raab/GP2023_chirp_detection
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different bootstrap approaches

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sprause 2023-01-24 20:49:57 +01:00
parent ad9cf9c785
commit 89823fdc28
1 changed files with 129 additions and 88 deletions
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code/eventchirpsplots.py
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@ -9,7 +9,7 @@ from IPython import embed
from pandas import read_csv
from modules.logger import makeLogger
from modules.plotstyle import PlotStyle
from modules.datahandling import causal_kde1d, acausal_kde1d
from modules.datahandling import causal_kde1d, acausal_kde1d, flatten
logger = makeLogger(__name__)
ps = PlotStyle()
@ -194,6 +194,7 @@ def main(datapath: str):
nrecording_physicals.append(physical_contacts)
# Define time window for chirps around event analysis
time_before_event = 30
time_after_event = 60
@ -212,7 +213,7 @@ def main(datapath: str):
nrecording_shuffled_convolved_offset_chirps = []
nrecording_shuffled_convolved_physical_chirps = []
nbootstrapping = 10
nbootstrapping = 100
for i in range(len(nrecording_chirps)):
chirps = nrecording_chirps[i]
@ -236,89 +237,124 @@ def main(datapath: str):
nshuffled_offset_chirps = []
nshuffled_physical_chirps = []
for j in tqdm(range(nbootstrapping)):
# Calculate interchirp intervals; add first chirp timestamp in beginning to get equal lengths
interchirp_intervals = np.append(np.array([chirps[0]]), np.diff(chirps))
np.random.shuffle(interchirp_intervals)
shuffled_chirps = np.cumsum(interchirp_intervals)
# Shuffled chasing onset chirps
_, _, cc_shuffled_onset_chirps = event_triggered_chirps(chasing_onsets, shuffled_chirps, time_before_event, time_after_event, dt, recording_width)
nshuffled_onset_chirps.append(cc_shuffled_onset_chirps)
# Shuffled chasing offset chirps
_, _, cc_shuffled_offset_chirps = event_triggered_chirps(chasing_offsets, shuffled_chirps, time_before_event, time_after_event, dt, recording_width)
nshuffled_offset_chirps.append(cc_shuffled_offset_chirps)
# Shuffled physical contact chirps
_, _, cc_shuffled_physical_chirps = event_triggered_chirps(physical_contacts, shuffled_chirps, time_before_event, time_after_event, dt, recording_width)
nshuffled_physical_chirps.append(cc_shuffled_physical_chirps)
rec_shuffled_q5_onset, rec_shuffled_median_onset, rec_shuffled_q95_onset = np.percentile(
nshuffled_onset_chirps, (5, 50, 95), axis=0)
rec_shuffled_q5_offset, rec_shuffled_median_offset, rec_shuffled_q95_offset = np.percentile(
nshuffled_offset_chirps, (5, 50, 95), axis=0)
rec_shuffled_q5_physical, rec_shuffled_median_physical, rec_shuffled_q95_physical = np.percentile(
nshuffled_physical_chirps, (5, 50, 95), axis=0)
#### Recording plots ####
fig, ax = plt.subplots(1, 3, figsize=(28*ps.cm, 16*ps.cm, ), constrained_layout=True, sharey='all')
ax[0].set_xlabel('Time[s]')
# Plot chasing onsets
ax[0].set_ylabel('Chirp rate [Hz]')
ax[0].plot(time, cc_chasing_onset_chirps, color=ps.yellow, zorder=2)
ax0 = ax[0].twinx()
ax0.eventplot(centered_chasing_onset_chirps, linelengths=0.2, colors=ps.gray, alpha=0.25, zorder=1)
ax0.vlines(0, 0, 1.5, ps.white, 'dashed')
ax[0].set_zorder(ax0.get_zorder()+1)
ax[0].patch.set_visible(False)
ax0.set_yticklabels([])
ax0.set_yticks([])
ax[0].fill_between(time, rec_shuffled_q5_onset, rec_shuffled_q95_onset, color=ps.gray, alpha=0.5)
ax[0].plot(time, rec_shuffled_median_onset, color=ps.black)
# Plot chasing offets
ax[1].set_xlabel('Time[s]')
ax[1].plot(time, cc_chasing_offset_chirps, color=ps.orange, zorder=2)
ax1 = ax[1].twinx()
ax1.eventplot(centered_chasing_offset_chirps, linelengths=0.2, colors=ps.gray, alpha=0.25, zorder=1)
ax1.vlines(0, 0, 1.5, ps.white, 'dashed')
ax[1].set_zorder(ax1.get_zorder()+1)
ax[1].patch.set_visible(False)
ax1.set_yticklabels([])
ax1.set_yticks([])
ax[1].fill_between(time, rec_shuffled_q5_offset, rec_shuffled_q95_offset, color=ps.gray, alpha=0.5)
ax[1].plot(time, rec_shuffled_median_offset, color=ps.black)
# Plot physical contacts
ax[2].set_xlabel('Time[s]')
ax[2].plot(time, cc_physical_chirps, color=ps.maroon, zorder=2)
ax2 = ax[2].twinx()
ax2.eventplot(centered_physical_chirps, linelengths=0.2, colors=ps.gray, alpha=0.25, zorder=1)
ax2.vlines(0, 0, 1.5, ps.white, 'dashed')
ax[2].set_zorder(ax2.get_zorder()+1)
ax[2].patch.set_visible(False)
ax2.set_yticklabels([])
ax2.set_yticks([])
ax[2].fill_between(time, rec_shuffled_q5_physical, rec_shuffled_q95_physical, color=ps.gray, alpha=0.5)
ax[2].plot(time, rec_shuffled_median_physical, ps.black)
fig.suptitle(f'Recording: {i}')
plt.show()
# for j in tqdm(range(nbootstrapping)):
# # Calculate interchirp intervals; add first chirp timestamp in beginning to get equal lengths
# interchirp_intervals = np.append(np.array([chirps[0]]), np.diff(chirps))
# np.random.shuffle(interchirp_intervals)
# shuffled_chirps = np.cumsum(interchirp_intervals)
# # Shuffled chasing onset chirps
# _, _, cc_shuffled_onset_chirps = event_triggered_chirps(chasing_onsets, shuffled_chirps, time_before_event, time_after_event, dt, recording_width)
# nshuffled_onset_chirps.append(cc_shuffled_onset_chirps)
# # Shuffled chasing offset chirps
# _, _, cc_shuffled_offset_chirps = event_triggered_chirps(chasing_offsets, shuffled_chirps, time_before_event, time_after_event, dt, recording_width)
# nshuffled_offset_chirps.append(cc_shuffled_offset_chirps)
# # Shuffled physical contact chirps
# _, _, cc_shuffled_physical_chirps = event_triggered_chirps(physical_contacts, shuffled_chirps, time_before_event, time_after_event, dt, recording_width)
# nshuffled_physical_chirps.append(cc_shuffled_physical_chirps)
# rec_shuffled_q5_onset, rec_shuffled_median_onset, rec_shuffled_q95_onset = np.percentile(
# nshuffled_onset_chirps, (5, 50, 95), axis=0)
# rec_shuffled_q5_offset, rec_shuffled_median_offset, rec_shuffled_q95_offset = np.percentile(
# nshuffled_offset_chirps, (5, 50, 95), axis=0)
# rec_shuffled_q5_physical, rec_shuffled_median_physical, rec_shuffled_q95_physical = np.percentile(
# nshuffled_physical_chirps, (5, 50, 95), axis=0)
# #### Recording plots ####
# fig, ax = plt.subplots(1, 3, figsize=(28*ps.cm, 16*ps.cm, ), constrained_layout=True, sharey='all')
# ax[0].set_xlabel('Time[s]')
# # Plot chasing onsets
# ax[0].set_ylabel('Chirp rate [Hz]')
# ax[0].plot(time, cc_chasing_onset_chirps, color=ps.yellow, zorder=2)
# ax0 = ax[0].twinx()
# ax0.eventplot(centered_chasing_onset_chirps, linelengths=0.2, colors=ps.gray, alpha=0.25, zorder=1)
# ax0.vlines(0, 0, 1.5, ps.white, 'dashed')
# ax[0].set_zorder(ax0.get_zorder()+1)
# ax[0].patch.set_visible(False)
# ax0.set_yticklabels([])
# ax0.set_yticks([])
# ######## median - q5, median + q95
# ax[0].fill_between(time, rec_shuffled_q5_onset, rec_shuffled_q95_onset, color=ps.gray, alpha=0.5)
# ax[0].plot(time, rec_shuffled_median_onset, color=ps.black)
# # Plot chasing offets
# ax[1].set_xlabel('Time[s]')
# ax[1].plot(time, cc_chasing_offset_chirps, color=ps.orange, zorder=2)
# ax1 = ax[1].twinx()
# ax1.eventplot(centered_chasing_offset_chirps, linelengths=0.2, colors=ps.gray, alpha=0.25, zorder=1)
# ax1.vlines(0, 0, 1.5, ps.white, 'dashed')
# ax[1].set_zorder(ax1.get_zorder()+1)
# ax[1].patch.set_visible(False)
# ax1.set_yticklabels([])
# ax1.set_yticks([])
# ax[1].fill_between(time, rec_shuffled_q5_offset, rec_shuffled_q95_offset, color=ps.gray, alpha=0.5)
# ax[1].plot(time, rec_shuffled_median_offset, color=ps.black)
# # Plot physical contacts
# ax[2].set_xlabel('Time[s]')
# ax[2].plot(time, cc_physical_chirps, color=ps.maroon, zorder=2)
# ax2 = ax[2].twinx()
# ax2.eventplot(centered_physical_chirps, linelengths=0.2, colors=ps.gray, alpha=0.25, zorder=1)
# ax2.vlines(0, 0, 1.5, ps.white, 'dashed')
# ax[2].set_zorder(ax2.get_zorder()+1)
# ax[2].patch.set_visible(False)
# ax2.set_yticklabels([])
# ax2.set_yticks([])
# ax[2].fill_between(time, rec_shuffled_q5_physical, rec_shuffled_q95_physical, color=ps.gray, alpha=0.5)
# ax[2].plot(time, rec_shuffled_median_physical, ps.black)
# fig.suptitle(f'Recording: {i}')
# # plt.show()
# plt.close()
nrecording_shuffled_convolved_onset_chirps.append(nshuffled_onset_chirps)
nrecording_shuffled_convolved_offset_chirps.append(nshuffled_offset_chirps)
nrecording_shuffled_convolved_physical_chirps.append(nshuffled_physical_chirps)
# nrecording_shuffled_convolved_onset_chirps.append(nshuffled_onset_chirps)
# nrecording_shuffled_convolved_offset_chirps.append(nshuffled_offset_chirps)
# nrecording_shuffled_convolved_physical_chirps.append(nshuffled_physical_chirps)
#### New shuffle approach ####
bootstrap_onset = []
bootstrap_offset = []
bootstrap_physical = []
# New bootstrapping approach
for n in range(nbootstrapping):
diff_onset = np.diff(np.sort(flatten(nrecording_centered_onset_chirps)))
diff_offset = np.diff(np.sort(flatten(nrecording_centered_offset_chirps)))
diff_physical = np.diff(np.sort(flatten(nrecording_centered_physical_chirps)))
np.random.shuffle(diff_onset)
shuffled_onset = np.cumsum(diff_onset)
np.random.shuffle(diff_offset)
shuffled_offset = np.cumsum(diff_offset)
np.random.shuffle(diff_physical)
shuffled_physical = np.cumsum(diff_physical)
kde_onset = (acausal_kde1d(shuffled_onset, time, width))/(27*100)
kde_offset = (acausal_kde1d(shuffled_offset, time, width))/(27*100)
kde_physical = (acausal_kde1d(shuffled_physical, time, width))/(27*100)
bootstrap_onset.append(kde_onset)
bootstrap_offset.append(kde_offset)
bootstrap_physical.append(kde_physical)
# New shuffle approach q5, q50, q95
onset_q5, onset_median, onset_q95 = np.percentile(bootstrap_onset, [5, 50, 95], axis=0)
offset_q5, offset_median, offset_q95 = np.percentile(bootstrap_offset, [5, 50, 95], axis=0)
physical_q5, physical_median, physical_q95 = np.percentile(bootstrap_physical, [5, 50, 95], axis=0)
# vstack um 1. Dim zu cutten
nrecording_shuffled_convolved_onset_chirps = np.vstack(nrecording_shuffled_convolved_onset_chirps)
nrecording_shuffled_convolved_offset_chirps = np.vstack(nrecording_shuffled_convolved_offset_chirps)
nrecording_shuffled_convolved_physical_chirps = np.vstack(nrecording_shuffled_convolved_physical_chirps)
# nrecording_shuffled_convolved_onset_chirps = np.vstack(nrecording_shuffled_convolved_onset_chirps)
# nrecording_shuffled_convolved_offset_chirps = np.vstack(nrecording_shuffled_convolved_offset_chirps)
# nrecording_shuffled_convolved_physical_chirps = np.vstack(nrecording_shuffled_convolved_physical_chirps)
shuffled_q5_onset, shuffled_median_onset, shuffled_q95_onset = np.percentile(
nrecording_shuffled_convolved_onset_chirps, (5, 50, 95), axis=0)
shuffled_q5_offset, shuffled_median_offset, shuffled_q95_offset = np.percentile(
nrecording_shuffled_convolved_offset_chirps, (5, 50, 95), axis=0)
shuffled_q5_physical, shuffled_median_physical, shuffled_q95_physical = np.percentile(
nrecording_shuffled_convolved_physical_chirps, (5, 50, 95), axis=0)
# shuffled_q5_onset, shuffled_median_onset, shuffled_q95_onset = np.percentile(
# nrecording_shuffled_convolved_onset_chirps, (5, 50, 95), axis=0)
# shuffled_q5_offset, shuffled_median_offset, shuffled_q95_offset = np.percentile(
# nrecording_shuffled_convolved_offset_chirps, (5, 50, 95), axis=0)
# shuffled_q5_physical, shuffled_median_physical, shuffled_q95_physical = np.percentile(
# nrecording_shuffled_convolved_physical_chirps, (5, 50, 95), axis=0)
# Flatten all chirps
all_chirps = np.concatenate(nrecording_chirps).ravel() # not centered
@ -339,7 +375,6 @@ def main(datapath: str):
all_offset_chirps_convolved = (acausal_kde1d(all_offset_chirps, time, width)) / len(all_offsets)
all_physical_chirps_convolved = (acausal_kde1d(all_physical_chirps, time, width)) / len(all_physicals)
# Plot all events with all shuffled
fig, ax = plt.subplots(1, 3, figsize=(28*ps.cm, 16*ps.cm, ), constrained_layout=True, sharey='all')
# offsets = np.arange(1,28,1)
@ -356,8 +391,10 @@ def main(datapath: str):
ax[0].patch.set_visible(False)
ax0.set_yticklabels([])
ax0.set_yticks([])
ax[0].fill_between(time, shuffled_q5_onset, shuffled_q95_onset, color=ps.gray, alpha=0.5)
ax[0].plot(time, shuffled_median_onset, color=ps.black)
# ax[0].fill_between(time, shuffled_q5_onset, shuffled_q95_onset, color=ps.gray, alpha=0.5)
# ax[0].plot(time, shuffled_median_onset, color=ps.black)
ax[0].fill_between(time, onset_q5, onset_q95, color=ps.gray, alpha=0.5)
ax[0].plot(time, onset_median, color=ps.black)
# Plot chasing offets
ax[1].set_xlabel('Time[s]')
@ -370,8 +407,10 @@ def main(datapath: str):
ax[1].patch.set_visible(False)
ax1.set_yticklabels([])
ax1.set_yticks([])
ax[1].fill_between(time, shuffled_q5_offset, shuffled_q95_offset, color=ps.gray, alpha=0.5)
ax[1].plot(time, shuffled_median_offset, color=ps.black)
# ax[1].fill_between(time, shuffled_q5_offset, shuffled_q95_offset, color=ps.gray, alpha=0.5)
# ax[1].plot(time, shuffled_median_offset, color=ps.black)
ax[1].fill_between(time, offset_q5, offset_q95, color=ps.gray, alpha=0.5)
ax[1].plot(time, offset_median, color=ps.black)
# Plot physical contacts
ax[2].set_xlabel('Time[s]')
@ -384,11 +423,13 @@ def main(datapath: str):
ax[2].patch.set_visible(False)
ax2.set_yticklabels([])
ax2.set_yticks([])
ax[2].fill_between(time, shuffled_q5_physical, shuffled_q95_physical, color=ps.gray, alpha=0.5)
ax[2].plot(time, shuffled_median_physical, ps.black)
# ax[2].fill_between(time, shuffled_q5_physical, shuffled_q95_physical, color=ps.gray, alpha=0.5)
# ax[2].plot(time, shuffled_median_physical, ps.black)
ax[2].fill_between(time, physical_q5, physical_q95, color=ps.gray, alpha=0.5)
ax[2].plot(time, physical_median, ps.black)
fig.suptitle('All recordings')
plt.show()
# plt.close()
plt.close()
embed()