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.gitignore

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-data/*
+data/*
+./_pycache_/

python/fig_pathway_stages.py

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+import glob
+import plotstyle_plt
+import numpy as np
+import matplotlib.pyplot as plt
+from thunderhopper.modeltools import load_data
+from IPython import embed
+
+# GENERAL SETTINGS:
+data_paths = glob.glob('../data/*.npz')
+channel = 0
+stages_pre = ['raw', 'filt', 'env', 'log', 'inv']
+stages_feat = ['conv', 'bi', 'feat', 'norm']
+
+# PLOT SETTINGS:
+fig_kwargs = dict(
+    figsize = np.array([16, 9]) * 0.75,
+    layout = 'constrained',
+    sharex = 'col',
+    sharey = 'row'
+)
+zoom_rel = np.array([0.4, 0.6])
+colors_pre = ['k' for _ in range(len(stages_pre))]
+colors_feat = ['k' for _ in range(len(stages_feat))]
+
+for data_path in data_paths:
+    # Load overall data:
+    data, config = load_data(data_path)
+    t_full = np.arange(data['raw'].shape[0]) / config['rate']
+
+    # Establish zoom frame:
+    zoom_abs = zoom_rel * t_full[-1]
+    zoom_mask = (t_full >= zoom_abs[0]) & (t_full <= zoom_abs[1])
+    t_zoom = t_full[zoom_mask]
+
+    # PART I: PREPROCESSING STAGE
+    fig, axes = plt.subplots(len(stages_pre), 2, **fig_kwargs)
+
+    for i, stage in enumerate(stages_pre):
+        signal = data[stage][:, channel]
+        ax_full, ax_zoom = axes[i, :]
+        ax_full.plot(t_full, signal, c=colors_pre[i])
+        ax_full.set_ylim(signal.min(), signal.max())
+
+        ax_zoom.plot(t_zoom, signal[zoom_mask], c=colors_pre[i])
+    ax_full.set_xlim(t_full[0], t_full[-1])
+
+    # PART II: FEATURE EXTRACTION STAGE:
+    fig, axes = plt.subplots(len(stages_feat), 2, **fig_kwargs)
+
+    for i, stage in enumerate(stages_feat):
+        signal = data[stage][:, ..., channel]
+        ax_full, ax_zoom = axes[i, :]
+        ax_full.plot(t_full, signal, c=colors_feat[i])
+        ax_full.set_ylim(signal.min(), signal.max())
+
+        ax_zoom.plot(t_zoom, signal[zoom_mask, ...], c=colors_feat[i])
+    ax_full.set_xlim(t_full[0], t_full[-1])
+    plt.show()
+
+

python/plotstyle_plt.py

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+import matplotlib as mpl
+
+# Latex rendering disabled:
+mpl.rcParams['text.usetex'] = False
+
+# Font style:
+mpl.rcParams['font.style'] = 'normal'
+mpl.rcParams['font.family'] = 'serif'
+mpl.rcParams['mathtext.fontset'] = 'cm'
+mpl.rcParams['mathtext.default'] = 'regular'
+# Font sizes:
+mpl.rcParams['font.size'] = 14
+mpl.rcParams['figure.titlesize'] = 15
+mpl.rcParams['axes.labelsize'] = 14
+mpl.rcParams['axes.titlesize'] = 14
+mpl.rcParams['xtick.labelsize'] = 13
+mpl.rcParams['ytick.labelsize'] = 13
+mpl.rcParams['legend.fontsize'] = 14
+mpl.rcParams['legend.title_fontsize'] = 14
+# Font weights:
+single_weight = ['normal', 'bold'][0]
+mpl.rcParams['font.weight'] = single_weight
+mpl.rcParams['axes.labelweight'] = single_weight
+mpl.rcParams['axes.titleweight'] = single_weight
+mpl.rcParams['figure.titleweight'] = single_weight
+
+# Figure parameters:
+mpl.rcParams['figure.figsize'] = (16/2.54, 9/2.54)
+mpl.rcParams['figure.autolayout'] = False
+mpl.rcParams['figure.raise_window'] = True
+# mpl.rcParams['figure.dpi'] = 100
+# mpl.rcParams['savefig.dpi'] = 500
+
+# Axes parameters:
+mpl.rcParams['axes.spines.top'] = False
+mpl.rcParams['axes.spines.right'] = False
+mpl.rcParams['axes.xmargin'] = 0
+mpl.rcParams['axes.ymargin'] = 0
+mpl.rcParams['axes.autolimit_mode'] = 'round_numbers'
+mpl.rcParams['axes.labelpad'] = 3
+
+# Tick parameters:
+mpl.rcParams['xtick.major.pad'] = 5
+mpl.rcParams['ytick.major.pad'] = 5
+
+# Legend parameters:
+mpl.rcParams['legend.frameon'] = False
+mpl.rcParams['legend.scatterpoints'] = 3