ncol=1, 
+    # plt.legend(loc='center', bbox_to_anchor=(0.5, -0.12), ncol=1, 
+    #            frameon = False, fontsize = fsize)
+    plt.legend(loc='upper left', ncol=1, 
                frameon = False, fontsize = fsize)
-    plt.yticks(np.arange(8)+0.5, [str(x)+'x' for x in range(1,9)])
+    plt.yticks(np.arange(8), [str(x)+'x' for x in range(1,9)])
     plt.xscale('log')
     plt.ylabel('Parameter $R$ in electrode distance', fontsize=fsize, labelpad = 15)
     plt.xlabel('$\lambda$',fontsize=fsize)
     ax = plt.subplot(gs[0:16, 6:12])
     set_axis(ax, -0.05, 1.05, letter='B')
-    plt.pcolormesh(lambdas, np.arange(9), errsy, cmap = 'Greys')
+    plt.pcolormesh(lambdas, np.arange(8), errsy, cmap='Greys', vmin=0.01, vmax=0.02)
     plt.colorbar()
     for i,m in enumerate(errsy.argmin(axis=1)):
-        plt.scatter([lambdas[m]], [i+0.5], s=50, color='red', alpha = 0.7)
+        plt.scatter([lambdas[m]], [i], s=50, color='red', alpha = 0.7)
         if i==7:
-            plt.scatter([lambdas[m]], [i+0.5], s=50, color='red', 
-                        label = 'Minimum Error', alpha = 0.7)
+            plt.scatter([lambdas[m]], [i], s=50, color='red', 
+                        label = 'Minimum \nError', alpha = 0.7)
     plt.xlim(lambdas[1],lambdas[-1])
-    plt.legend(loc='center', bbox_to_anchor=(0.5, -0.12), ncol=1, 
+    # plt.legend(loc='center', bbox_to_anchor=(0.5, -0.12), ncol=1, 
+    #            frameon = False, fontsize = fsize)
+    plt.legend(loc='upper left', ncol=1, 
                frameon = False, fontsize = fsize)
     plt.title('Cross-validation regularization', fontsize = fsize)
-    plt.yticks(np.arange(8)+0.5, [str(x)+'x' for x in range(1,9)])
+    plt.yticks(np.arange(8), [str(x)+'x' for x in range(1,9)])
     plt.xscale('log')
     plt.xlabel('$\lambda$', fontsize=fsize)
     fig.savefig(save_as+'.png')
 
 if __name__=='__main__':
-#    os.chdir("./LCurve/")
+    os.chdir("./LCurve/")
     noises = 3
     noise_lvl = np.linspace(0, 0.5, noises)
-#    df = np.load('LC2/data_fig4_and_fig13_lc_noise25.0.npz')
+    print(os.getcwd())
+    df = np.load(os.path.join('LC2', 'data_fig4_and_fig13_LC_noise25.0.npz'))
+
     Rs = np.linspace(0.025, 8*0.025, 8)
     title = ['nazwa_pliku']
     save_as = 'noise'
-#    plot_surface(df['curve_surf'], df['errsy'], save_as+'surf')
-    plt.close('all')
+    plot_surface(df['curve_surf'], df['errsy'], save_as+'surf')
+    plt.close('all')

figures/kCSD_properties/figure_LCandCVperformance.py

@@ -25,10 +25,10 @@ def make_plot_perf(sim_results):
     lam_lc = sim_results[0, 0]
     rms_cv = sim_results[1, 2]
     lam_cv = sim_results[1, 0]
-    fig = plt.figure(figsize = (9,12), dpi = 300)
-    widths = [10]
-    heights = [1, 1]
-    gs = gridspec.GridSpec(2, 1, height_ratios=heights, width_ratios=widths,
+    fig = plt.figure(figsize = (12,7), dpi = 300)
+    widths = [1, 1]
+    heights = [1]
+    gs = gridspec.GridSpec(1, 2, height_ratios=heights, width_ratios=widths,
                            hspace=0.45, wspace=0.3)
     ax1 = plt.subplot(gs[0])
     if np.min(rms_cv) < np.min(rms_lc):
@@ -50,7 +50,8 @@ def make_plot_perf(sim_results):
     ax1.spines['right'].set_visible(False)
     ax1.spines['top'].set_visible(False)
     set_axis(ax1, -0.05, 1.05, letter='A')
-    plt.title('Performance of regularization methods')
+    ax1.legend(loc='upper left', frameon=False)
+    # plt.title('Performance of regularization methods')
 
     '''second plot'''
     ax2 = plt.subplot(gs[1])
@@ -69,14 +70,15 @@ def make_plot_perf(sim_results):
     plt.xlabel('Relative Noise Level', labelpad = 15)
     set_axis(ax2, -0.05, 1.05, letter='B')
     ht, lh = ax2.get_legend_handles_labels()
-    fig.legend(ht, lh, loc='lower center', ncol=2, frameon=False)
+    #fig.legend(ht, lh, loc='upper center', ncol=2, frameon=False)
     ax2.spines['right'].set_visible(False)
     ax2.spines['top'].set_visible(False)
+    ax2.legend(loc='upper left', frameon=False)
     fig.savefig('stats.png')
 
 if __name__=='__main__':
-#    os.chdir("./LCurve/")
+    os.chdir("./LCurve/")
     noises = 9
     noise_lvl = np.linspace(0, 0.5, noises)
-#    sim_results = np.load('sim_results.npy')
-#    make_plot_perf(sim_results)
+    sim_results = np.load('sim_results.npy')
+    make_plot_perf(sim_results)

figures/kCSD_properties/figure_properties.py

@@ -17,3 +17,5 @@
 })
 
 
+def cm_to_inches(vals):
+    return [0.393701*ii for ii in vals]

figures/kCSD_properties/sources_electrodes.odg

@@ -36,7 +36,7 @@ def grid(x, y, z):
 def set_axis(ax, letter=None):
     ax.text(
         -0.05,
-        1.05,
+        1.10,
         letter,
         fontsize=20,
         weight='bold',
@@ -63,7 +63,7 @@ def make_subplot(ax, val_type, xs, ys, values, cax, title=None, ele_pos=None, xl
     if ylabel:
         ax.set_ylabel('Y (mm)')
     if title is not None:
-        ax.set_title(title)
+        ax.set_title(title, pad=10)
     ax.set_xticks([0, 0.5, 1])
     ax.set_yticks([0, 0.5, 1])
     ticks = np.linspace(-1 * t_max, t_max, 3, endpoint=True)
@@ -128,6 +128,7 @@ def generate_figure(small_seed, large_seed):
     cax = plt.subplot(gs[1, 0])
     t_max_1 = 0.50
     make_subplot(ax, 'csd', csd_x, csd_y, true_csd, cax, 'True CSD', xlabel=True, ylabel=True, letter='A', t_max=t_max_1)
+    ax.text(-0.4, 0.5, 'Small sources', fontsize=20, rotation=90, va='center')
     ax = plt.subplot(gs[0, 1])
     cax = plt.subplot(gs[1, 1])
     make_subplot(ax, 'pot', pot_X, pot_Y, pot_Z, cax, 'Interpolated potentials', xlabel=True, ele_pos=ele_pos, letter='B')
@@ -145,9 +146,10 @@ def generate_figure(small_seed, large_seed):
     cax = plt.subplot(gs[1, 0])
     t_max_2 = 0.52
     make_subplot(ax, 'csd', csd_x, csd_y, true_csd, cax,  ylabel=True, xlabel=True, letter='E', t_max=t_max_2)
+    ax.text(-0.4, 0.5, 'Large sources', fontsize=20, rotation=90, va='center')
     ax = plt.subplot(gs[0, 1])
     cax = plt.subplot(gs[1, 1])
-    make_subplot(ax, 'pot', pot_X, pot_Y, pot_Z, cax,  xlabel=True, ele_pos=ele_pos, letter='F')
+    make_subplot(ax, 'pot', pot_X, pot_Y, pot_Z, cax,  xlabel=True, ele_pos=ele_pos, letter='F', t_max=1)
     ax = plt.subplot(gs[0, 2])
     cax = plt.subplot(gs[1, 2])
     make_subplot(ax, 'csd', k.estm_x, k.estm_y, est_csd_pre_cv[:, :, 0], cax, xlabel=True, letter='G', t_max=t_max_2)

figures/kCSD_properties/tutorial_basic.py

@@ -40,7 +40,7 @@ def load_files(folderpaths, seeds):
 def set_axis(ax, letter=None):
     ax.text(
         -0.05,
-        1.05,
+        1.1,
         letter,
         fontsize=20,
         weight='bold',
@@ -121,7 +121,7 @@ def make_subplot(ax, val_type, xs, ys, values, cax, title=None, ele_pos=None, xl
     if ylabel:
         ax.set_ylabel('Y (mm)')
     if title is not None:
-        ax.set_title(title)
+        ax.set_title(title, pad=10)
     ax.set_xticks([0, 0.5, 1])
     ax.set_yticks([0, 0.5, 1])
     ticks = np.linspace(0, t_max, 3, endpoint=True)
@@ -154,6 +154,7 @@ def generate_figure():
     make_subplot(ax, 'err', csd_x, csd_y, errs[0], ele_pos=electrode_positions(missing_ele=0),
                  cax=cax, title='Error CSD', xlabel=True, ylabel=True, letter='A',
                  t_max=err_max)
+    ax.text(-0.4, 0.5, 'Small sources', fontsize=20, rotation=90, va='center')
     ax = plt.subplot(gs[0, 1])
     cax = plt.subplot(gs[1, 1])
     make_subplot(ax, 'err', csd_x, csd_y, errs[1], ele_pos=electrode_positions(missing_ele=5),
@@ -179,6 +180,7 @@ def generate_figure():
     make_subplot(ax, 'err', csd_x, csd_y, errs[0], ele_pos=electrode_positions(missing_ele=0),
                  cax=cax, xlabel=True, ylabel=True, letter='E',
                  t_max=err_max)
+    ax.text(-0.4, 0.5, 'Large sources', fontsize=20, rotation=90, va='center')
     ax = plt.subplot(gs[0, 1])
     cax = plt.subplot(gs[1, 1])
     make_subplot(ax, 'err', csd_x, csd_y, errs[1], ele_pos=electrode_positions(missing_ele=5),

figures/kCSD_properties/tutorial_broken_electrodes.py

@@ -38,7 +38,7 @@ def load_files(folderpaths, seeds):
 def set_axis(ax, letter=None):
     ax.text(
         -0.05,
-        1.05,
+        1.10,
         letter,
         fontsize=20,
         weight='bold',
@@ -145,7 +145,7 @@ def make_subplot(ax, val_type, xs, ys, values, cax, title=None, ele_pos=None,
     if ylabel:
         ax.set_ylabel('Y (mm)')
     if title is not None:
-        ax.set_title(title)
+        ax.set_title(title, pad=10)
     ax.set_xticks([0, 0.5, 1])
     ax.set_yticks([0, 0.5, 1])
     ticks = np.linspace(0, t_max, 3, endpoint=True)
@@ -277,20 +277,22 @@ def generate_figure2():
     make_subplot(ax, 'err', csd_x, csd_y, errs[0], ele_pos=electrode_positions(missing_ele=0),
                  cax=cax, title='Error CSD', xlabel=True, ylabel=True, letter='A',
                  t_max=.2)
+    ax.text(-0.4, 0.5, 'Small+Large sources', fontsize=20, rotation=90, va='center')
+
     ax = plt.subplot(gs[0, 1])
     cax = plt.subplot(gs[1, 1])
     make_subplot(ax, 'err', csd_x, csd_y, abs(errs[1] - errs[0]), ele_pos=electrode_positions(missing_ele=5),
-                 cax=cax, title='Error Diff CSD 5 broken', xlabel=True,  letter='B',
+                 cax=cax, title='5 broken - Error CSD ', xlabel=True,  letter='B',
                  t_max=err_max)
     ax = plt.subplot(gs[0, 2])
     cax = plt.subplot(gs[1, 2])
     make_subplot(ax, 'err', csd_x, csd_y, abs(errs[2] - errs[0]), ele_pos=electrode_positions(missing_ele=10),
-                 cax=cax, title='Error Diff CSD 10 broken', xlabel=True, letter='C',
+                 cax=cax, title='10 broken - Error CSD', xlabel=True, letter='C',
                  t_max=err_max)
     ax = plt.subplot(gs[0, 3])
     cax = plt.subplot(gs[1, 3])
     make_subplot(ax, 'err', csd_x, csd_y, abs(errs[3] - errs[0]), ele_pos=electrode_positions(missing_ele=20),
-                 cax=cax, title='Error Diff CSD 20 broken', xlabel=True, letter='D',
+                 cax=cax, title='20 broken - Error CSD', xlabel=True, letter='D',
                  t_max=err_max)
 
     errs = fetch_values('small')
@@ -302,6 +304,7 @@ def generate_figure2():
     make_subplot(ax, 'err', csd_x, csd_y, errs[0], ele_pos=electrode_positions(missing_ele=0),
                  cax=cax, xlabel=True, ylabel=True, letter='E',
                  t_max=.2)
+    ax.text(-0.4, 0.5, 'Small sources', fontsize=20, rotation=90, va='center')
     ax = plt.subplot(gs[0, 1])
     cax = plt.subplot(gs[1, 1])
     make_subplot(ax, 'err', csd_x, csd_y, abs(errs[1] - errs[0]), ele_pos=electrode_positions(missing_ele=5),
@@ -327,6 +330,7 @@ def generate_figure2():
     make_subplot(ax, 'err', csd_x, csd_y, errs[0], ele_pos=electrode_positions(missing_ele=0),
                  cax=cax, xlabel=True, ylabel=True, letter='I',
                  t_max=.2)
+    ax.text(-0.4, 0.5, 'Large sources', fontsize=20, rotation=90, va='center')
     ax = plt.subplot(gs[0, 1])
     cax = plt.subplot(gs[1, 1])
     make_subplot(ax, 'err', csd_x, csd_y, abs(errs[1] - errs[0]), ele_pos=electrode_positions(missing_ele=5),

figures/kCSD_properties/tutorial_broken_electrodes_diff_err.py

@@ -36,7 +36,7 @@ def grid(x, y, z):
 def set_axis(ax, letter=None):
     ax.text(
         -0.05,
-        1.05,
+        1.1,
         letter,
         fontsize=20,
         weight='bold',
@@ -77,7 +77,7 @@ def make_subplot(ax, val_type, xs, ys, values, cax, title=None, ele_pos=None, xl
     if ylabel:
         ax.set_ylabel('Y (mm)')
     if title is not None:
-        ax.set_title(title)
+        ax.set_title(title, pad=10)
     ax.set_xticks([0, 0.5, 1])
     ax.set_yticks([0, 0.5, 1])
     ticks = np.linspace(0, t_max, 3, endpoint=True)
@@ -97,12 +97,11 @@ def do_kcsd(CSD_PROFILE, csd_seed, noise_level):
 #        R_final = np.linspace(0.1, 1.5, 15)
         R_final = np.linspace(0.05, 1., 20)
     # True CSD_PROFILE
-    csd_at = np.mgrid[0.:1.:100j,
-                      0.:1.:100j]
+    csd_at = np.mgrid[0.:1.:101j,
+                      0.:1.:101j]
     csd_x, csd_y = csd_at
     # Small source
     true_csd = CSD_PROFILE(csd_at, seed=csd_seed) 
-
     # Electrode positions
     ele_x, ele_y = np.mgrid[0.05: 0.95: 10j,
                             0.05: 0.95: 10j]
@@ -153,12 +152,12 @@ def generate_figure(small_seed, large_seed):
     cax = plt.subplot(gs[1, 0])
     make_subplot(ax, 'err', csd_x, csd_y, err, ele_pos=ele_pos,
                  cax=cax, title='Error CSD', xlabel=True, ylabel=True, letter='A', t_max=t_max_1)
-    
+    ax.text(-0.4, 0.5, 'Small sources', fontsize=20, rotation=90, va='center')
     csd_x, csd_y, err, ele_pos = do_kcsd(CSD.gauss_2d_small, csd_seed=small_seed, noise_level=5)
     ax = plt.subplot(gs[0, 1])
     cax = plt.subplot(gs[1, 1])
     make_subplot(ax, 'err', csd_x, csd_y, err, ele_pos=ele_pos,
-                 cax=cax, title='Error CSD 5% noise', xlabel=True, ylabel=True, letter='B', t_max=t_max_1)
+                 cax=cax, title='Error CSD 5% noise', xlabel=True, letter='B', t_max=t_max_1)
 
     csd_x, csd_y, err, ele_pos = do_kcsd(CSD.gauss_2d_small, csd_seed=small_seed, noise_level=10)
     ax = plt.subplot(gs[0, 2])
@@ -180,7 +179,7 @@ def generate_figure(small_seed, large_seed):
     cax = plt.subplot(gs[1, 0])
     make_subplot(ax, 'err', csd_x, csd_y, err, ele_pos=ele_pos,
                  cax=cax, xlabel=True, ylabel=True, letter='E', t_max=0.55)
-    
+    ax.text(-0.4, 0.5, 'Large sources', fontsize=20, rotation=90, va='center')
     csd_x, csd_y, err, ele_pos = do_kcsd(CSD.gauss_2d_large, csd_seed=large_seed, noise_level=5)
     ax = plt.subplot(gs[0, 1])
     cax = plt.subplot(gs[1, 1])
@@ -199,7 +198,7 @@ def generate_figure(small_seed, large_seed):
     make_subplot(ax, 'err', csd_x, csd_y, err, ele_pos=ele_pos,
                  cax=cax,  xlabel=True,  letter='H', t_max=0.55)
     plt.savefig('tutorial_noise.png', dpi=300)
-    plt.show()
+    # plt.show()
 
 if __name__ == '__main__':
     small_seed = 15