Colored the hopper. Lots of polishing.
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|
||||
***********
|
||||
LaTeX2e <2023-11-01> patch level 1
|
||||
L3 programming layer <2024-01-22>
|
||||
@ -772,18 +772,18 @@ Package logreq Info: Writing requests to 'main.run.xml'.
|
||||
|
||||
)
|
||||
Here is how much of TeX's memory you used:
|
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20729 strings out of 474222
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42713 multiletter control sequences out of 15000+600000
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569394 words of font info for 79 fonts, out of 8000000 for 9000
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1143 hyphenation exceptions out of 8191
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94i,19n,93p,955b,1732s stack positions out of 10000i,1000n,20000p,200000b,200000s
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|
||||
Output written on main.pdf (14 pages, 14132974 bytes).
|
||||
Output written on main.pdf (14 pages, 14001839 bytes).
|
||||
PDF statistics:
|
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1210 PDF objects out of 1440 (max. 8388607)
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737 compressed objects within 8 object streams
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1226 PDF objects out of 1440 (max. 8388607)
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745 compressed objects within 8 object streams
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0 named destinations out of 1000 (max. 500000)
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28 words of extra memory for PDF output out of 10000 (max. 10000000)
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|
||||
BIN
main.synctex.gz
BIN
main.synctex.gz
Binary file not shown.
7
main.tex
7
main.tex
@ -339,8 +339,7 @@ outlined in the following sections.
|
||||
|
||||
\begin{figure}[!ht]
|
||||
\centering
|
||||
\def\svgwidth{\textwidth}
|
||||
\import{figures/}{fig_auditory_pathway.pdf_tex}
|
||||
\includegraphics[width=\textwidth]{figures/fig_auditory_pathway.pdf}
|
||||
\caption{\textbf{Schematic organisation of the song recognition pathway in
|
||||
grasshoppers compared to the structure of the functional
|
||||
model pathway.}
|
||||
@ -412,7 +411,7 @@ following feature extraction stage.
|
||||
% Cite somewhere:
|
||||
\begin{figure}[!ht]
|
||||
\centering
|
||||
\includegraphics[width=\textwidth]{figures/pathway_stages_pre.pdf}
|
||||
\includegraphics[width=\textwidth]{figures/fig_pre_stages.pdf}
|
||||
\caption{\textbf{Representations of a song of \textit{O. rufipes} during
|
||||
the preprocessing stage.}
|
||||
\textbf{a}:~Bandpass-filtered tympanal signal.
|
||||
@ -526,7 +525,7 @@ can be read out by a simple linear classifier.
|
||||
% Cite somewhere:
|
||||
\begin{figure}[!ht]
|
||||
\centering
|
||||
\includegraphics[width=\textwidth]{figures/pathway_stages_feat.pdf}
|
||||
\includegraphics[width=\textwidth]{figures/fig_feat_stages.pdf}
|
||||
\caption{\textbf{Representations of a song of \textit{O. rufipes} during
|
||||
the feature extraction stage.}
|
||||
\textbf{a}:~Kernel-specific filter responses.
|
||||
|
||||
@ -1,5 +1,3 @@
|
||||
from math import log
|
||||
|
||||
import plotstyle_plt
|
||||
import glob
|
||||
import numpy as np
|
||||
@ -118,6 +116,40 @@ def reorder_traces(handles, signal, zlow=2, zhigh=2.5):
|
||||
handles[ind].set_zorder(z)
|
||||
return None
|
||||
|
||||
def choose_kernels(kern_specs, features, kern_types, per_type=2, thresh=0.01):
|
||||
embed()
|
||||
mean_feat = features.mean(axis=0)
|
||||
feat_diff = np.abs(mean_feat[:, None] - mean_feat[None, :])
|
||||
feat_diff[features.max(axis=0) < thresh, :] = np.nan
|
||||
feat_diff = np.nanmean(feat_diff, axis=0)
|
||||
|
||||
ranking = np.argsort(feat_diff)
|
||||
|
||||
kern_inds = []
|
||||
for type_id in kern_types:
|
||||
type_inds = np.nonzero(kern_specs[:, 0] == type_id)[0]
|
||||
rank_inds = np.nonzero(np.isin(ranking, type_inds))[0][-per_type:]
|
||||
kern_inds.extend(ranking[rank_inds])
|
||||
return np.array(kern_inds)
|
||||
|
||||
|
||||
mean_feat = features.mean(axis=0)
|
||||
mean_feat -= mean_feat.min()
|
||||
mean_feat /= mean_feat.max()
|
||||
|
||||
feat_diff = np.abs(mean_feat[:, None] - mean_feat[None, :]).mean(axis=0)
|
||||
feat_diff -= feat_diff.min()
|
||||
feat_diff /= feat_diff.max()
|
||||
|
||||
ranking = np.argsort(mean_feat + feat_diff)
|
||||
|
||||
kern_inds = []
|
||||
for type_id in kern_types:
|
||||
type_inds = np.nonzero(kern_specs[:, 0] == type_id)[0]
|
||||
rank_inds = np.nonzero(np.isin(ranking, type_inds))[0][-per_type:]
|
||||
kern_inds.extend(ranking[rank_inds])
|
||||
return np.array(kern_inds)
|
||||
|
||||
def letter_subplots(axes, labels='abcd', x=0.02, y=1, ha='left', va='bottom',
|
||||
fontsize=16, fontweight='bold', **kwargs):
|
||||
for ax, label in zip(axes, labels):
|
||||
@ -130,7 +162,7 @@ def letter_subplots(axes, labels='abcd', x=0.02, y=1, ha='left', va='bottom',
|
||||
target = 'Omocestus_rufipes'
|
||||
data_paths = glob.glob(f'../data/processed/{target}*.npz')
|
||||
stages = ['filt', 'env', 'log', 'inv', 'conv', 'bi', 'feat']
|
||||
save_name = '../figures/pathway_stages'
|
||||
save_path = None#'../figures/'
|
||||
|
||||
# PLOT SETTINGS:
|
||||
fig_kwargs = dict(
|
||||
@ -196,13 +228,27 @@ zoom_kwargs = dict(
|
||||
zorder=0,
|
||||
linewidth=0
|
||||
)
|
||||
# kernels = np.array([
|
||||
# [-2, 0.016],
|
||||
# [3, 0.032]
|
||||
# ])
|
||||
kern_types = np.array([1, -1, 2, -2, 3, -3, 4, -4])
|
||||
kern_sigmas = np.array([0.008, 0.032])
|
||||
kernels = np.array([[k, s] for k in kern_types for s in kern_sigmas])
|
||||
kernels = np.array([
|
||||
[1, 0.002],
|
||||
[1, 0.016],
|
||||
[-1, 0.002],
|
||||
[-1, 0.016],
|
||||
[2, 0.004],
|
||||
[2, 0.032],
|
||||
[-2, 0.004],
|
||||
[-2, 0.032],
|
||||
[3, 0.004],
|
||||
[3, 0.032],
|
||||
[-3, 0.004],
|
||||
[-3, 0.032],
|
||||
[4, 0.004],
|
||||
[4, 0.032],
|
||||
[-4, 0.004],
|
||||
[-4, 0.032]
|
||||
])
|
||||
# t = [1, 2, 3, 4]
|
||||
# s = [0.001, 0.002, 0.004, 0.008, 0.032]
|
||||
# kernels = np.array([[i, j] for i in t for j in s])
|
||||
conv_colors = load_colors('../data/conv_colors.npz')
|
||||
bi_colors = load_colors('../data/bi_colors.npz')
|
||||
feat_colors = load_colors('../data/feat_colors.npz')
|
||||
@ -266,9 +312,8 @@ for data_path in data_paths:
|
||||
indicate_zoom(fig, axes[0, 0], axes[-1, 0], zoom_abs, **zoom_kwargs)
|
||||
indicate_zoom(fig, axes[0, 1], axes[-1, 1], zoom_abs, **zoom_kwargs)
|
||||
letter_subplots(axes[:, 0])
|
||||
# fig.align_ylabels(axes[:, 0])
|
||||
if save_name is not None:
|
||||
fig.savefig(f'{save_name}_pre.pdf')
|
||||
if save_path is not None:
|
||||
fig.savefig(f'{save_path}fig_pre_stages.pdf')
|
||||
|
||||
|
||||
# PART II: FEATURE EXTRACTION STAGE:
|
||||
@ -312,9 +357,8 @@ for data_path in data_paths:
|
||||
indicate_zoom(fig, axes[0, 0], axes[-1, 0], zoom_abs, **zoom_kwargs)
|
||||
indicate_zoom(fig, axes[0, 1], axes[-1, 1], zoom_abs, **zoom_kwargs)
|
||||
letter_subplots(axes[:, 0])
|
||||
# fig.align_ylabels(axes[:, 0])
|
||||
if save_name is not None:
|
||||
fig.savefig(f'{save_name}_feat.pdf')
|
||||
if save_path is not None:
|
||||
fig.savefig(f'{save_path}fig_feat_stages.pdf')
|
||||
plt.show()
|
||||
|
||||
|
||||
|
||||
140
python/save_figure_texts.py
Normal file
140
python/save_figure_texts.py
Normal file
@ -0,0 +1,140 @@
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
# Fixed RCs:
|
||||
plt.rcParams['font.style'] = 'normal'
|
||||
plt.rcParams['mathtext.fontset'] = 'cm'
|
||||
plt.rcParams['svg.fonttype'] = 'path'
|
||||
plt.rc('text.latex', preamble=r'\usepackage{amsmath}')
|
||||
|
||||
# Context RCs:
|
||||
show_figs = True
|
||||
rc_tex = {
|
||||
'text.usetex': True,
|
||||
'font.family': 'computer modern roman',
|
||||
}
|
||||
rc_plt = {
|
||||
'text.usetex': False,
|
||||
'font.family': 'sans-serif',
|
||||
}
|
||||
|
||||
# Instance configs:
|
||||
title_props = dict(
|
||||
use_tex=False,
|
||||
figsize=(5, 2.5),
|
||||
fs=53,
|
||||
fw='normal',
|
||||
)
|
||||
letter_props = dict(
|
||||
use_tex=False,
|
||||
figsize=(1, 1),
|
||||
fs=70,
|
||||
fw='bold',
|
||||
)
|
||||
element_props = dict(
|
||||
use_tex=True,
|
||||
figsize=(3, 3),
|
||||
fs=80,
|
||||
fw='normal',
|
||||
)
|
||||
line_props = dict(
|
||||
use_tex=True,
|
||||
figsize=(3, 2),
|
||||
fs=75,
|
||||
fw='normal',
|
||||
)
|
||||
|
||||
# Auxiliary configs:
|
||||
fig_kwargs = dict(
|
||||
gridspec_kw={'left': 0, 'right': 1, 'top': 1, 'bottom': 0},
|
||||
facecolor='none',
|
||||
edgecolor='none',
|
||||
frameon=False,
|
||||
)
|
||||
ax_kwargs = dict(
|
||||
facecolor='none',
|
||||
frame_on=False,
|
||||
)
|
||||
text_kwargs = dict(
|
||||
color='k',
|
||||
x=0.5,
|
||||
y=0.5,
|
||||
ha='center',
|
||||
va='center',
|
||||
)
|
||||
|
||||
# Targets:
|
||||
texts = {
|
||||
### PLAIN FONT ###
|
||||
|
||||
# TITLES (NEURONAL CIRCUIT):
|
||||
'neuron_titles_tympanum': ('Tympanal\nMembrane', title_props),
|
||||
'neuron_titles_receptors': ('Receptor\nNeurons', title_props),
|
||||
'neuron_titles_interneurons': ('Local\nInterneurons', title_props),
|
||||
'neuron_titles_ascending': ('Ascending\nNeurons', title_props),
|
||||
'neuron_titles_brain': ('Central\nBrain', title_props),
|
||||
|
||||
# TITLES (MODEL CIRCUIT):
|
||||
'model_titles_bandpass': ('Bandpass\nFiltering', title_props),
|
||||
'model_titles_envelope': ('Envelope\nExtraction', title_props),
|
||||
'model_titles_logarithm': ('Logarithmic\nCompression', title_props),
|
||||
'model_titles_adaptation': ('Intensity\nAdaptation', title_props),
|
||||
'model_titles_convolution': ('Convolutional\nFiltering', title_props),
|
||||
'model_titles_nonlinear': ('Threshold\nNonlinearity', title_props),
|
||||
'model_titles_integration': ('Temporal\nAveraging', title_props),
|
||||
'model_titles_readout': ('Weighted\nReadout', title_props),
|
||||
|
||||
# SUBPLOT LETTERS:
|
||||
'subplot_a': ('a', letter_props),
|
||||
'subplot_b': ('b', letter_props),
|
||||
'subplot_c': ('c', letter_props),
|
||||
'subplot_d': ('d', letter_props),
|
||||
|
||||
### TEX FONT ###
|
||||
|
||||
# ELEMENT LABELS (MODEL CIRCUIT):
|
||||
'model_elements_filt': (r'$x_{\text{filt}}$', element_props),
|
||||
'model_elements_env': (r'$x_{\text{env}}$', element_props),
|
||||
'model_elements_log': (r'$x_{\text{dB}}$', element_props),
|
||||
'model_elements_adapt': (r'$x_{\text{adapt}}$', element_props),
|
||||
'model_elements_c1': (r'$c_1$', element_props),
|
||||
'model_elements_c2': (r'$c_2$', element_props),
|
||||
'model_elements_c3': (r'$c_3$', element_props),
|
||||
'model_elements_b1': (r'$b_1$', element_props),
|
||||
'model_elements_b2': (r'$b_2$', element_props),
|
||||
'model_elements_b3': (r'$b_3$', element_props),
|
||||
'model_elements_f1': (r'$f_1$', element_props),
|
||||
'model_elements_f2': (r'$f_2$', element_props),
|
||||
'model_elements_f3': (r'$f_3$', element_props),
|
||||
'model_elements_out': (r'$\hat{y}$', element_props),
|
||||
|
||||
# LINE LABELS (MODEL CIRCUIT):
|
||||
'model_lines_env': (r'$\lvert\cdot\lvert,h_{\text{LP}}$', line_props),
|
||||
'model_lines_log': (r'$\text{log}$', line_props),
|
||||
'model_lines_hp': (r'$h_{\text{HP}}$', line_props),
|
||||
'model_lines_k1': (r'$k_1$', line_props),
|
||||
'model_lines_k2': (r'$k_2$', line_props),
|
||||
'model_lines_k3': (r'$k_3$', line_props),
|
||||
'model_lines_t1': (r'$\Theta_1$', line_props),
|
||||
'model_lines_t2': (r'$\Theta_2$', line_props),
|
||||
'model_lines_t3': (r'$\Theta_3$', line_props),
|
||||
# 'model_lines_H1': (r'$H(c_1-\Theta_1)$', line_props),
|
||||
# 'model_lines_H2': (r'$H(c_2-\Theta_2)$', line_props),
|
||||
# 'model_lines_H3': (r'$H(c_3-\Theta_3)$', line_props),
|
||||
'model_lines_lp': (r'$h_{\text{LP}}$', line_props),
|
||||
'model_lines_w1': (r'$\omega_1$', line_props),
|
||||
'model_lines_w2': (r'$\omega_2$', line_props),
|
||||
'model_lines_w3': (r'$\omega_3$', line_props),
|
||||
}
|
||||
|
||||
# Save each target string:
|
||||
for name, (text, props) in texts.items():
|
||||
plt.rcParams.update(rc_tex if props['use_tex'] else rc_plt)
|
||||
fig, ax = plt.subplots(figsize=props['figsize'], **fig_kwargs)
|
||||
ax.set(**ax_kwargs)
|
||||
ax.axis('off')
|
||||
ax.text(s=text, size=props['fs'], weight=props['fw'], **text_kwargs)
|
||||
fig.savefig(f'../figures/{name}_text.svg', dpi=300,
|
||||
bbox_inches='tight', pad_inches=0)
|
||||
if show_figs:
|
||||
plt.show()
|
||||
plt.close(fig)
|
||||
@ -13,4 +13,6 @@ stage_colors = load_colors('../data/stage_colors.npz')
|
||||
for stage in stages:
|
||||
colors = shade_colors(stage_colors[stage], shade_factors)
|
||||
colors = {str(k): c for k, c in zip(kern_types, colors)}
|
||||
print(f'\n{stage} colors:')
|
||||
print(colors)
|
||||
np.savez(f'../data/{stage}_colors.npz', **colors)
|
||||
|
||||
@ -1,103 +0,0 @@
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
plt.rcParams['text.usetex'] = True
|
||||
plt.rcParams['font.family'] = 'computer modern roman'
|
||||
plt.rcParams['mathtext.fontset'] = 'cm'
|
||||
plt.rcParams['mathtext.default'] = 'regular'
|
||||
plt.rcParams['svg.fonttype'] = 'path'
|
||||
plt.rc('text.latex', preamble=r'\usepackage{amsmath}')
|
||||
|
||||
# Settings:
|
||||
titles_fontsize = 65
|
||||
titles_figsize = (5, 2.5)
|
||||
elements_fontsize = 80
|
||||
elements_figsize = (3, 3)
|
||||
lines_fontsize = 75
|
||||
lines_figsize = (3, 2)
|
||||
show_figs = True
|
||||
grid_props = dict(left=0, right=1, top=1, bottom=0)
|
||||
|
||||
fig_props = {
|
||||
'facecolor': 'none',
|
||||
'edgecolor': 'none',
|
||||
'frameon': False,
|
||||
}
|
||||
|
||||
ax_props = {
|
||||
'facecolor': 'none',
|
||||
'frame_on': False,
|
||||
}
|
||||
|
||||
text_props = {
|
||||
'color': 'k',
|
||||
'x': 0.5,
|
||||
'y': 0.5,
|
||||
'ha': 'center',
|
||||
'va': 'center',
|
||||
}
|
||||
|
||||
# Targets:
|
||||
texts = {
|
||||
# # TITLES (NEURONAL CIRCUIT):
|
||||
# 'neuron_titles_tympanum': ('Tympanal\nMembrane', titles_fontsize, titles_figsize),
|
||||
# 'neuron_titles_receptors': ('Receptor\nNeurons', titles_fontsize, titles_figsize),
|
||||
# 'neuron_titles_interneurons': ('Local\nInterneurons', titles_fontsize, titles_figsize),
|
||||
# 'neuron_titles_ascending': ('Ascending\nNeurons', titles_fontsize, titles_figsize),
|
||||
# 'neuron_titles_brain': ('Central\nBrain', titles_fontsize, titles_figsize),
|
||||
|
||||
# # TITLES (MODEL CIRCUIT):
|
||||
# 'model_titles_bandpass': ('Bandpass\nFiltering', titles_fontsize, titles_figsize),
|
||||
# 'model_titles_envelope': ('Envelope\nExtraction', titles_fontsize, titles_figsize),
|
||||
# 'model_titles_logarithm': ('Logarithmic\nCompression', titles_fontsize, titles_figsize),
|
||||
# 'model_titles_adaptation': ('Intensity\nAdaptation', titles_fontsize, titles_figsize),
|
||||
# 'model_titles_convolution': ('Convolutional\nFiltering', titles_fontsize, titles_figsize),
|
||||
# 'model_titles_nonlinear': ('Threshold\nNonlinearity', titles_fontsize, titles_figsize),
|
||||
# 'model_titles_integration': ('Temporal\nAveraging', titles_fontsize, titles_figsize),
|
||||
# 'model_titles_readout': ('Weighted\nReadout', titles_fontsize, titles_figsize),
|
||||
|
||||
# # ELEMENT LABELS (MODEL CIRCUIT):
|
||||
# 'model_elements_filt': (r'$x_{\text{filt}}$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_env': (r'$x_{\text{env}}$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_log': (r'$x_{\text{dB}}$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_adapt': (r'$x_{\text{adapt}}$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_c1': (r'$c_1$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_c2': (r'$c_2$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_c3': (r'$c_3$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_b1': (r'$b_1$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_b2': (r'$b_2$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_b3': (r'$b_3$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_f1': (r'$f_1$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_f2': (r'$f_2$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_f3': (r'$f_3$', elements_fontsize, elements_figsize),
|
||||
# 'model_elements_out': (r'$\hat{y}$', elements_fontsize, elements_figsize),
|
||||
|
||||
# LINE LABELS (MODEL CIRCUIT):
|
||||
'model_lines_env': (r'$\lvert\cdot\lvert,h_{\text{LP}}$', lines_fontsize, lines_figsize),
|
||||
'model_lines_log': (r'$\text{log}$', lines_fontsize, lines_figsize),
|
||||
'model_lines_hp': (r'$h_{\text{HP}}$', lines_fontsize, lines_figsize),
|
||||
'model_lines_k1': (r'$k_1$', lines_fontsize, lines_figsize),
|
||||
'model_lines_k2': (r'$k_2$', lines_fontsize, lines_figsize),
|
||||
'model_lines_k3': (r'$k_3$', lines_fontsize, lines_figsize),
|
||||
'model_lines_t1': (r'$\Theta_1$', lines_fontsize, lines_figsize),
|
||||
'model_lines_t2': (r'$\Theta_2$', lines_fontsize, lines_figsize),
|
||||
'model_lines_t3': (r'$\Theta_3$', lines_fontsize, lines_figsize),
|
||||
# 'model_lines_H1': (r'$H(c_1-\Theta_1)$', lines_fontsize, lines_figsize),
|
||||
# 'model_lines_H2': (r'$H(c_2-\Theta_2)$', lines_fontsize, lines_figsize),
|
||||
# 'model_lines_H3': (r'$H(c_3-\Theta_3)$', lines_fontsize, lines_figsize),
|
||||
'model_lines_lp': (r'$h_{\text{LP}}$', lines_fontsize, lines_figsize),
|
||||
'model_lines_w1': (r'$\omega_1$', lines_fontsize, lines_figsize),
|
||||
'model_lines_w2': (r'$\omega_2$', lines_fontsize, lines_figsize),
|
||||
'model_lines_w3': (r'$\omega_3$', lines_fontsize, lines_figsize),
|
||||
}
|
||||
|
||||
# Save each target string:
|
||||
for name, (text, fs, size) in texts.items():
|
||||
fig, ax = plt.subplots(figsize=size, gridspec_kw=grid_props, **fig_props)
|
||||
ax.set(**ax_props)
|
||||
ax.axis('off')
|
||||
ax.text(s=text, fontsize=fs, **text_props)
|
||||
fig.savefig(f'../figures/{name}_text.svg', dpi=300,
|
||||
bbox_inches='tight', pad_inches=0)
|
||||
if show_figs:
|
||||
plt.show()
|
||||
plt.close(fig)
|
||||
@ -1,10 +1,10 @@
|
||||
import matplotlib.pyplot as plt
|
||||
from color_functions import load_colors, color_selector
|
||||
from color_functions import load_colors, color_selector, hex_to_rgb
|
||||
from IPython import embed
|
||||
|
||||
# Settings:
|
||||
stages = ['filt', 'env', 'log', 'inv', 'conv', 'bi', 'feat']
|
||||
file_name = None#'../data/stage_colors'
|
||||
stages = ['filt', 'env', 'log', 'inv', 'conv', 'bi', 'feat', 'out']
|
||||
file_name = '../data/stage_colors'
|
||||
colors = None
|
||||
if True:
|
||||
colors = load_colors('../data/stage_colors.npz')
|
||||
@ -12,4 +12,4 @@ if True:
|
||||
# Execution:
|
||||
colors = color_selector(len(stages), colors, file_name, labels=stages, hex=True)
|
||||
plt.show()
|
||||
embed()
|
||||
embed()
|
||||
Loading…
Reference in New Issue
Block a user