136 lines
4.5 KiB
Python
136 lines
4.5 KiB
Python
import numpy as np
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import matplotlib.pyplot as plt
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from thunderhopper.filetools import search_files
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from thunderhopper.modeltools import load_data, save_data
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from misc_functions import shorten_species, sort_files_by_rec
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from IPython import embed
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# GENERAL SETTINGS:
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target_species = [
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'Chorthippus_biguttulus',
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'Chorthippus_mollis',
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'Chrysochraon_dispar',
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'Euchorthippus_declivus',
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'Gomphocerippus_rufus',
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'Omocestus_rufipes',
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'Pseudochorthippus_parallelus',
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]
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sources = [
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'BM04',
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'BM93',
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'DJN',
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'GBC',
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'FTN'
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]
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search_path = '../data/inv/thresh_lp/'
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save_path = '../data/inv/thresh_lp/condensed/'
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# ANALYSIS SETTINGS:
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with_noise = True
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plot_overview = True
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thresh_rel = np.array([0.5, 1, 3])
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# PREPARATION:
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if plot_overview:
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kern_colors = ['r', 'g', 'b']
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all_figs, all_axes = {}, {}
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for thresh in thresh_rel:
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fig, axes = plt.subplots(3, len(target_species), figsize=(16, 9),
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sharex=True, sharey=True, layout='constrained')
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fig.suptitle(f'rel. thresh: {thresh}')
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axes[0, 0].set_ylim(0, 1)
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axes[0, 0].set_ylabel('songs')
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axes[1, 0].set_ylabel('recordings\n(mean ± SD)')
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axes[2, 0].set_ylabel('total\n(mean ± SD)')
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all_figs[thresh] = fig
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all_axes[thresh] = axes
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# EXECUTION:
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for i, species in enumerate(target_species):
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print(f'Processing {species}')
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if plot_overview:
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for thresh in thresh_rel:
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all_axes[thresh][0, i].set_title(shorten_species(species))
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# Fetch all species-specific song files:
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incl = 'noise' if with_noise else 'pure'
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all_paths = search_files(species, incl=incl, ext='npz', dir=search_path)
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# Sort song files by recording (one or more per source):
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sorted_paths = sort_files_by_rec(all_paths, sources)
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# Condense across song files per recording:
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for j, rec_paths in enumerate(sorted_paths):
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for k, path in enumerate(rec_paths):
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# Load invariance data:
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data, config = load_data(path, ['scales', 'measure_feat'])
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scales, measure = data['scales'], data['measure_feat']
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if k == 0:
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# Prepare song file-specific storage:
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shape = measure.shape + (len(rec_paths),)
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file_data = np.zeros(shape, dtype=float)
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if j == 0:
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# Prepare recording-specific storage:
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shape = measure.shape + (len(sorted_paths),)
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rec_mean = np.zeros(shape, dtype=float)
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rec_sd = np.zeros(shape, dtype=float)
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# Log song file data:
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file_data[..., k] = measure
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if plot_overview:
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for l, thresh in enumerate(thresh_rel):
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axes = all_axes[thresh]
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for m, c in enumerate(kern_colors):
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axes[0, i].plot(scales, measure[:, m, l], c=c, alpha=0.5)
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# Get recording statistics:
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rec_mean[..., j] = file_data.mean(axis=-1)
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rec_sd[..., j] = file_data.std(axis=-1)
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if plot_overview:
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for l, thresh in enumerate(thresh_rel):
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axes = all_axes[thresh]
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for m, c in enumerate(kern_colors):
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axes[1, i].plot(scales, rec_mean[:, m, l, j], c=c)
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spread = (rec_mean[:, m, l, j] - rec_sd[:, m, l, j],
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rec_mean[:, m, l, j] + rec_sd[:, m, l, j])
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axes[1, i].fill_between(scales, *spread, color=c, alpha=0.2)
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# Save condensed recording data:
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save_name = save_path + species
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if with_noise:
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save_name += '_noise'
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else:
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save_name += '_pure'
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archive = dict(
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scales=scales,
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mean_feat=rec_mean,
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sd_feat=rec_sd,
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thresh_rel=thresh_rel,)
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save_data(save_name, archive, config)
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if plot_overview:
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spec_mean = rec_mean.mean(axis=-1)
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spec_sd = rec_mean.std(axis=-1)
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for l, thresh in enumerate(thresh_rel):
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axes = all_axes[thresh]
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for m, c in enumerate(kern_colors):
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axes[2, i].plot(scales, spec_mean[:, m, l], c=c)
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spread = (spec_mean[:, m, l] - spec_sd[:, m, l],
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spec_mean[:, m, l] + spec_sd[:, m, l])
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axes[2, i].fill_between(scales, *spread, color=c, alpha=0.2)
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print('Done.')
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if plot_overview:
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for thresh in thresh_rel:
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axes = all_axes[thresh]
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axes[0, 0].set_xscale('log')
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axes[0, 0].set_xlim(scales[1], scales[-1])
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plt.show()
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