raab/GP2023_chirp_detection
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weygoldt 2023-04-11 15:33:07 +02:00
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26 changed files with 1177 additions and 810 deletions
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10
chirp_instantaneous_freq/filters.py
View File

@ -92,6 +92,7 @@ def inst_freq(signal, fs):
return freq
def bandpass_filter(
signal: np.ndarray,
samplerate: float,
@ -150,9 +151,7 @@ def highpass_filter(
def lowpass_filter(
signal: np.ndarray,
samplerate: float,
cutoff: float
signal: np.ndarray, samplerate: float, cutoff: float
) -> np.ndarray:
"""Lowpass filter a signal.
@ -176,9 +175,8 @@ def lowpass_filter(
return filtered_signal
def envelope(signal: np.ndarray,
samplerate: float,
cutoff_frequency: float
def envelope(
signal: np.ndarray, samplerate: float, cutoff_frequency: float
) -> np.ndarray:
"""Calculate the envelope of a signal using a lowpass filter.

30
chirp_instantaneous_freq/fish_signal.py
View File

@ -384,16 +384,14 @@ def chirps(
frequency = eodf * np.ones(n)
am = np.ones(n)
for time, width, size, kurtosis, contrast in zip(chirp_times, chirp_width, chirp_size, chirp_kurtosis, chirp_contrast):
for time, width, size, kurtosis, contrast in zip(
chirp_times, chirp_width, chirp_size, chirp_kurtosis, chirp_contrast
):
# chirp frequency waveform:
chirp_t = np.arange(-2.0 * width, 2.0 * width, 1.0 / samplerate)
chirp_sig = (
0.5 * width / (2.0 * np.log(10.0)) ** (0.5 / kurtosis)
)
chirp_sig = 0.5 * width / (2.0 * np.log(10.0)) ** (0.5 / kurtosis)
gauss = np.exp(-0.5 * ((chirp_t / chirp_sig) ** 2.0) ** kurtosis)
# add chirps on baseline eodf:
index = int(time * samplerate)
i0 = index - len(gauss) // 2
@ -452,15 +450,12 @@ def rises(
# baseline eod frequency:
frequency = eodf * np.ones(n)
for time, size, riset, decayt in zip(rise_times, rise_size, rise_tau, decay_tau):
for time, size, riset, decayt in zip(
rise_times, rise_size, rise_tau, decay_tau
):
# rise frequency waveform:
rise_t = np.arange(0.0, 5.0 * decayt, 1.0 / samplerate)
rise = (
size
* (1.0 - np.exp(-rise_t / riset))
* np.exp(-rise_t / decayt)
)
rise = size * (1.0 - np.exp(-rise_t / riset)) * np.exp(-rise_t / decayt)
# add rises on baseline eodf:
index = int(time * samplerate)
@ -472,6 +467,7 @@ def rises(
frequency[index : index + len(rise)] += rise
return frequency
class FishSignal:
def __init__(self, samplerate, duration, eodf, nchirps, nrises):
time = np.arange(0, duration, 1 / samplerate)
@ -534,7 +530,6 @@ class FishSignal:
self.eodf = eodf
def visualize(self):
spec, freqs, spectime = ps.spectrogram(
data=self.signal,
ratetime=self.samplerate,
@ -549,7 +544,12 @@ class FishSignal:
ax1.set_xlabel("Time (s)")
ax1.set_title("EOD signal")
ax2.imshow(ps.decibel(spec), origin='lower', aspect="auto", extent=[spectime[0], spectime[-1], freqs[0], freqs[-1]])
ax2.imshow(
ps.decibel(spec),
origin="lower",
aspect="auto",
extent=[spectime[0], spectime[-1], freqs[0], freqs[-1]],
)
ax2.set_ylabel("Frequency (Hz)")
ax2.set_xlabel("Time (s)")
ax2.set_title("Spectrogram")

84
chirp_instantaneous_freq/test_parameters.py
View File

@ -6,18 +6,18 @@ from IPython import embed
def switch_test(test, defaultparams, testparams):
if test == 'width':
defaultparams['chirp_width'] = testparams['chirp_width']
key = 'chirp_width'
elif test == 'size':
defaultparams['chirp_size'] = testparams['chirp_size']
key = 'chirp_size'
elif test == 'kurtosis':
defaultparams['chirp_kurtosis'] = testparams['chirp_kurtosis']
key = 'chirp_kurtosis'
elif test == 'contrast':
defaultparams['chirp_contrast'] = testparams['chirp_contrast']
key = 'chirp_contrast'
if test == "width":
defaultparams["chirp_width"] = testparams["chirp_width"]
key = "chirp_width"
elif test == "size":
defaultparams["chirp_size"] = testparams["chirp_size"]
key = "chirp_size"
elif test == "kurtosis":
defaultparams["chirp_kurtosis"] = testparams["chirp_kurtosis"]
key = "chirp_kurtosis"
elif test == "contrast":
defaultparams["chirp_contrast"] = testparams["chirp_contrast"]
key = "chirp_contrast"
else:
raise ValueError("Test not recognized")
@ -29,9 +29,18 @@ def extract_dict(dict, index):
def main(test1, test2, resolution=10):
assert test1 in ['width', 'size', 'kurtosis', 'contrast'], "Test1 not recognized"
assert test2 in ['width', 'size', 'kurtosis', 'contrast'], "Test2 not recognized"
assert test1 in [
"width",
"size",
"kurtosis",
"contrast",
], "Test1 not recognized"
assert test2 in [
"width",
"size",
"kurtosis",
"contrast",
], "Test2 not recognized"
# Define the parameters for the chirp simulations
ntest = resolution
@ -64,39 +73,59 @@ def main(test1, test2, resolution=10):
distances = np.full((ntest, ntest), np.nan)
fig, axs = plt.subplots(ntest, ntest, figsize = (10, 10), sharex = True, sharey = True)
fig, axs = plt.subplots(
ntest, ntest, figsize=(10, 10), sharex=True, sharey=True
)
axs = axs.flatten()
iter0 = 0
for iter1, test1_param in enumerate(chirp_params[key1]):
for iter2, test2_param in enumerate(chirp_params[key2]):
# get the chirp parameters for the current test
inner_chirp_params = extract_dict(chirp_params, iter2)
inner_chirp_params[key1] = test1_param
inner_chirp_params[key2] = test2_param
# make the chirp trace for the current chirp parameters
sizes = np.ones(len(chirp_times)) * inner_chirp_params['chirp_size']
widths = np.ones(len(chirp_times)) * inner_chirp_params['chirp_width']
kurtosis = np.ones(len(chirp_times)) * inner_chirp_params['chirp_kurtosis']
contrast = np.ones(len(chirp_times)) * inner_chirp_params['chirp_contrast']
sizes = np.ones(len(chirp_times)) * inner_chirp_params["chirp_size"]
widths = (
np.ones(len(chirp_times)) * inner_chirp_params["chirp_width"]
)
kurtosis = (
np.ones(len(chirp_times)) * inner_chirp_params["chirp_kurtosis"]
)
contrast = (
np.ones(len(chirp_times)) * inner_chirp_params["chirp_contrast"]
)
# make the chirp trace
chirp_trace, ampmod = chirps(eodf, samplerate, duration, chirp_times, sizes, widths, kurtosis, contrast)
chirp_trace, ampmod = chirps(
eodf,
samplerate,
duration,
chirp_times,
sizes,
widths,
kurtosis,
contrast,
)
signal = wavefish_eods(
fish="Alepto",
frequency=chirp_trace,
samplerate=samplerate,
duration=duration,
phase0=0.0,
noise_std=0.05
noise_std=0.05,
)
signal = signal * ampmod
# apply broadband filter
wide_signal = bandpass_filter(signal, samplerate, eodf - wide_cutoffs, eodf + wide_cutoffs)
tight_signal = bandpass_filter(signal, samplerate, eodf - tight_cutoffs, eodf + tight_cutoffs)
wide_signal = bandpass_filter(
signal, samplerate, eodf - wide_cutoffs, eodf + wide_cutoffs
)
tight_signal = bandpass_filter(
signal, samplerate, eodf - tight_cutoffs, eodf + tight_cutoffs
)
# get the instantaneous frequency
wide_frequency = inst_freq(wide_signal, samplerate)
@ -111,8 +140,9 @@ def main(test1, test2, resolution=10):
iter0 += 1
fig, ax = plt.subplots()
ax.imshow(distances, cmap = 'jet')
ax.imshow(distances, cmap="jet")
plt.show()
if __name__ == "__main__":
main('width', 'size')
main("width", "size")

57
code/analysis.py
View File

@ -10,12 +10,12 @@ from modules.filters import bandpass_filter
def main(folder):
file = os.path.join(folder, 'traces-grid.raw')
file = os.path.join(folder, "traces-grid.raw")
data = open_data(folder, 60.0, 0, channel=-1)
time = np.load(folder + 'times.npy', allow_pickle=True)
freq = np.load(folder + 'fund_v.npy', allow_pickle=True)
ident = np.load(folder + 'ident_v.npy', allow_pickle=True)
idx = np.load(folder + 'idx_v.npy', allow_pickle=True)
time = np.load(folder + "times.npy", allow_pickle=True)
freq = np.load(folder + "fund_v.npy", allow_pickle=True)
ident = np.load(folder + "ident_v.npy", allow_pickle=True)
idx = np.load(folder + "idx_v.npy", allow_pickle=True)
t0 = 3 * 60 * 60 + 6 * 60 + 43.5
dt = 60
@ -24,16 +24,23 @@ def main(folder):
for i in [10]:
# getting the spectogramm
spec_power, spec_freqs, spec_times = spectrogram(
data_oi[:, i], ratetime=data.samplerate, freq_resolution=50, overlap_frac=0.0)
data_oi[:, i],
ratetime=data.samplerate,
freq_resolution=50,
overlap_frac=0.0,
)
fig, ax = plt.subplots(figsize=(20 / 2.54, 12 / 2.54))
ax.pcolormesh(spec_times, spec_freqs, decibel(
spec_power), vmin=-100, vmax=-50)
ax.pcolormesh(
spec_times, spec_freqs, decibel(spec_power), vmin=-100, vmax=-50
)
for track_id in np.unique(ident):
# window_index for time array in time window
window_index = np.arange(len(idx))[(ident == track_id) &
(time[idx] >= t0) &
(time[idx] <= (t0+dt))]
window_index = np.arange(len(idx))[
(ident == track_id)
& (time[idx] >= t0)
& (time[idx] <= (t0 + dt))
]
freq_temp = freq[window_index]
time_temp = time[idx[window_index]]
# mean_freq = np.mean(freq_temp)
@ -43,18 +50,22 @@ def main(folder):
ax.set_ylim(500, 1000)
plt.show()
# filter plot
id = 10.
id = 10.0
i = 10
window_index = np.arange(len(idx))[(ident == id) &
(time[idx] >= t0) &
(time[idx] <= (t0+dt))]
window_index = np.arange(len(idx))[
(ident == id) & (time[idx] >= t0) & (time[idx] <= (t0 + dt))
]
freq_temp = freq[window_index]
time_temp = time[idx[window_index]]
mean_freq = np.mean(freq_temp)
fdata = bandpass_filter(
data_oi[:, i], rate=data.samplerate, lowf=mean_freq-5, highf=mean_freq+200)
data_oi[:, i],
rate=data.samplerate,
lowf=mean_freq - 5,
highf=mean_freq + 200,
)
fig, ax = plt.subplots()
ax.plot(np.arange(len(fdata))/data.samplerate, fdata, marker='*')
ax.plot(np.arange(len(fdata)) / data.samplerate, fdata, marker="*")
# plt.show()
# freqency analyis of filtered data
@ -63,8 +74,8 @@ def main(folder):
period_index = np.arange(len(fdata))[(roll_fdata < 0) & (fdata >= 0)]
plt.plot(time_fdata, fdata)
plt.scatter(time_fdata[period_index], fdata[period_index], c='r')
plt.scatter(time_fdata[period_index-1], fdata[period_index-1], c='r')
plt.scatter(time_fdata[period_index], fdata[period_index], c="r")
plt.scatter(time_fdata[period_index - 1], fdata[period_index - 1], c="r")
upper_bound = np.abs(fdata[period_index])
lower_bound = np.abs(fdata[period_index - 1])
@ -84,7 +95,7 @@ def main(folder):
inst_freq = 1 / np.diff(true_zero)
filtered_inst_freq = gaussian_filter1d(inst_freq, 0.005)
fig, ax = plt.subplots()
ax.plot(filtered_inst_freq, marker='.')
ax.plot(filtered_inst_freq, marker=".")
# in 5 sekunden welcher fisch auf einer elektrode am
embed()
@ -99,5 +110,7 @@ def main(folder):
pass
if __name__ == '__main__':
main('/Users/acfw/Documents/uni_tuebingen/chirpdetection/gp_benda/data/2022-06-02-10_00/')
if __name__ == "__main__":
main(
"/Users/acfw/Documents/uni_tuebingen/chirpdetection/gp_benda/data/2022-06-02-10_00/"
)

14
code/band_pass_problem.py
View File

@ -22,15 +22,17 @@ def main(folder):
axs[0].plot(np.arange(data_oi.shape[0]) / data.raw_rate, data_oi)
for tr, track_id in enumerate(np.unique(data.ident[~np.isnan(data.ident)])):
rack_window_index = np.arange(len(data.idx))[
(data.ident == track_id) &
(data.time[data.idx] >= t0) &
(data.time[data.idx] <= (t0+dt))]
(data.ident == track_id)
& (data.time[data.idx] >= t0)
& (data.time[data.idx] <= (t0 + dt))
]
freq_fish = data.freq[rack_window_index]
axs[1].plot(np.arange(freq_fish.shape[0]) / data.raw_rate, freq_fish)
plt.show()
if __name__ == '__main__':
main('/Users/acfw/Documents/uni_tuebingen/chirpdetection/GP2023_chirp_detection/data/2022-06-02-10_00/')
if __name__ == "__main__":
main(
"/Users/acfw/Documents/uni_tuebingen/chirpdetection/GP2023_chirp_detection/data/2022-06-02-10_00/"
)

165
code/behavior.py
View File

@ -11,6 +11,7 @@ from scipy.ndimage import gaussian_filter1d
logger = makeLogger(__name__)
class Behavior:
"""Load behavior data from csv file as class attributes
Attributes
@ -31,23 +32,35 @@ class Behavior:
"""
def __init__(self, folder_path: str) -> None:
LED_on_time_BORIS = np.load(os.path.join(folder_path, 'LED_on_time.npy'), allow_pickle=True)
self.time = np.load(os.path.join(folder_path, "times.npy"), allow_pickle=True)
csv_filename = [f for f in os.listdir(folder_path) if f.endswith('.csv')][0] # check if there are more than one csv file
LED_on_time_BORIS = np.load(
os.path.join(folder_path, "LED_on_time.npy"), allow_pickle=True
)
self.time = np.load(
os.path.join(folder_path, "times.npy"), allow_pickle=True
)
csv_filename = [
f for f in os.listdir(folder_path) if f.endswith(".csv")
][
0
] # check if there are more than one csv file
self.dataframe = read_csv(os.path.join(folder_path, csv_filename))
self.chirps = np.load(os.path.join(folder_path, 'chirps.npy'), allow_pickle=True)
self.chirps_ids = np.load(os.path.join(folder_path, 'chirps_ids.npy'), allow_pickle=True)
self.chirps = np.load(
os.path.join(folder_path, "chirps.npy"), allow_pickle=True
)
self.chirps_ids = np.load(
os.path.join(folder_path, "chirps_ids.npy"), allow_pickle=True
)
for k, key in enumerate(self.dataframe.keys()):
key = key.lower()
if ' ' in key:
key = key.replace(' ', '_')
if '(' in key:
key = key.replace('(', '')
key = key.replace(')', '')
setattr(self, key, np.array(self.dataframe[self.dataframe.keys()[k]]))
if " " in key:
key = key.replace(" ", "_")
if "(" in key:
key = key.replace("(", "")
key = key.replace(")", "")
setattr(
self, key, np.array(self.dataframe[self.dataframe.keys()[k]])
)
last_LED_t_BORIS = LED_on_time_BORIS[-1]
real_time_range = self.time[-1] - self.time[0]
@ -56,6 +69,7 @@ class Behavior:
self.start_s = (self.start_s - shift) / factor
self.stop_s = (self.stop_s - shift) / factor
"""
1 - chasing onset
2 - chasing offset
@ -83,44 +97,41 @@ temporal encpding needs to be corrected ... not exactly 25FPS.
behavior = data['Behavior']
"""
def correct_chasing_events(
category: np.ndarray,
timestamps: np.ndarray
category: np.ndarray, timestamps: np.ndarray
) -> tuple[np.ndarray, np.ndarray]:
onset_ids = np.arange(
len(category))[category == 0]
offset_ids = np.arange(
len(category))[category == 1]
onset_ids = np.arange(len(category))[category == 0]
offset_ids = np.arange(len(category))[category == 1]
# Check whether on- or offset is longer and calculate length difference
if len(onset_ids) > len(offset_ids):
len_diff = len(onset_ids) - len(offset_ids)
longer_array = onset_ids
shorter_array = offset_ids
logger.info(f'Onsets are greater than offsets by {len_diff}')
logger.info(f"Onsets are greater than offsets by {len_diff}")
elif len(onset_ids) < len(offset_ids):
len_diff = len(offset_ids) - len(onset_ids)
longer_array = offset_ids
shorter_array = onset_ids
logger.info(f'Offsets are greater than offsets by {len_diff}')
logger.info(f"Offsets are greater than offsets by {len_diff}")
elif len(onset_ids) == len(offset_ids):
logger.info('Chasing events are equal')
logger.info("Chasing events are equal")
return category, timestamps
# Correct the wrong chasing events; delete double events
wrong_ids = []
for i in range(len(longer_array) - (len_diff + 1)):
if (shorter_array[i] > longer_array[i]) & (shorter_array[i] < longer_array[i+1]):
if (shorter_array[i] > longer_array[i]) & (
shorter_array[i] < longer_array[i + 1]
):
pass
else:
wrong_ids.append(longer_array[i])
longer_array = np.delete(longer_array, i)
category = np.delete(
category, wrong_ids)
timestamps = np.delete(
timestamps, wrong_ids)
category = np.delete(category, wrong_ids)
timestamps = np.delete(timestamps, wrong_ids)
return category, timestamps
@ -128,29 +139,32 @@ def event_triggered_chirps(
event: np.ndarray,
chirps: np.ndarray,
time_before_event: int,
time_after_event: int
time_after_event: int,
) -> tuple[np.ndarray, np.ndarray]:
event_chirps = [] # chirps that are in specified window around event
centered_chirps = [] # timestamps of chirps around event centered on the event timepoint
centered_chirps = (
[]
) # timestamps of chirps around event centered on the event timepoint
for event_timestamp in event:
start = event_timestamp - time_before_event # timepoint of window start
stop = event_timestamp + time_after_event # timepoint of window ending
chirps_around_event = [c for c in chirps if (c >= start) & (c <= stop)] # get chirps that are in a -5 to +5 sec window around event
chirps_around_event = [
c for c in chirps if (c >= start) & (c <= stop)
] # get chirps that are in a -5 to +5 sec window around event
event_chirps.append(chirps_around_event)
if len(chirps_around_event) == 0:
continue
else:
centered_chirps.append(chirps_around_event - event_timestamp)
centered_chirps = np.concatenate(centered_chirps, axis=0) # convert list of arrays to one array for plotting
centered_chirps = np.concatenate(
centered_chirps, axis=0
) # convert list of arrays to one array for plotting
return event_chirps, centered_chirps
def main(datapath: str):
# behavior is pandas dataframe with all the data
bh = Behavior(datapath)
@ -172,10 +186,34 @@ def main(datapath: str):
# First overview plot
fig1, ax1 = plt.subplots()
ax1.scatter(chirps, np.ones_like(chirps), marker='*', color='royalblue', label='Chirps')
ax1.scatter(chasing_onset, np.ones_like(chasing_onset)*2, marker='.', color='forestgreen', label='Chasing onset')
ax1.scatter(chasing_offset, np.ones_like(chasing_offset)*2.5, marker='.', color='firebrick', label='Chasing offset')
ax1.scatter(physical_contact, np.ones_like(physical_contact)*3, marker='x', color='black', label='Physical contact')
ax1.scatter(
chirps,
np.ones_like(chirps),
marker="*",
color="royalblue",
label="Chirps",
)
ax1.scatter(
chasing_onset,
np.ones_like(chasing_onset) * 2,
marker=".",
color="forestgreen",
label="Chasing onset",
)
ax1.scatter(
chasing_offset,
np.ones_like(chasing_offset) * 2.5,
marker=".",
color="firebrick",
label="Chasing offset",
)
ax1.scatter(
physical_contact,
np.ones_like(physical_contact) * 3,
marker="x",
color="black",
label="Physical contact",
)
plt.legend()
# plt.show()
plt.close()
@ -194,22 +232,33 @@ def main(datapath: str):
# chirps = chirps[chirps_fish_ids == fish]
# print(fish)
chasing_chirps, centered_chasing_chirps = event_triggered_chirps(chasing_onset, chirps, time_around_event, time_around_event)
physical_chirps, centered_physical_chirps = event_triggered_chirps(physical_contact, chirps, time_around_event, time_around_event)
chasing_chirps, centered_chasing_chirps = event_triggered_chirps(
chasing_onset, chirps, time_around_event, time_around_event
)
physical_chirps, centered_physical_chirps = event_triggered_chirps(
physical_contact, chirps, time_around_event, time_around_event
)
# Kernel density estimation ???
# centered_chasing_chirps_convolved = gaussian_filter1d(centered_chasing_chirps, 5)
# centered_chasing = chasing_onset[0] - chasing_onset[0] ## get the 0 timepoint for plotting; set one chasing event to 0
offsets = [0.5, 1]
fig4, ax4 = plt.subplots(figsize=(20 / 2.54, 12 / 2.54), constrained_layout=True)
ax4.eventplot(np.array([centered_chasing_chirps, centered_physical_chirps]), lineoffsets=offsets, linelengths=0.25, colors=['g', 'r'])
ax4.vlines(0, 0, 1.5, 'tab:grey', 'dashed', 'Timepoint of event')
fig4, ax4 = plt.subplots(
figsize=(20 / 2.54, 12 / 2.54), constrained_layout=True
)
ax4.eventplot(
np.array([centered_chasing_chirps, centered_physical_chirps]),
lineoffsets=offsets,
linelengths=0.25,
colors=["g", "r"],
)
ax4.vlines(0, 0, 1.5, "tab:grey", "dashed", "Timepoint of event")
# ax4.plot(centered_chasing_chirps_convolved)
ax4.set_yticks(offsets)
ax4.set_yticklabels(['Chasings', 'Physical \n contacts'])
ax4.set_xlabel('Time[s]')
ax4.set_ylabel('Type of event')
ax4.set_yticklabels(["Chasings", "Physical \n contacts"])
ax4.set_xlabel("Time[s]")
ax4.set_ylabel("Type of event")
plt.show()
# Associate chirps to inidividual fish
@ -227,14 +276,13 @@ def main(datapath: str):
#### Chirp counts per fish general #####
fig2, ax2 = plt.subplots()
x = ['Fish1', 'Fish2']
x = ["Fish1", "Fish2"]
width = 0.35
ax2.bar(x, fish, width=width)
ax2.set_ylabel('Chirp count')
ax2.set_ylabel("Chirp count")
# plt.show()
plt.close()
##### Count chirps emitted during chasing events and chirps emitted out of chasing events #####
chirps_in_chasings = []
for onset, offset in zip(chasing_onset, chasing_offset):
@ -252,22 +300,23 @@ def main(datapath: str):
# chirps in chasing events
fig3, ax3 = plt.subplots()
ax3.bar(['Chirps in chasing events', 'Chasing events without Chirps'], [counts_chirps_chasings, chasings_without_chirps], width=width)
plt.ylabel('Count')
ax3.bar(
["Chirps in chasing events", "Chasing events without Chirps"],
[counts_chirps_chasings, chasings_without_chirps],
width=width,
)
plt.ylabel("Count")
# plt.show()
plt.close()
# comparison between chasing events with and without chirps
embed()
exit()
if __name__ == '__main__':
if __name__ == "__main__":
# Path to the data
datapath = '../data/mount_data/2020-05-13-10_00/'
datapath = '../data/mount_data/2020-05-13-10_00/'
datapath = "../data/mount_data/2020-05-13-10_00/"
datapath = "../data/mount_data/2020-05-13-10_00/"
main(datapath)

9
code/chirp_sim.py
View File

@ -8,11 +8,12 @@ from modules.datahandling import instantaneous_frequency
from modules.simulations import create_chirp
# trying thunderfish fakefish chirp simulation ---------------------------------
samplerate = 44100
freq, ampl = fakefish.chirps(eodf=500, chirp_contrast=0.2)
data = fakefish.wavefish_eods(fish='Alepto', frequency=freq, phase0=3, samplerate=samplerate)
data = fakefish.wavefish_eods(
fish="Alepto", frequency=freq, phase0=3, samplerate=samplerate
)
# filter signal with bandpass_filter
data_filterd = bandpass_filter(data * ampl + 1, samplerate, 0.01, 1.99)
@ -31,7 +32,3 @@ ax[3].plot(data_freq_time, data_freq)
plt.show()
embed()

118
code/chirpdetection.py
View File

@ -7,6 +7,7 @@ import matplotlib.pyplot as plt
import matplotlib.gridspec as gr
from scipy.signal import find_peaks
from thunderfish.powerspectrum import spectrogram, decibel
# from sklearn.preprocessing import normalize
from modules.filters import bandpass_filter, envelope, highpass_filter
@ -59,7 +60,6 @@ class ChirpPlotBuffer:
frequency_peaks: np.ndarray
def plot_buffer(self, chirps: np.ndarray, plot: str) -> None:
logger.debug("Starting plotting")
# make data for plotting
@ -135,7 +135,6 @@ class ChirpPlotBuffer:
ax0.set_ylim(np.min(self.frequency) - 100, np.max(self.frequency) + 200)
for track_id in self.data.ids:
t0_track = self.t0_old - 5
dt_track = self.dt + 10
window_idx = np.arange(len(self.data.idx))[
@ -176,10 +175,16 @@ class ChirpPlotBuffer:
# )
ax0.axhline(
q50 - self.config.minimal_bandwidth / 2, color=ps.gblue1, lw=1, ls="dashed"
q50 - self.config.minimal_bandwidth / 2,
color=ps.gblue1,
lw=1,
ls="dashed",
)
ax0.axhline(
q50 + self.config.minimal_bandwidth / 2, color=ps.gblue1, lw=1, ls="dashed"
q50 + self.config.minimal_bandwidth / 2,
color=ps.gblue1,
lw=1,
ls="dashed",
)
ax0.axhline(search_lower, color=ps.gblue2, lw=1, ls="dashed")
ax0.axhline(search_upper, color=ps.gblue2, lw=1, ls="dashed")
@ -205,7 +210,11 @@ class ChirpPlotBuffer:
# plot waveform of filtered signal
ax1.plot(
self.time, self.baseline * waveform_scaler, c=ps.gray, lw=lw, alpha=0.5
self.time,
self.baseline * waveform_scaler,
c=ps.gray,
lw=lw,
alpha=0.5,
)
ax1.plot(
self.time,
@ -216,7 +225,13 @@ class ChirpPlotBuffer:
)
# plot waveform of filtered search signal
ax2.plot(self.time, self.search * waveform_scaler, c=ps.gray, lw=lw, alpha=0.5)
ax2.plot(
self.time,
self.search * waveform_scaler,
c=ps.gray,
lw=lw,
alpha=0.5,
)
ax2.plot(
self.time,
self.search_envelope_unfiltered * waveform_scaler,
@ -238,9 +253,7 @@ class ChirpPlotBuffer:
# ax4.plot(
# self.time, self.baseline_envelope * waveform_scaler, c=ps.gblue1, lw=lw
# )
ax4.plot(
self.time, self.baseline_envelope, c=ps.gblue1, lw=lw
)
ax4.plot(self.time, self.baseline_envelope, c=ps.gblue1, lw=lw)
ax4.scatter(
(self.time)[self.baseline_peaks],
# (self.baseline_envelope * waveform_scaler)[self.baseline_peaks],
@ -269,7 +282,9 @@ class ChirpPlotBuffer:
)
# plot filtered instantaneous frequency
ax6.plot(self.frequency_time, self.frequency_filtered, c=ps.gblue3, lw=lw)
ax6.plot(
self.frequency_time, self.frequency_filtered, c=ps.gblue3, lw=lw
)
ax6.scatter(
self.frequency_time[self.frequency_peaks],
self.frequency_filtered[self.frequency_peaks],
@ -303,7 +318,9 @@ class ChirpPlotBuffer:
# ax7.spines.bottom.set_bounds((0, 5))
ax0.set_xlim(0, self.config.window)
plt.subplots_adjust(left=0.165, right=0.975, top=0.98, bottom=0.074, hspace=0.2)
plt.subplots_adjust(
left=0.165, right=0.975, top=0.98, bottom=0.074, hspace=0.2
)
fig.align_labels()
if plot == "show":
@ -408,7 +425,9 @@ def extract_frequency_bands(
q25, q75 = q50 - minimal_bandwidth / 2, q50 + minimal_bandwidth / 2
# filter baseline
filtered_baseline = bandpass_filter(raw_data, samplerate, lowf=q25, highf=q75)
filtered_baseline = bandpass_filter(
raw_data, samplerate, lowf=q25, highf=q75
)
# filter search area
filtered_search_freq = bandpass_filter(
@ -453,12 +472,14 @@ def window_median_all_track_ids(
track_ids = []
for _, track_id in enumerate(np.unique(data.ident[~np.isnan(data.ident)])):
# the window index combines the track id and the time window
window_idx = np.arange(len(data.idx))[
(data.ident == track_id)
& (data.time[data.idx] >= window_start_seconds)
& (data.time[data.idx] <= (window_start_seconds + window_duration_seconds))
& (
data.time[data.idx]
<= (window_start_seconds + window_duration_seconds)
)
]
if len(data.freq[window_idx]) > 0:
@ -595,15 +616,15 @@ def find_searchband(
# iterate through theses tracks
if check_track_ids.size != 0:
for j, check_track_id in enumerate(check_track_ids):
q25_temp = q25[percentiles_ids == check_track_id]
q75_temp = q75[percentiles_ids == check_track_id]
bool_lower[search_window > q25_temp - config.search_res] = False
bool_upper[search_window < q75_temp + config.search_res] = False
search_window_bool[(bool_lower == False) & (bool_upper == False)] = False
search_window_bool[
(bool_lower == False) & (bool_upper == False)
] = False
# find gaps in search window
search_window_indices = np.arange(len(search_window))
@ -622,7 +643,9 @@ def find_searchband(
# if the first value is -1, the array starst with true, so a gap
if nonzeros[0] == -1:
stops = search_window_indices[search_window_gaps == -1]
starts = np.append(0, search_window_indices[search_window_gaps == 1])
starts = np.append(
0, search_window_indices[search_window_gaps == 1]
)
# if the last value is -1, the array ends with true, so a gap
if nonzeros[-1] == 1:
@ -659,7 +682,6 @@ def find_searchband(
def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
assert plot in [
"save",
"show",
@ -729,7 +751,6 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
multiwindow_ids = []
for st, window_start_index in enumerate(window_start_indices):
logger.info(f"Processing window {st+1} of {len(window_start_indices)}")
window_start_seconds = window_start_index / data.raw_rate
@ -744,8 +765,9 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
)
# iterate through all fish
for tr, track_id in enumerate(np.unique(data.ident[~np.isnan(data.ident)])):
for tr, track_id in enumerate(
np.unique(data.ident[~np.isnan(data.ident)])
):
logger.debug(f"Processing track {tr} of {len(data.ids)}")
# get index of track data in this time window
@ -773,16 +795,17 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
nanchecker = np.unique(np.isnan(current_powers))
if (len(nanchecker) == 1) and nanchecker[0] is True:
logger.warning(
f"No powers available for track {track_id} window {st}," "skipping."
f"No powers available for track {track_id} window {st},"
"skipping."
)
continue
# find the strongest electrodes for the current fish in the current
# window
best_electrode_index = np.argsort(np.nanmean(current_powers, axis=0))[
-config.number_electrodes :
]
best_electrode_index = np.argsort(
np.nanmean(current_powers, axis=0)
)[-config.number_electrodes :]
# find a frequency above the baseline of the current fish in which
# no other fish is active to search for chirps there
@ -802,9 +825,9 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
# iterate through electrodes
for el, electrode_index in enumerate(best_electrode_index):
logger.debug(
f"Processing electrode {el+1} of " f"{len(best_electrode_index)}"
f"Processing electrode {el+1} of "
f"{len(best_electrode_index)}"
)
# LOAD DATA FOR CURRENT ELECTRODE AND CURRENT FISH ------------
@ -813,7 +836,9 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
current_raw_data = data.raw[
window_start_index:window_stop_index, electrode_index
]
current_raw_time = raw_time[window_start_index:window_stop_index]
current_raw_time = raw_time[
window_start_index:window_stop_index
]
# EXTRACT FEATURES --------------------------------------------
@ -839,8 +864,7 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
# because the instantaneous frequency is not reliable there
amplitude_mask = mask_low_amplitudes(
baseline_envelope_unfiltered,
config.baseline_min_amplitude
baseline_envelope_unfiltered, config.baseline_min_amplitude
)
# highpass filter baseline envelope to remove slower
@ -879,7 +903,7 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
baseline_frequency = instantaneous_frequency(
baselineband,
data.raw_rate,
config.baseline_frequency_smoothing
config.baseline_frequency_smoothing,
)
# Take the absolute of the instantaneous frequency to invert
@ -897,7 +921,10 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
# to enter normalization, where small changes due to noise
# would be amplified
if not has_chirp(baseline_frequency_filtered[amplitude_mask], config.baseline_frequency_peakheight):
if not has_chirp(
baseline_frequency_filtered[amplitude_mask],
config.baseline_frequency_peakheight,
):
continue
# CUT OFF OVERLAP ---------------------------------------------
@ -912,14 +939,20 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
current_raw_time = current_raw_time[no_edges]
baselineband = baselineband[no_edges]
baseline_envelope_unfiltered = baseline_envelope_unfiltered[no_edges]
baseline_envelope_unfiltered = baseline_envelope_unfiltered[
no_edges
]
searchband = searchband[no_edges]
baseline_envelope = baseline_envelope[no_edges]
search_envelope_unfiltered = search_envelope_unfiltered[no_edges]
search_envelope_unfiltered = search_envelope_unfiltered[
no_edges
]
search_envelope = search_envelope[no_edges]
baseline_frequency = baseline_frequency[no_edges]
baseline_frequency_filtered = baseline_frequency_filtered[no_edges]
baseline_frequency_filtered = baseline_frequency_filtered[
no_edges
]
baseline_frequency_time = current_raw_time
# # get instantaneous frequency withoup edges
@ -960,13 +993,16 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
)
# detect peaks inst_freq_filtered
frequency_peak_indices, _ = find_peaks(
baseline_frequency_filtered, prominence=config.frequency_prominence
baseline_frequency_filtered,
prominence=config.frequency_prominence,
)
# DETECT CHIRPS IN SEARCH WINDOW ------------------------------
# get the peak timestamps from the peak indices
baseline_peak_timestamps = current_raw_time[baseline_peak_indices]
baseline_peak_timestamps = current_raw_time[
baseline_peak_indices
]
search_peak_timestamps = current_raw_time[search_peak_indices]
frequency_peak_timestamps = baseline_frequency_time[
@ -1015,7 +1051,6 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
)
if chirp_detected or (debug != "elecrode"):
logger.debug("Detected chirp, ititialize buffer ...")
# save data to Buffer
@ -1107,7 +1142,6 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
multiwindow_chirps_flat = []
multiwindow_ids_flat = []
for track_id in np.unique(multiwindow_ids):
# get chirps for this fish and flatten the list
current_track_bool = np.asarray(multiwindow_ids) == track_id
current_track_chirps = flatten(
@ -1116,7 +1150,9 @@ def chirpdetection(datapath: str, plot: str, debug: str = "false") -> None:
# add flattened chirps to the list
multiwindow_chirps_flat.extend(current_track_chirps)
multiwindow_ids_flat.extend(list(np.ones_like(current_track_chirps) * track_id))
multiwindow_ids_flat.extend(
list(np.ones_like(current_track_chirps) * track_id)
)
# purge duplicates, i.e. chirps that are very close to each other
# duplites arise due to overlapping windows

1
code/chirpdetector_conf.yml
View File

@ -44,4 +44,3 @@ frequency_prominence: 0.3 # peak prominence threshold for baseline freq
# Classify events as chirps if they are less than this time apart
chirp_window_threshold: 0.02

252
code/eventchirpsplots.py
View File

@ -35,28 +35,36 @@ class Behavior:
"""
def __init__(self, folder_path: str) -> None:
print(f'{folder_path}')
LED_on_time_BORIS = np.load(os.path.join(
folder_path, 'LED_on_time.npy'), allow_pickle=True)
self.time = np.load(os.path.join(
folder_path, "times.npy"), allow_pickle=True)
csv_filename = [f for f in os.listdir(folder_path) if f.endswith(
'.csv')][0] # check if there are more than one csv file
print(f"{folder_path}")
LED_on_time_BORIS = np.load(
os.path.join(folder_path, "LED_on_time.npy"), allow_pickle=True
)
self.time = np.load(
os.path.join(folder_path, "times.npy"), allow_pickle=True
)
csv_filename = [
f for f in os.listdir(folder_path) if f.endswith(".csv")
][
0
] # check if there are more than one csv file
self.dataframe = read_csv(os.path.join(folder_path, csv_filename))
self.chirps = np.load(os.path.join(
folder_path, 'chirps.npy'), allow_pickle=True)
self.chirps_ids = np.load(os.path.join(
folder_path, 'chirp_ids.npy'), allow_pickle=True)
self.chirps = np.load(
os.path.join(folder_path, "chirps.npy"), allow_pickle=True
)
self.chirps_ids = np.load(
os.path.join(folder_path, "chirp_ids.npy"), allow_pickle=True
)
for k, key in enumerate(self.dataframe.keys()):
key = key.lower()
if ' ' in key:
key = key.replace(' ', '_')
if '(' in key:
key = key.replace('(', '')
key = key.replace(')', '')
setattr(self, key, np.array(
self.dataframe[self.dataframe.keys()[k]]))
if " " in key:
key = key.replace(" ", "_")
if "(" in key:
key = key.replace("(", "")
key = key.replace(")", "")
setattr(
self, key, np.array(self.dataframe[self.dataframe.keys()[k]])
)
last_LED_t_BORIS = LED_on_time_BORIS[-1]
real_time_range = self.time[-1] - self.time[0]
@ -95,17 +103,14 @@ temporal encpding needs to be corrected ... not exactly 25FPS.
def correct_chasing_events(
category: np.ndarray,
timestamps: np.ndarray
category: np.ndarray, timestamps: np.ndarray
) -> tuple[np.ndarray, np.ndarray]:
onset_ids = np.arange(len(category))[category == 0]
offset_ids = np.arange(len(category))[category == 1]
onset_ids = np.arange(
len(category))[category == 0]
offset_ids = np.arange(
len(category))[category == 1]
wrong_bh = np.arange(len(category))[
category != 2][:-1][np.diff(category[category != 2]) == 0]
wrong_bh = np.arange(len(category))[category != 2][:-1][
np.diff(category[category != 2]) == 0
]
if onset_ids[0] > offset_ids[0]:
offset_ids = np.delete(offset_ids, 0)
help_index = offset_ids[0]
@ -117,12 +122,12 @@ def correct_chasing_events(
# Check whether on- or offset is longer and calculate length difference
if len(onset_ids) > len(offset_ids):
len_diff = len(onset_ids) - len(offset_ids)
logger.info(f'Onsets are greater than offsets by {len_diff}')
logger.info(f"Onsets are greater than offsets by {len_diff}")
elif len(onset_ids) < len(offset_ids):
len_diff = len(offset_ids) - len(onset_ids)
logger.info(f'Offsets are greater than onsets by {len_diff}')
logger.info(f"Offsets are greater than onsets by {len_diff}")
elif len(onset_ids) == len(offset_ids):
logger.info('Chasing events are equal')
logger.info("Chasing events are equal")
return category, timestamps
@ -135,7 +140,6 @@ def event_triggered_chirps(
dt: float,
width: float,
) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
event_chirps = [] # chirps that are in specified window around event
# timestamps of chirps around event centered on the event timepoint
centered_chirps = []
@ -159,16 +163,19 @@ def event_triggered_chirps(
else:
# convert list of arrays to one array for plotting
centered_chirps = np.concatenate(centered_chirps, axis=0)
centered_chirps_convolved = (acausal_kde1d(
centered_chirps, time, width)) / len(event)
centered_chirps_convolved = (
acausal_kde1d(centered_chirps, time, width)
) / len(event)
return event_chirps, centered_chirps, centered_chirps_convolved
def main(datapath: str):
foldernames = [
datapath + x + '/' for x in os.listdir(datapath) if os.path.isdir(datapath + x)]
datapath + x + "/"
for x in os.listdir(datapath)
if os.path.isdir(datapath + x)
]
nrecording_chirps = []
nrecording_chirps_fish_ids = []
@ -179,7 +186,7 @@ def main(datapath: str):
# Iterate over all recordings and save chirp- and event-timestamps
for folder in foldernames:
# exclude folder with empty LED_on_time.npy
if folder == '../data/mount_data/2020-05-12-10_00/':
if folder == "../data/mount_data/2020-05-12-10_00/":
continue
bh = Behavior(folder)
@ -232,18 +239,47 @@ def main(datapath: str):
physical_contacts = nrecording_physicals[i]
# Chirps around chasing onsets
_, centered_chasing_onset_chirps, cc_chasing_onset_chirps = event_triggered_chirps(
chasing_onsets, chirps, time_before_event, time_after_event, dt, recording_width)
(
_,
centered_chasing_onset_chirps,
cc_chasing_onset_chirps,
) = event_triggered_chirps(
chasing_onsets,
chirps,
time_before_event,
time_after_event,
dt,
recording_width,
)
# Chirps around chasing offsets
_, centered_chasing_offset_chirps, cc_chasing_offset_chirps = event_triggered_chirps(
chasing_offsets, chirps, time_before_event, time_after_event, dt, recording_width)
(
_,
centered_chasing_offset_chirps,
cc_chasing_offset_chirps,
) = event_triggered_chirps(
chasing_offsets,
chirps,
time_before_event,
time_after_event,
dt,
recording_width,
)
# Chirps around physical contacts
_, centered_physical_chirps, cc_physical_chirps = event_triggered_chirps(
physical_contacts, chirps, time_before_event, time_after_event, dt, recording_width)
(
_,
centered_physical_chirps,
cc_physical_chirps,
) = event_triggered_chirps(
physical_contacts,
chirps,
time_before_event,
time_after_event,
dt,
recording_width,
)
nrecording_centered_onset_chirps.append(centered_chasing_onset_chirps)
nrecording_centered_offset_chirps.append(
centered_chasing_offset_chirps)
nrecording_centered_offset_chirps.append(centered_chasing_offset_chirps)
nrecording_centered_physical_chirps.append(centered_physical_chirps)
## Shuffled chirps ##
@ -331,12 +367,13 @@ def main(datapath: str):
# New bootstrapping approach
for n in range(nbootstrapping):
diff_onset = np.diff(
np.sort(flatten(nrecording_centered_onset_chirps)))
diff_onset = np.diff(np.sort(flatten(nrecording_centered_onset_chirps)))
diff_offset = np.diff(
np.sort(flatten(nrecording_centered_offset_chirps)))
np.sort(flatten(nrecording_centered_offset_chirps))
)
diff_physical = np.diff(
np.sort(flatten(nrecording_centered_physical_chirps)))
np.sort(flatten(nrecording_centered_physical_chirps))
)
np.random.shuffle(diff_onset)
shuffled_onset = np.cumsum(diff_onset)
@ -347,7 +384,9 @@ def main(datapath: str):
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)
kde_physical = (acausal_kde1d(shuffled_physical, time, width)) / (
27 * 100
)
bootstrap_onset.append(kde_onset)
bootstrap_offset.append(kde_offset)
@ -355,11 +394,14 @@ def main(datapath: str):
# New shuffle approach q5, q50, q95
onset_q5, onset_median, onset_q95 = np.percentile(
bootstrap_onset, [5, 50, 95], axis=0)
bootstrap_onset, [5, 50, 95], axis=0
)
offset_q5, offset_median, offset_q95 = np.percentile(
bootstrap_offset, [5, 50, 95], axis=0)
bootstrap_offset, [5, 50, 95], axis=0
)
physical_q5, physical_median, physical_q95 = np.percentile(
bootstrap_physical, [5, 50, 95], axis=0)
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)
@ -378,44 +420,65 @@ def main(datapath: str):
# Flatten event timestamps
all_onsets = np.concatenate(
nrecording_chasing_onsets).ravel() # not centered
nrecording_chasing_onsets
).ravel() # not centered
all_offsets = np.concatenate(
nrecording_chasing_offsets).ravel() # not centered
all_physicals = np.concatenate(
nrecording_physicals).ravel() # not centered
nrecording_chasing_offsets
).ravel() # not centered
all_physicals = np.concatenate(nrecording_physicals).ravel() # not centered
# Flatten all chirps around events
all_onset_chirps = np.concatenate(
nrecording_centered_onset_chirps).ravel() # centered
nrecording_centered_onset_chirps
).ravel() # centered
all_offset_chirps = np.concatenate(
nrecording_centered_offset_chirps).ravel() # centered
nrecording_centered_offset_chirps
).ravel() # centered
all_physical_chirps = np.concatenate(
nrecording_centered_physical_chirps).ravel() # centered
nrecording_centered_physical_chirps
).ravel() # centered
# Convolute all chirps
# Divide by total number of each event over all recordings
all_onset_chirps_convolved = (acausal_kde1d(
all_onset_chirps, time, width)) / len(all_onsets)
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)
all_onset_chirps_convolved = (
acausal_kde1d(all_onset_chirps, time, width)
) / len(all_onsets)
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')
fig, ax = plt.subplots(
1,
3,
figsize=(
28 * ps.cm,
16 * ps.cm,
),
constrained_layout=True,
sharey="all",
)
# offsets = np.arange(1,28,1)
ax[0].set_xlabel('Time[s]')
ax[0].set_xlabel("Time[s]")
# Plot chasing onsets
ax[0].set_ylabel('Chirp rate [Hz]')
ax[0].set_ylabel("Chirp rate [Hz]")
ax[0].plot(time, all_onset_chirps_convolved, color=ps.yellow, zorder=2)
ax0 = ax[0].twinx()
nrecording_centered_onset_chirps = np.asarray(
nrecording_centered_onset_chirps, dtype=object)
ax0.eventplot(np.array(nrecording_centered_onset_chirps),
linelengths=0.5, colors=ps.gray, alpha=0.25, zorder=1)
ax0.vlines(0, 0, 1.5, ps.white, 'dashed')
nrecording_centered_onset_chirps, dtype=object
)
ax0.eventplot(
np.array(nrecording_centered_onset_chirps),
linelengths=0.5,
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([])
@ -426,14 +489,20 @@ def main(datapath: str):
ax[0].plot(time, onset_median, color=ps.black)
# Plot chasing offets
ax[1].set_xlabel('Time[s]')
ax[1].set_xlabel("Time[s]")
ax[1].plot(time, all_offset_chirps_convolved, color=ps.orange, zorder=2)
ax1 = ax[1].twinx()
nrecording_centered_offset_chirps = np.asarray(
nrecording_centered_offset_chirps, dtype=object)
ax1.eventplot(np.array(nrecording_centered_offset_chirps),
linelengths=0.5, colors=ps.gray, alpha=0.25, zorder=1)
ax1.vlines(0, 0, 1.5, ps.white, 'dashed')
nrecording_centered_offset_chirps, dtype=object
)
ax1.eventplot(
np.array(nrecording_centered_offset_chirps),
linelengths=0.5,
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([])
@ -444,24 +513,31 @@ def main(datapath: str):
ax[1].plot(time, offset_median, color=ps.black)
# Plot physical contacts
ax[2].set_xlabel('Time[s]')
ax[2].set_xlabel("Time[s]")
ax[2].plot(time, all_physical_chirps_convolved, color=ps.maroon, zorder=2)
ax2 = ax[2].twinx()
nrecording_centered_physical_chirps = np.asarray(
nrecording_centered_physical_chirps, dtype=object)
ax2.eventplot(np.array(nrecording_centered_physical_chirps),
linelengths=0.5, colors=ps.gray, alpha=0.25, zorder=1)
ax2.vlines(0, 0, 1.5, ps.white, 'dashed')
nrecording_centered_physical_chirps, dtype=object
)
ax2.eventplot(
np.array(nrecording_centered_physical_chirps),
linelengths=0.5,
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, 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].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')
fig.suptitle("All recordings")
plt.show()
plt.close()
@ -587,7 +663,7 @@ def main(datapath: str):
#### Chirps around events, only losers, one recording ####
if __name__ == '__main__':
if __name__ == "__main__":
# Path to the data
datapath = '../data/mount_data/'
datapath = "../data/mount_data/"
main(datapath)

35
code/extract_chirps.py
View File

@ -8,50 +8,51 @@ from IPython import embed
def get_valid_datasets(dataroot):
datasets = sorted([name for name in os.listdir(dataroot) if os.path.isdir(
os.path.join(dataroot, name))])
datasets = sorted(
[
name
for name in os.listdir(dataroot)
if os.path.isdir(os.path.join(dataroot, name))
]
)
valid_datasets = []
for dataset in datasets:
path = os.path.join(dataroot, dataset)
csv_name = '-'.join(dataset.split('-')[:3]) + '.csv'
csv_name = "-".join(dataset.split("-")[:3]) + ".csv"
if os.path.exists(os.path.join(path, csv_name)) is False:
continue
if os.path.exists(os.path.join(path, 'ident_v.npy')) is False:
if os.path.exists(os.path.join(path, "ident_v.npy")) is False:
continue
ident = np.load(os.path.join(path, 'ident_v.npy'))
ident = np.load(os.path.join(path, "ident_v.npy"))
number_of_fish = len(np.unique(ident[~np.isnan(ident)]))
if number_of_fish != 2:
continue
valid_datasets.append(dataset)
datapaths = [os.path.join(dataroot, dataset) +
'/' for dataset in valid_datasets]
datapaths = [
os.path.join(dataroot, dataset) + "/" for dataset in valid_datasets
]
return datapaths, valid_datasets
def main(datapaths):
for path in datapaths:
chirpdetection(path, plot='show')
if __name__ == '__main__':
chirpdetection(path, plot="show")
dataroot = '../data/mount_data/'
if __name__ == "__main__":
dataroot = "../data/mount_data/"
datapaths, valid_datasets = get_valid_datasets(dataroot)
recs = pd.DataFrame(columns=['recording'], data=valid_datasets)
recs.to_csv('../recs.csv', index=False)
recs = pd.DataFrame(columns=["recording"], data=valid_datasets)
recs.to_csv("../recs.csv", index=False)
# datapaths = ['../data/mount_data/2020-03-25-10_00/']
main(datapaths)

34
code/get_behaviour.py
View File

@ -7,29 +7,41 @@ from pandas import read_csv
ssh = SSHClient()
ssh.load_system_host_keys()
ssh.connect(hostname='kraken',
username='efish',
password='fwNix4U',
ssh.connect(
hostname="kraken",
username="efish",
password="fwNix4U",
)
# SCPCLient takes a paramiko transport as its only argument
scp = SCPClient(ssh.get_transport())
data = read_csv('../recs.csv')
foldernames = data['recording'].values
data = read_csv("../recs.csv")
foldernames = data["recording"].values
directory = f'/Users/acfw/Documents/uni_tuebingen/chirpdetection/GP2023_chirp_detection/data/mount_data/'
directory = f"/Users/acfw/Documents/uni_tuebingen/chirpdetection/GP2023_chirp_detection/data/mount_data/"
for foldername in foldernames:
if not os.path.exists(directory + foldername):
os.makedirs(directory + foldername)
files = [('-').join(foldername.split('-')[:3])+'.csv','chirp_ids.npy', 'chirps.npy', 'fund_v.npy', 'ident_v.npy', 'idx_v.npy', 'times.npy', 'spec.npy', 'LED_on_time.npy', 'sign_v.npy']
files = [
("-").join(foldername.split("-")[:3]) + ".csv",
"chirp_ids.npy",
"chirps.npy",
"fund_v.npy",
"ident_v.npy",
"idx_v.npy",
"times.npy",
"spec.npy",
"LED_on_time.npy",
"sign_v.npy",
]
for f in files:
scp.get(f'/home/efish/behavior/2019_tube_competition/{foldername}/{f}',
directory+foldername)
scp.get(
f"/home/efish/behavior/2019_tube_competition/{foldername}/{f}",
directory + foldername,
)
scp.close()

94
code/modules/behaviour_handling.py
View File

@ -30,12 +30,12 @@ class Behavior:
"""
def __init__(self, folder_path: str) -> None:
LED_on_time_BORIS = np.load(os.path.join(
folder_path, 'LED_on_time.npy'), allow_pickle=True)
LED_on_time_BORIS = np.load(
os.path.join(folder_path, "LED_on_time.npy"), allow_pickle=True
)
csv_filename = os.path.split(folder_path[:-1])[-1]
csv_filename = '-'.join(csv_filename.split('-')[:-1]) + '.csv'
csv_filename = "-".join(csv_filename.split("-")[:-1]) + ".csv"
# embed()
# csv_filename = [f for f in os.listdir(
@ -43,31 +43,39 @@ class Behavior:
# logger.info(f'CSV file: {csv_filename}')
self.dataframe = read_csv(os.path.join(folder_path, csv_filename))
self.chirps = np.load(os.path.join(
folder_path, 'chirps.npy'), allow_pickle=True)
self.chirps_ids = np.load(os.path.join(
folder_path, 'chirp_ids.npy'), allow_pickle=True)
self.ident = np.load(os.path.join(
folder_path, 'ident_v.npy'), allow_pickle=True)
self.idx = np.load(os.path.join(
folder_path, 'idx_v.npy'), allow_pickle=True)
self.freq = np.load(os.path.join(
folder_path, 'fund_v.npy'), allow_pickle=True)
self.time = np.load(os.path.join(
folder_path, "times.npy"), allow_pickle=True)
self.spec = np.load(os.path.join(
folder_path, "spec.npy"), allow_pickle=True)
self.chirps = np.load(
os.path.join(folder_path, "chirps.npy"), allow_pickle=True
)
self.chirps_ids = np.load(
os.path.join(folder_path, "chirp_ids.npy"), allow_pickle=True
)
self.ident = np.load(
os.path.join(folder_path, "ident_v.npy"), allow_pickle=True
)
self.idx = np.load(
os.path.join(folder_path, "idx_v.npy"), allow_pickle=True
)
self.freq = np.load(
os.path.join(folder_path, "fund_v.npy"), allow_pickle=True
)
self.time = np.load(
os.path.join(folder_path, "times.npy"), allow_pickle=True
)
self.spec = np.load(
os.path.join(folder_path, "spec.npy"), allow_pickle=True
)
for k, key in enumerate(self.dataframe.keys()):
key = key.lower()
if ' ' in key:
key = key.replace(' ', '_')
if '(' in key:
key = key.replace('(', '')
key = key.replace(')', '')
setattr(self, key, np.array(
self.dataframe[self.dataframe.keys()[k]]))
if " " in key:
key = key.replace(" ", "_")
if "(" in key:
key = key.replace("(", "")
key = key.replace(")", "")
setattr(
self, key, np.array(self.dataframe[self.dataframe.keys()[k]])
)
last_LED_t_BORIS = LED_on_time_BORIS[-1]
real_time_range = self.time[-1] - self.time[0]
@ -78,22 +86,19 @@ class Behavior:
def correct_chasing_events(
category: np.ndarray,
timestamps: np.ndarray
category: np.ndarray, timestamps: np.ndarray
) -> tuple[np.ndarray, np.ndarray]:
onset_ids = np.arange(len(category))[category == 0]
offset_ids = np.arange(len(category))[category == 1]
onset_ids = np.arange(
len(category))[category == 0]
offset_ids = np.arange(
len(category))[category == 1]
wrong_bh = np.arange(len(category))[
category != 2][:-1][np.diff(category[category != 2]) == 0]
wrong_bh = np.arange(len(category))[category != 2][:-1][
np.diff(category[category != 2]) == 0
]
if category[category != 2][-1] == 0:
wrong_bh = np.append(
wrong_bh,
np.arange(len(category))[category != 2][-1])
wrong_bh, np.arange(len(category))[category != 2][-1]
)
if onset_ids[0] > offset_ids[0]:
offset_ids = np.delete(offset_ids, 0)
@ -103,18 +108,16 @@ def correct_chasing_events(
category = np.delete(category, wrong_bh)
timestamps = np.delete(timestamps, wrong_bh)
new_onset_ids = np.arange(
len(category))[category == 0]
new_offset_ids = np.arange(
len(category))[category == 1]
new_onset_ids = np.arange(len(category))[category == 0]
new_offset_ids = np.arange(len(category))[category == 1]
# Check whether on- or offset is longer and calculate length difference
if len(new_onset_ids) > len(new_offset_ids):
embed()
logger.warning('Onsets are greater than offsets')
logger.warning("Onsets are greater than offsets")
elif len(new_onset_ids) < len(new_offset_ids):
logger.warning('Offsets are greater than onsets')
logger.warning("Offsets are greater than onsets")
elif len(new_onset_ids) == len(new_offset_ids):
# logger.info('Chasing events are equal')
pass
@ -130,13 +133,11 @@ def center_chirps(
# dt: float,
# width: float,
) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
event_chirps = [] # chirps that are in specified window around event
# timestamps of chirps around event centered on the event timepoint
centered_chirps = []
for event_timestamp in events:
start = event_timestamp - time_before_event
stop = event_timestamp + time_after_event
chirps_around_event = [c for c in chirps if (c >= start) & (c <= stop)]
@ -152,7 +153,8 @@ def center_chirps(
if len(centered_chirps) != len(event_chirps):
raise ValueError(
'Non centered chirps and centered chirps are not equal')
"Non centered chirps and centered chirps are not equal"
)
# time = np.arange(-time_before_event, time_after_event, dt)

21
code/modules/datahandling.py
View File

@ -23,7 +23,9 @@ def minmaxnorm(data):
return (data - np.min(data)) / (np.max(data) - np.min(data))
def instantaneous_frequency2(signal: np.ndarray, fs: float, interpolation: str = 'linear') -> np.ndarray:
def instantaneous_frequency2(
signal: np.ndarray, fs: float, interpolation: str = "linear"
) -> np.ndarray:
"""
Compute the instantaneous frequency of a periodic signal using zero crossings and resample the frequency using linear
or cubic interpolation to match the dimensions of the input array.
@ -55,10 +57,10 @@ def instantaneous_frequency2(signal: np.ndarray, fs: float, interpolation: str =
orig_len = len(signal)
freq = resample(freq, orig_len)
if interpolation == 'linear':
if interpolation == "linear":
freq = np.interp(np.arange(0, orig_len), np.arange(0, orig_len), freq)
elif interpolation == 'cubic':
freq = resample(freq, orig_len, window='cubic')
elif interpolation == "cubic":
freq = resample(freq, orig_len, window="cubic")
return freq
@ -67,7 +69,7 @@ def instantaneous_frequency(
signal: np.ndarray,
samplerate: int,
smoothing_window: int,
interpolation: str = 'linear',
interpolation: str = "linear",
) -> np.ndarray:
"""
Compute the instantaneous frequency of a signal that is approximately
@ -120,11 +122,10 @@ def instantaneous_frequency(
orig_len = len(signal)
freq = resample(instantaneous_frequency, orig_len)
if interpolation == 'linear':
if interpolation == "linear":
freq = np.interp(np.arange(0, orig_len), np.arange(0, orig_len), freq)
elif interpolation == 'cubic':
freq = resample(freq, orig_len, window='cubic')
elif interpolation == "cubic":
freq = resample(freq, orig_len, window="cubic")
return freq
@ -160,7 +161,6 @@ def purge_duplicates(
group = [timestamps[0]]
for i in range(1, len(timestamps)):
# check the difference between current timestamp and previous
# timestamp is less than the threshold
if timestamps[i] - timestamps[i - 1] < threshold:
@ -379,7 +379,6 @@ def acausal_kde1d(spikes, time, width):
if __name__ == "__main__":
timestamps = [
[1.2, 1.5, 1.3],
[],

1
code/modules/filehandling.py
View File

@ -35,7 +35,6 @@ class LoadData:
"""
def __init__(self, datapath: str) -> None:
# load raw data
self.datapath = datapath
self.file = os.path.join(datapath, "traces-grid1.raw")

9
code/modules/filters.py
View File

@ -60,9 +60,7 @@ def highpass_filter(
def lowpass_filter(
signal: np.ndarray,
samplerate: float,
cutoff: float
signal: np.ndarray, samplerate: float, cutoff: float
) -> np.ndarray:
"""Lowpass filter a signal.
@ -86,9 +84,8 @@ def lowpass_filter(
return filtered_signal
def envelope(signal: np.ndarray,
samplerate: float,
cutoff_frequency: float
def envelope(
signal: np.ndarray, samplerate: float, cutoff_frequency: float
) -> np.ndarray:
"""Calculate the envelope of a signal using a lowpass filter.

8
code/modules/logger.py
View File

@ -2,12 +2,13 @@ import logging
def makeLogger(name: str):
# create logger formats for file and terminal
file_formatter = logging.Formatter(
"[ %(levelname)s ] ~ %(asctime)s ~ %(module)s.%(funcName)s: %(message)s")
"[ %(levelname)s ] ~ %(asctime)s ~ %(module)s.%(funcName)s: %(message)s"
)
console_formatter = logging.Formatter(
"[ %(levelname)s ] in %(module)s.%(funcName)s: %(message)s")
"[ %(levelname)s ] in %(module)s.%(funcName)s: %(message)s"
)
# create logging file if loglevel is debug
file_handler = logging.FileHandler(f"gridtools_log.log", mode="w")
@ -29,7 +30,6 @@ def makeLogger(name: str):
if __name__ == "__main__":
# initiate logger
mylogger = makeLogger(__name__)

16
code/modules/plotstyle.py
View File

@ -7,7 +7,6 @@ from matplotlib.colors import ListedColormap
def PlotStyle() -> None:
class style:
# lightcmap = cmocean.tools.lighten(cmocean.cm.haline, 0.8)
# units
@ -76,13 +75,15 @@ def PlotStyle() -> None:
va="center",
zorder=1000,
bbox=dict(
boxstyle=f"circle, pad={padding}", fc="white", ec="black", lw=1
boxstyle=f"circle, pad={padding}",
fc="white",
ec="black",
lw=1,
),
)
@classmethod
def fade_cmap(cls, cmap):
my_cmap = cmap(np.arange(cmap.N))
my_cmap[:, -1] = np.linspace(0, 1, cmap.N)
my_cmap = ListedColormap(my_cmap)
@ -295,7 +296,6 @@ def PlotStyle() -> None:
if __name__ == "__main__":
s = PlotStyle()
import matplotlib.cbook as cbook
@ -347,7 +347,8 @@ if __name__ == "__main__":
for ax in axs:
ax.yaxis.grid(True)
ax.set_xticks(
[y + 1 for y in range(len(all_data))], labels=["x1", "x2", "x3", "x4"]
[y + 1 for y in range(len(all_data))],
labels=["x1", "x2", "x3", "x4"],
)
ax.set_xlabel("Four separate samples")
ax.set_ylabel("Observed values")
@ -396,7 +397,10 @@ if __name__ == "__main__":
grid = np.random.rand(4, 4)
fig, axs = plt.subplots(
nrows=3, ncols=6, figsize=(9, 6), subplot_kw={"xticks": [], "yticks": []}
nrows=3,
ncols=6,
figsize=(9, 6),
subplot_kw={"xticks": [], "yticks": []},
)
for ax, interp_method in zip(axs.flat, methods):

16
code/modules/plotstyle1.py
View File

@ -7,7 +7,6 @@ from matplotlib.colors import ListedColormap
def PlotStyle() -> None:
class style:
# lightcmap = cmocean.tools.lighten(cmocean.cm.haline, 0.8)
# units
@ -76,13 +75,15 @@ def PlotStyle() -> None:
va="center",
zorder=1000,
bbox=dict(
boxstyle=f"circle, pad={padding}", fc="white", ec="black", lw=1
boxstyle=f"circle, pad={padding}",
fc="white",
ec="black",
lw=1,
),
)
@classmethod
def fade_cmap(cls, cmap):
my_cmap = cmap(np.arange(cmap.N))
my_cmap[:, -1] = np.linspace(0, 1, cmap.N)
my_cmap = ListedColormap(my_cmap)
@ -295,7 +296,6 @@ def PlotStyle() -> None:
if __name__ == "__main__":
s = PlotStyle()
import matplotlib.cbook as cbook
@ -347,7 +347,8 @@ if __name__ == "__main__":
for ax in axs:
ax.yaxis.grid(True)
ax.set_xticks(
[y + 1 for y in range(len(all_data))], labels=["x1", "x2", "x3", "x4"]
[y + 1 for y in range(len(all_data))],
labels=["x1", "x2", "x3", "x4"],
)
ax.set_xlabel("Four separate samples")
ax.set_ylabel("Observed values")
@ -396,7 +397,10 @@ if __name__ == "__main__":
grid = np.random.rand(4, 4)
fig, axs = plt.subplots(
nrows=3, ncols=6, figsize=(9, 6), subplot_kw={"xticks": [], "yticks": []}
nrows=3,
ncols=6,
figsize=(9, 6),
subplot_kw={"xticks": [], "yticks": []},
)
for ax, interp_method in zip(axs.flat, methods):

16
code/modules/plotstyle_dark.py
View File

@ -7,7 +7,6 @@ from matplotlib.colors import ListedColormap
def PlotStyle() -> None:
class style:
# lightcmap = cmocean.tools.lighten(cmocean.cm.haline, 0.8)
# units
@ -76,13 +75,15 @@ def PlotStyle() -> None:
va="center",
zorder=1000,
bbox=dict(
boxstyle=f"circle, pad={padding}", fc="white", ec="black", lw=1
boxstyle=f"circle, pad={padding}",
fc="white",
ec="black",
lw=1,
),
)
@classmethod
def fade_cmap(cls, cmap):
my_cmap = cmap(np.arange(cmap.N))
my_cmap[:, -1] = np.linspace(0, 1, cmap.N)
my_cmap = ListedColormap(my_cmap)
@ -295,7 +296,6 @@ def PlotStyle() -> None:
if __name__ == "__main__":
s = PlotStyle()
import matplotlib.cbook as cbook
@ -347,7 +347,8 @@ if __name__ == "__main__":
for ax in axs:
ax.yaxis.grid(True)
ax.set_xticks(
[y + 1 for y in range(len(all_data))], labels=["x1", "x2", "x3", "x4"]
[y + 1 for y in range(len(all_data))],
labels=["x1", "x2", "x3", "x4"],
)
ax.set_xlabel("Four separate samples")
ax.set_ylabel("Observed values")
@ -396,7 +397,10 @@ if __name__ == "__main__":
grid = np.random.rand(4, 4)
fig, axs = plt.subplots(
nrows=3, ncols=6, figsize=(9, 6), subplot_kw={"xticks": [], "yticks": []}
nrows=3,
ncols=6,
figsize=(9, 6),
subplot_kw={"xticks": [], "yticks": []},
)
for ax, interp_method in zip(axs.flat, methods):

289
code/plot_chirp_size.py
View File

@ -16,26 +16,25 @@ logger = makeLogger(__name__)
def get_chirp_winner_loser(folder_name, Behavior, order_meta_df):
foldername = folder_name.split('/')[-2]
winner_row = order_meta_df[order_meta_df['recording'] == foldername]
winner = winner_row['winner'].values[0].astype(int)
winner_fish1 = winner_row['fish1'].values[0].astype(int)
winner_fish2 = winner_row['fish2'].values[0].astype(int)
foldername = folder_name.split("/")[-2]
winner_row = order_meta_df[order_meta_df["recording"] == foldername]
winner = winner_row["winner"].values[0].astype(int)
winner_fish1 = winner_row["fish1"].values[0].astype(int)
winner_fish2 = winner_row["fish2"].values[0].astype(int)
if winner > 0:
if winner == winner_fish1:
winner_fish_id = winner_row['rec_id1'].values[0]
loser_fish_id = winner_row['rec_id2'].values[0]
winner_fish_id = winner_row["rec_id1"].values[0]
loser_fish_id = winner_row["rec_id2"].values[0]
elif winner == winner_fish2:
winner_fish_id = winner_row['rec_id2'].values[0]
loser_fish_id = winner_row['rec_id1'].values[0]
winner_fish_id = winner_row["rec_id2"].values[0]
loser_fish_id = winner_row["rec_id1"].values[0]
chirp_winner = len(
Behavior.chirps[Behavior.chirps_ids == winner_fish_id])
chirp_loser = len(
Behavior.chirps[Behavior.chirps_ids == loser_fish_id])
Behavior.chirps[Behavior.chirps_ids == winner_fish_id]
)
chirp_loser = len(Behavior.chirps[Behavior.chirps_ids == loser_fish_id])
return chirp_winner, chirp_loser
else:
@ -43,24 +42,24 @@ def get_chirp_winner_loser(folder_name, Behavior, order_meta_df):
def get_chirp_size(folder_name, Behavior, order_meta_df, id_meta_df):
foldername = folder_name.split('/')[-2]
folder_row = order_meta_df[order_meta_df['recording'] == foldername]
fish1 = folder_row['fish1'].values[0].astype(int)
fish2 = folder_row['fish2'].values[0].astype(int)
winner = folder_row['winner'].values[0].astype(int)
groub = folder_row['group'].values[0].astype(int)
size_fish1_row = id_meta_df[(id_meta_df['group'] == groub) & (
id_meta_df['fish'] == fish1)]
size_fish2_row = id_meta_df[(id_meta_df['group'] == groub) & (
id_meta_df['fish'] == fish2)]
size_winners = [size_fish1_row[col].values[0]
for col in ['l1', 'l2', 'l3']]
foldername = folder_name.split("/")[-2]
folder_row = order_meta_df[order_meta_df["recording"] == foldername]
fish1 = folder_row["fish1"].values[0].astype(int)
fish2 = folder_row["fish2"].values[0].astype(int)
winner = folder_row["winner"].values[0].astype(int)
groub = folder_row["group"].values[0].astype(int)
size_fish1_row = id_meta_df[
(id_meta_df["group"] == groub) & (id_meta_df["fish"] == fish1)
]
size_fish2_row = id_meta_df[
(id_meta_df["group"] == groub) & (id_meta_df["fish"] == fish2)
]
size_winners = [size_fish1_row[col].values[0] for col in ["l1", "l2", "l3"]]
size_fish1 = np.nanmean(size_winners)
size_losers = [size_fish2_row[col].values[0] for col in ['l1', 'l2', 'l3']]
size_losers = [size_fish2_row[col].values[0] for col in ["l1", "l2", "l3"]]
size_fish2 = np.nanmean(size_losers)
if winner == fish1:
@ -75,8 +74,8 @@ def get_chirp_size(folder_name, Behavior, order_meta_df, id_meta_df):
size_diff_bigger = 0
size_diff_smaller = 0
winner_fish_id = folder_row['rec_id1'].values[0]
loser_fish_id = folder_row['rec_id2'].values[0]
winner_fish_id = folder_row["rec_id1"].values[0]
loser_fish_id = folder_row["rec_id2"].values[0]
elif winner == fish2:
if size_fish2 > size_fish1:
@ -90,39 +89,39 @@ def get_chirp_size(folder_name, Behavior, order_meta_df, id_meta_df):
size_diff_bigger = 0
size_diff_smaller = 0
winner_fish_id = folder_row['rec_id2'].values[0]
loser_fish_id = folder_row['rec_id1'].values[0]
winner_fish_id = folder_row["rec_id2"].values[0]
loser_fish_id = folder_row["rec_id1"].values[0]
else:
size_diff_bigger = np.nan
size_diff_smaller = np.nan
winner_fish_id = np.nan
loser_fish_id = np.nan
return size_diff_bigger, size_diff_smaller, winner_fish_id, loser_fish_id
return (
size_diff_bigger,
size_diff_smaller,
winner_fish_id,
loser_fish_id,
)
chirp_winner = len(
Behavior.chirps[Behavior.chirps_ids == winner_fish_id])
chirp_loser = len(
Behavior.chirps[Behavior.chirps_ids == loser_fish_id])
chirp_winner = len(Behavior.chirps[Behavior.chirps_ids == winner_fish_id])
chirp_loser = len(Behavior.chirps[Behavior.chirps_ids == loser_fish_id])
return size_diff_bigger, chirp_winner, size_diff_smaller, chirp_loser
def get_chirp_freq(folder_name, Behavior, order_meta_df):
foldername = folder_name.split("/")[-2]
folder_row = order_meta_df[order_meta_df["recording"] == foldername]
fish1 = folder_row["fish1"].values[0].astype(int)
fish2 = folder_row["fish2"].values[0].astype(int)
foldername = folder_name.split('/')[-2]
folder_row = order_meta_df[order_meta_df['recording'] == foldername]
fish1 = folder_row['fish1'].values[0].astype(int)
fish2 = folder_row['fish2'].values[0].astype(int)
fish1_freq = folder_row['rec_id1'].values[0].astype(int)
fish2_freq = folder_row['rec_id2'].values[0].astype(int)
fish1_freq = folder_row["rec_id1"].values[0].astype(int)
fish2_freq = folder_row["rec_id2"].values[0].astype(int)
chirp_freq_fish1 = np.nanmedian(
Behavior.freq[Behavior.ident == fish1_freq])
chirp_freq_fish2 = np.nanmedian(
Behavior.freq[Behavior.ident == fish2_freq])
winner = folder_row['winner'].values[0].astype(int)
chirp_freq_fish1 = np.nanmedian(Behavior.freq[Behavior.ident == fish1_freq])
chirp_freq_fish2 = np.nanmedian(Behavior.freq[Behavior.ident == fish2_freq])
winner = folder_row["winner"].values[0].astype(int)
if winner == fish1:
# if chirp_freq_fish1 > chirp_freq_fish2:
@ -138,9 +137,9 @@ def get_chirp_freq(folder_name, Behavior, order_meta_df):
# winner_fish_id = np.nan
# loser_fish_id = np.nan
winner_fish_id = folder_row['rec_id1'].values[0]
winner_fish_id = folder_row["rec_id1"].values[0]
winner_fish_freq = chirp_freq_fish1
loser_fish_id = folder_row['rec_id2'].values[0]
loser_fish_id = folder_row["rec_id2"].values[0]
loser_fish_freq = chirp_freq_fish2
elif winner == fish2:
@ -157,9 +156,9 @@ def get_chirp_freq(folder_name, Behavior, order_meta_df):
# winner_fish_id = np.nan
# loser_fish_id = np.nan
winner_fish_id = folder_row['rec_id2'].values[0]
winner_fish_id = folder_row["rec_id2"].values[0]
winner_fish_freq = chirp_freq_fish2
loser_fish_id = folder_row['rec_id1'].values[0]
loser_fish_id = folder_row["rec_id1"].values[0]
loser_fish_freq = chirp_freq_fish1
else:
winner_fish_freq = np.nan
@ -168,25 +167,25 @@ def get_chirp_freq(folder_name, Behavior, order_meta_df):
loser_fish_id = np.nan
return winner_fish_freq, winner_fish_id, loser_fish_freq, loser_fish_id
chirp_winner = len(
Behavior.chirps[Behavior.chirps_ids == winner_fish_id])
chirp_loser = len(
Behavior.chirps[Behavior.chirps_ids == loser_fish_id])
chirp_winner = len(Behavior.chirps[Behavior.chirps_ids == winner_fish_id])
chirp_loser = len(Behavior.chirps[Behavior.chirps_ids == loser_fish_id])
return winner_fish_freq, chirp_winner, loser_fish_freq, chirp_loser
def main(datapath: str):
foldernames = [
datapath + x + '/' for x in os.listdir(datapath) if os.path.isdir(datapath+x)]
datapath + x + "/"
for x in os.listdir(datapath)
if os.path.isdir(datapath + x)
]
foldernames, _ = get_valid_datasets(datapath)
path_order_meta = (
'/').join(foldernames[0].split('/')[:-2]) + '/order_meta.csv'
path_order_meta = ("/").join(
foldernames[0].split("/")[:-2]
) + "/order_meta.csv"
order_meta_df = read_csv(path_order_meta)
order_meta_df['recording'] = order_meta_df['recording'].str[1:-1]
path_id_meta = (
'/').join(foldernames[0].split('/')[:-2]) + '/id_meta.csv'
order_meta_df["recording"] = order_meta_df["recording"].str[1:-1]
path_id_meta = ("/").join(foldernames[0].split("/")[:-2]) + "/id_meta.csv"
id_meta_df = read_csv(path_id_meta)
chirps_winner = []
@ -202,10 +201,9 @@ def main(datapath: str):
freq_chirps_winner = []
freq_chirps_loser = []
for foldername in foldernames:
# behabvior is pandas dataframe with all the data
if foldername == '../data/mount_data/2020-05-12-10_00/':
if foldername == "../data/mount_data/2020-05-12-10_00/":
continue
bh = Behavior(foldername)
# chirps are not sorted in time (presumably due to prior groupings)
@ -217,15 +215,24 @@ def main(datapath: str):
category, timestamps = correct_chasing_events(category, timestamps)
winner_chirp, loser_chirp = get_chirp_winner_loser(
foldername, bh, order_meta_df)
foldername, bh, order_meta_df
)
chirps_winner.append(winner_chirp)
chirps_loser.append(loser_chirp)
size_diff_bigger, chirp_winner, size_diff_smaller, chirp_loser = get_chirp_size(
foldername, bh, order_meta_df, id_meta_df)
(
size_diff_bigger,
chirp_winner,
size_diff_smaller,
chirp_loser,
) = get_chirp_size(foldername, bh, order_meta_df, id_meta_df)
freq_winner, chirp_freq_winner, freq_loser, chirp_freq_loser = get_chirp_freq(
foldername, bh, order_meta_df)
(
freq_winner,
chirp_freq_winner,
freq_loser,
chirp_freq_loser,
) = get_chirp_freq(foldername, bh, order_meta_df)
freq_diffs_higher.append(freq_winner)
freq_diffs_lower.append(freq_loser)
@ -242,82 +249,124 @@ def main(datapath: str):
pearsonr(size_diffs_winner, size_chirps_winner)
pearsonr(size_diffs_loser, size_chirps_loser)
fig, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(
21*ps.cm, 7*ps.cm), width_ratios=[1, 0.8, 0.8], sharey=True)
plt.subplots_adjust(left=0.11, right=0.948, top=0.86,
wspace=0.343, bottom=0.198)
fig, (ax1, ax2, ax3) = plt.subplots(
1,
3,
figsize=(21 * ps.cm, 7 * ps.cm),
width_ratios=[1, 0.8, 0.8],
sharey=True,
)
plt.subplots_adjust(
left=0.11, right=0.948, top=0.86, wspace=0.343, bottom=0.198
)
scatterwinner = 1.15
scatterloser = 1.85
chirps_winner = np.asarray(chirps_winner)[~np.isnan(chirps_winner)]
chirps_loser = np.asarray(chirps_loser)[~np.isnan(chirps_loser)]
embed()
exit()
freq_diffs_higher = np.asarray(
freq_diffs_higher)[~np.isnan(freq_diffs_higher)]
freq_diffs_lower = np.asarray(freq_diffs_lower)[
~np.isnan(freq_diffs_lower)]
freq_chirps_winner = np.asarray(
freq_chirps_winner)[~np.isnan(freq_chirps_winner)]
freq_chirps_loser = np.asarray(
freq_chirps_loser)[~np.isnan(freq_chirps_loser)]
freq_diffs_higher = np.asarray(freq_diffs_higher)[
~np.isnan(freq_diffs_higher)
]
freq_diffs_lower = np.asarray(freq_diffs_lower)[~np.isnan(freq_diffs_lower)]
freq_chirps_winner = np.asarray(freq_chirps_winner)[
~np.isnan(freq_chirps_winner)
]
freq_chirps_loser = np.asarray(freq_chirps_loser)[
~np.isnan(freq_chirps_loser)
]
stat = wilcoxon(chirps_winner, chirps_loser)
print(stat)
winner_color = ps.gblue2
loser_color = ps.gblue1
bplot1 = ax1.boxplot(chirps_winner, positions=[
0.9], showfliers=False, patch_artist=True)
bplot2 = ax1.boxplot(chirps_loser, positions=[
2.1], showfliers=False, patch_artist=True)
ax1.scatter(np.ones(len(chirps_winner)) *
scatterwinner, chirps_winner, color=winner_color)
ax1.scatter(np.ones(len(chirps_loser)) *
scatterloser, chirps_loser, color=loser_color)
ax1.set_xticklabels(['Winner', 'Loser'])
ax1.text(0.1, 0.85, f'n={len(chirps_loser)}',
transform=ax1.transAxes, color=ps.white)
bplot1 = ax1.boxplot(
chirps_winner, positions=[0.9], showfliers=False, patch_artist=True
)
bplot2 = ax1.boxplot(
chirps_loser, positions=[2.1], showfliers=False, patch_artist=True
)
ax1.scatter(
np.ones(len(chirps_winner)) * scatterwinner,
chirps_winner,
color=winner_color,
)
ax1.scatter(
np.ones(len(chirps_loser)) * scatterloser,
chirps_loser,
color=loser_color,
)
ax1.set_xticklabels(["Winner", "Loser"])
ax1.text(
0.1,
0.85,
f"n={len(chirps_loser)}",
transform=ax1.transAxes,
color=ps.white,
)
for w, l in zip(chirps_winner, chirps_loser):
ax1.plot([scatterwinner, scatterloser], [w, l],
color=ps.white, alpha=0.6, linewidth=1, zorder=-1)
ax1.set_ylabel('Chirp counts', color=ps.white)
ax1.set_xlabel('Competition outcome', color=ps.white)
ax1.plot(
[scatterwinner, scatterloser],
[w, l],
color=ps.white,
alpha=0.6,
linewidth=1,
zorder=-1,
)
ax1.set_ylabel("Chirp counts", color=ps.white)
ax1.set_xlabel("Competition outcome", color=ps.white)
ps.set_boxplot_color(bplot1, winner_color)
ps.set_boxplot_color(bplot2, loser_color)
ax2.scatter(size_diffs_winner, size_chirps_winner,
color=winner_color, label='Winner')
ax2.scatter(size_diffs_loser, size_chirps_loser,
color=loser_color, label='Loser')
ax2.text(0.05, 0.85, f'n={len(size_chirps_loser)}',
transform=ax2.transAxes, color=ps.white)
ax2.set_xlabel('Size difference [cm]')
ax2.scatter(
size_diffs_winner,
size_chirps_winner,
color=winner_color,
label="Winner",
)
ax2.scatter(
size_diffs_loser, size_chirps_loser, color=loser_color, label="Loser"
)
ax2.text(
0.05,
0.85,
f"n={len(size_chirps_loser)}",
transform=ax2.transAxes,
color=ps.white,
)
ax2.set_xlabel("Size difference [cm]")
# ax2.set_xticks(np.arange(-10, 10.1, 2))
ax3.scatter(freq_diffs_higher, freq_chirps_winner, color=winner_color)
ax3.scatter(freq_diffs_lower, freq_chirps_loser, color=loser_color)
ax3.text(0.1, 0.85, f'n={len(np.asarray(freq_chirps_winner)[~np.isnan(freq_chirps_loser)])}',
transform=ax3.transAxes, color=ps.white)
ax3.text(
0.1,
0.85,
f"n={len(np.asarray(freq_chirps_winner)[~np.isnan(freq_chirps_loser)])}",
transform=ax3.transAxes,
color=ps.white,
)
ax3.set_xlabel('EODf [Hz]')
ax3.set_xlabel("EODf [Hz]")
handles, labels = ax2.get_legend_handles_labels()
fig.legend(handles, labels, loc='upper center',
ncol=2, bbox_to_anchor=(0.5, 1.04))
fig.legend(
handles, labels, loc="upper center", ncol=2, bbox_to_anchor=(0.5, 1.04)
)
# pearson r
plt.savefig('../poster/figs/chirps_winner_loser.pdf')
plt.savefig("../poster/figs/chirps_winner_loser.pdf")
plt.show()
if __name__ == '__main__':
if __name__ == "__main__":
# Path to the data
datapath = '../data/mount_data/'
datapath = "../data/mount_data/"
main(datapath)

68
code/plot_chirps_in_chasing.py
View File

@ -21,14 +21,16 @@ logger = makeLogger(__name__)
def main(datapath: str):
foldernames = [
datapath + x + '/' for x in os.listdir(datapath) if os.path.isdir(datapath+x)]
datapath + x + "/"
for x in os.listdir(datapath)
if os.path.isdir(datapath + x)
]
time_precents = []
chirps_percents = []
for foldername in foldernames:
# behabvior is pandas dataframe with all the data
if foldername == '../data/mount_data/2020-05-12-10_00/':
if foldername == "../data/mount_data/2020-05-12-10_00/":
continue
bh = Behavior(foldername)
@ -46,21 +48,27 @@ def main(datapath: str):
chirps_in_chasings = []
for onset, offset in zip(chasing_onset, chasing_offset):
chirps_in_chasing = [
c for c in bh.chirps if (c > onset) & (c < offset)]
c for c in bh.chirps if (c > onset) & (c < offset)
]
chirps_in_chasings.append(chirps_in_chasing)
try:
time_chasing = np.sum(
chasing_offset[chasing_offset < 3*60*60] - chasing_onset[chasing_onset < 3*60*60])
chasing_offset[chasing_offset < 3 * 60 * 60]
- chasing_onset[chasing_onset < 3 * 60 * 60]
)
except:
time_chasing = np.sum(
chasing_offset[chasing_offset < 3*60*60] - chasing_onset[chasing_onset < 3*60*60][:-1])
chasing_offset[chasing_offset < 3 * 60 * 60]
- chasing_onset[chasing_onset < 3 * 60 * 60][:-1]
)
time_chasing_percent = (time_chasing / (3 * 60 * 60)) * 100
chirps_chasing = np.asarray(flatten(chirps_in_chasings))
chirps_chasing_new = chirps_chasing[chirps_chasing < 3 * 60 * 60]
chirps_percent = (len(chirps_chasing_new) /
len(bh.chirps[bh.chirps < 3*60*60]))*100
chirps_percent = (
len(chirps_chasing_new) / len(bh.chirps[bh.chirps < 3 * 60 * 60])
) * 100
time_precents.append(time_chasing_percent)
chirps_percents.append(chirps_percent)
@ -69,27 +77,41 @@ def main(datapath: str):
scatter_time = 1.20
scatter_chirps = 1.80
size = 10
bplot1 = ax.boxplot([time_precents, chirps_percents],
showfliers=False, patch_artist=True)
bplot1 = ax.boxplot(
[time_precents, chirps_percents], showfliers=False, patch_artist=True
)
ps.set_boxplot_color(bplot1, ps.gray)
ax.set_xticklabels(['Time \nchasing', 'Chirps \nin chasing'])
ax.set_ylabel('Percent')
ax.scatter(np.ones(len(time_precents))*scatter_time, time_precents,
facecolor=ps.white, s=size)
ax.scatter(np.ones(len(chirps_percents))*scatter_chirps, chirps_percents,
facecolor=ps.white, s=size)
ax.set_xticklabels(["Time \nchasing", "Chirps \nin chasing"])
ax.set_ylabel("Percent")
ax.scatter(
np.ones(len(time_precents)) * scatter_time,
time_precents,
facecolor=ps.white,
s=size,
)
ax.scatter(
np.ones(len(chirps_percents)) * scatter_chirps,
chirps_percents,
facecolor=ps.white,
s=size,
)
for i in range(len(time_precents)):
ax.plot([scatter_time, scatter_chirps], [time_precents[i],
chirps_percents[i]], alpha=0.6, linewidth=1, color=ps.white)
ax.text(0.1, 0.9, f'n={len(time_precents)}', transform=ax.transAxes)
ax.plot(
[scatter_time, scatter_chirps],
[time_precents[i], chirps_percents[i]],
alpha=0.6,
linewidth=1,
color=ps.white,
)
ax.text(0.1, 0.9, f"n={len(time_precents)}", transform=ax.transAxes)
plt.subplots_adjust(left=0.221, bottom=0.186, right=0.97, top=0.967)
plt.savefig('../poster/figs/chirps_in_chasing.pdf')
plt.savefig("../poster/figs/chirps_in_chasing.pdf")
plt.show()
if __name__ == '__main__':
if __name__ == "__main__":
# Path to the data
datapath = '../data/mount_data/'
datapath = "../data/mount_data/"
main(datapath)

80
code/plot_event_timeline.py
View File

@ -13,6 +13,7 @@ from modules.plotstyle import PlotStyle
from modules.behaviour_handling import Behavior, correct_chasing_events
from extract_chirps import get_valid_datasets
ps = PlotStyle()
logger = makeLogger(__name__)
@ -20,13 +21,16 @@ logger = makeLogger(__name__)
def main(datapath: str):
foldernames = [
datapath + x + '/' for x in os.listdir(datapath) if os.path.isdir(datapath+x)]
datapath + x + "/"
for x in os.listdir(datapath)
if os.path.isdir(datapath + x)
]
foldernames, _ = get_valid_datasets(datapath)
for foldername in foldernames[3:4]:
print(foldername)
# foldername = foldernames[0]
if foldername == '../data/mount_data/2020-05-12-10_00/':
if foldername == "../data/mount_data/2020-05-12-10_00/":
continue
# behabvior is pandas dataframe with all the data
bh = Behavior(foldername)
@ -52,18 +56,43 @@ def main(datapath: str):
exit()
fish1_color = ps.gblue2
fish2_color = ps.gblue1
fig, ax = plt.subplots(5, 1, figsize=(
21*ps.cm, 10*ps.cm), height_ratios=[0.5, 0.5, 0.5, 0.2, 6], sharex=True)
fig, ax = plt.subplots(
5,
1,
figsize=(21 * ps.cm, 10 * ps.cm),
height_ratios=[0.5, 0.5, 0.5, 0.2, 6],
sharex=True,
)
# marker size
s = 80
ax[0].scatter(physical_contact, np.ones(
len(physical_contact)), color=ps.gray, marker='|', s=s)
ax[1].scatter(chasing_onset, np.ones(len(chasing_onset)),
color=ps.gray, marker='|', s=s)
ax[2].scatter(fish1, np.ones(len(fish1))-0.25,
color=fish1_color, marker='|', s=s)
ax[2].scatter(fish2, np.zeros(len(fish2))+0.25,
color=fish2_color, marker='|', s=s)
ax[0].scatter(
physical_contact,
np.ones(len(physical_contact)),
color=ps.gray,
marker="|",
s=s,
)
ax[1].scatter(
chasing_onset,
np.ones(len(chasing_onset)),
color=ps.gray,
marker="|",
s=s,
)
ax[2].scatter(
fish1,
np.ones(len(fish1)) - 0.25,
color=fish1_color,
marker="|",
s=s,
)
ax[2].scatter(
fish2,
np.zeros(len(fish2)) + 0.25,
color=fish2_color,
marker="|",
s=s,
)
freq_temp = bh.freq[bh.ident == fish1_id]
time_temp = bh.time[bh.idx[bh.ident == fish1_id]]
@ -94,35 +123,38 @@ def main(datapath: str):
ax[2].set_xticks([])
ps.hide_ax(ax[2])
ax[4].axvspan(0, 3, 0, 5, facecolor='grey', alpha=0.5)
ax[4].axvspan(0, 3, 0, 5, facecolor="grey", alpha=0.5)
ax[4].set_xticks(np.arange(0, 6.1, 0.5))
ps.hide_ax(ax[3])
labelpad = 30
fsize = 12
ax[0].set_ylabel('Contact', rotation=0,
labelpad=labelpad, fontsize=fsize)
ax[0].set_ylabel(
"Contact", rotation=0, labelpad=labelpad, fontsize=fsize
)
ax[0].yaxis.set_label_coords(-0.062, -0.08)
ax[1].set_ylabel('Chasing', rotation=0,
labelpad=labelpad, fontsize=fsize)
ax[1].set_ylabel(
"Chasing", rotation=0, labelpad=labelpad, fontsize=fsize
)
ax[1].yaxis.set_label_coords(-0.06, -0.08)
ax[2].set_ylabel('Chirps', rotation=0,
labelpad=labelpad, fontsize=fsize)
ax[2].set_ylabel(
"Chirps", rotation=0, labelpad=labelpad, fontsize=fsize
)
ax[2].yaxis.set_label_coords(-0.07, -0.08)
ax[4].set_ylabel('EODf')
ax[4].set_ylabel("EODf")
ax[4].set_xlabel('Time [h]')
ax[4].set_xlabel("Time [h]")
# ax[0].set_title(foldername.split('/')[-2])
# 2020-03-31-9_59
plt.subplots_adjust(left=0.158, right=0.987, top=0.918, bottom=0.136)
plt.savefig('../poster/figs/timeline.svg')
plt.savefig("../poster/figs/timeline.svg")
plt.show()
# plot chirps
if __name__ == '__main__':
if __name__ == "__main__":
# Path to the data
datapath = '../data/mount_data/'
datapath = "../data/mount_data/"
main(datapath)

44
code/plot_introduction_specs.py
View File

@ -11,7 +11,6 @@ ps = PlotStyle()
def main():
# Load data
datapath = "../data/2022-06-02-10_00/"
data = LoadData(datapath)
@ -24,26 +23,31 @@ def main():
timescaler = 1000
raw = data.raw[window_start_index:window_start_index +
window_duration_index, 10]
raw = data.raw[
window_start_index : window_start_index + window_duration_index, 10
]
fig, (ax1, ax2) = plt.subplots(
1, 2, figsize=(21 * ps.cm, 8*ps.cm), sharex=True, sharey=True)
1, 2, figsize=(21 * ps.cm, 8 * ps.cm), sharex=True, sharey=True
)
# plot instantaneous frequency
filtered1 = bandpass_filter(
signal=raw, lowf=750, highf=1200, samplerate=data.raw_rate)
signal=raw, lowf=750, highf=1200, samplerate=data.raw_rate
)
filtered2 = bandpass_filter(
signal=raw, lowf=550, highf=700, samplerate=data.raw_rate)
signal=raw, lowf=550, highf=700, samplerate=data.raw_rate
)
freqtime1, freq1 = instantaneous_frequency(
filtered1, data.raw_rate, smoothing_window=3)
filtered1, data.raw_rate, smoothing_window=3
)
freqtime2, freq2 = instantaneous_frequency(
filtered2, data.raw_rate, smoothing_window=3)
filtered2, data.raw_rate, smoothing_window=3
)
ax1.plot(freqtime1 * timescaler, freq1, color=ps.g, lw=2, label="Fish 1")
ax1.plot(freqtime2*timescaler, freq2, color=ps.gray,
lw=2, label="Fish 2")
ax1.plot(freqtime2 * timescaler, freq2, color=ps.gray, lw=2, label="Fish 2")
# ax.legend(bbox_to_anchor=(1.04, 1), borderaxespad=0)
# # ps.hide_xax(ax1)
@ -99,8 +103,7 @@ def main():
)
# ps.hide_xax(ax3)
ax2.plot(freqtime1 * timescaler, freq1, color=ps.g, lw=2, label="_")
ax2.plot(freqtime2*timescaler, freq2, color=ps.gray,
lw=2, label="_")
ax2.plot(freqtime2 * timescaler, freq2, color=ps.gray, lw=2, label="_")
ax2.set_xlim(75, 200)
ax1.set_ylim(400, 1200)
@ -109,15 +112,22 @@ def main():
fig.supylabel("Frequency [Hz]", fontsize=14)
handles, labels = ax1.get_legend_handles_labels()
ax2.legend(handles, labels, bbox_to_anchor=(1.04, 1), loc="upper left", ncol=1,)
ax2.legend(
handles,
labels,
bbox_to_anchor=(1.04, 1),
loc="upper left",
ncol=1,
)
ps.letter_subplots(xoffset=[-0.27, -0.1], yoffset=1.05)
plt.subplots_adjust(left=0.12, right=0.85, top=0.89,
bottom=0.18, hspace=0.35)
plt.subplots_adjust(
left=0.12, right=0.85, top=0.89, bottom=0.18, hspace=0.35
)
plt.savefig('../poster/figs/introplot.pdf')
plt.savefig("../poster/figs/introplot.pdf")
if __name__ == '__main__':
if __name__ == "__main__":
main()

170
code/plot_kdes.py
View File

@ -1,7 +1,9 @@
from modules.plotstyle import PlotStyle
from modules.behaviour_handling import (
Behavior, correct_chasing_events, center_chirps)
Behavior,
correct_chasing_events,
center_chirps,
)
from modules.datahandling import flatten, causal_kde1d, acausal_kde1d
from modules.logger import makeLogger
from pandas import read_csv
@ -18,8 +20,15 @@ logger = makeLogger(__name__)
ps = PlotStyle()
def bootstrap(data, nresamples, kde_time, kernel_width, event_times, time_before, time_after):
def bootstrap(
data,
nresamples,
kde_time,
kernel_width,
event_times,
time_before,
time_after,
):
bootstrapped_kdes = []
data = data[data <= 3 * 60 * 60] # only night time
@ -28,28 +37,36 @@ def bootstrap(data, nresamples, kde_time, kernel_width, event_times, time_before
# mean_chirprate = (len(data) - 1) / (data[-1] - data[0])
for i in tqdm(range(nresamples)):
np.random.shuffle(diff_data)
bootstrapped_data = np.cumsum(diff_data)
# bootstrapped_data = data + np.random.randn(len(data)) * 10
bootstrap_data_centered = center_chirps(
bootstrapped_data, event_times, time_before, time_after)
bootstrapped_data, event_times, time_before, time_after
)
bootstrapped_kde = acausal_kde1d(
bootstrap_data_centered, time=kde_time, width=kernel_width)
bootstrap_data_centered, time=kde_time, width=kernel_width
)
bootstrapped_kde = list(np.asarray(
bootstrapped_kde) / len(event_times))
bootstrapped_kde = list(np.asarray(bootstrapped_kde) / len(event_times))
bootstrapped_kdes.append(bootstrapped_kde)
return bootstrapped_kdes
def jackknife(data, nresamples, subsetsize, kde_time, kernel_width, event_times, time_before, time_after):
def jackknife(
data,
nresamples,
subsetsize,
kde_time,
kernel_width,
event_times,
time_before,
time_after,
):
jackknife_kdes = []
data = data[data <= 3 * 60 * 60] # only night time
subsetsize = int(len(data) * subsetsize)
@ -57,41 +74,39 @@ def jackknife(data, nresamples, subsetsize, kde_time, kernel_width, event_times,
diff_data = np.diff(np.sort(data), prepend=0)
for i in tqdm(range(nresamples)):
jackknifed_data = np.random.choice(
diff_data, subsetsize, replace=False)
jackknifed_data = np.random.choice(diff_data, subsetsize, replace=False)
jackknifed_data = np.cumsum(jackknifed_data)
jackknifed_data_centered = center_chirps(
jackknifed_data, event_times, time_before, time_after)
jackknifed_data, event_times, time_before, time_after
)
jackknifed_kde = acausal_kde1d(
jackknifed_data_centered, time=kde_time, width=kernel_width)
jackknifed_data_centered, time=kde_time, width=kernel_width
)
jackknifed_kde = list(np.asarray(
jackknifed_kde) / len(event_times))
jackknifed_kde = list(np.asarray(jackknifed_kde) / len(event_times))
jackknife_kdes.append(jackknifed_kde)
return jackknife_kdes
def get_chirp_winner_loser(folder_name, Behavior, order_meta_df):
foldername = folder_name.split('/')[-2]
winner_row = order_meta_df[order_meta_df['recording'] == foldername]
winner = winner_row['winner'].values[0].astype(int)
winner_fish1 = winner_row['fish1'].values[0].astype(int)
winner_fish2 = winner_row['fish2'].values[0].astype(int)
foldername = folder_name.split("/")[-2]
winner_row = order_meta_df[order_meta_df["recording"] == foldername]
winner = winner_row["winner"].values[0].astype(int)
winner_fish1 = winner_row["fish1"].values[0].astype(int)
winner_fish2 = winner_row["fish2"].values[0].astype(int)
if winner > 0:
if winner == winner_fish1:
winner_fish_id = winner_row['rec_id1'].values[0]
loser_fish_id = winner_row['rec_id2'].values[0]
winner_fish_id = winner_row["rec_id1"].values[0]
loser_fish_id = winner_row["rec_id2"].values[0]
elif winner == winner_fish2:
winner_fish_id = winner_row['rec_id2'].values[0]
loser_fish_id = winner_row['rec_id1'].values[0]
winner_fish_id = winner_row["rec_id2"].values[0]
loser_fish_id = winner_row["rec_id1"].values[0]
chirp_winner = Behavior.chirps[Behavior.chirps_ids == winner_fish_id]
chirp_loser = Behavior.chirps[Behavior.chirps_ids == loser_fish_id]
@ -101,7 +116,6 @@ def get_chirp_winner_loser(folder_name, Behavior, order_meta_df):
def main(dataroot):
foldernames, _ = np.asarray(get_valid_datasets(dataroot))
plot_all = True
time_before = 90
@ -111,10 +125,9 @@ def main(dataroot):
kde_time = np.arange(-time_before, time_after, dt)
nbootstraps = 50
meta_path = (
'/').join(foldernames[0].split('/')[:-2]) + '/order_meta.csv'
meta_path = ("/").join(foldernames[0].split("/")[:-2]) + "/order_meta.csv"
meta = pd.read_csv(meta_path)
meta['recording'] = meta['recording'].str[1:-1]
meta["recording"] = meta["recording"].str[1:-1]
winner_onsets = []
winner_offsets = []
@ -143,16 +156,16 @@ def main(dataroot):
# loser_onset_chirpcount = 0
# loser_offset_chirpcount = 0
# loser_physical_chirpcount = 0
fig, ax = plt.subplots(1, 2, figsize=(
14 * ps.cm, 7*ps.cm), sharey=True, sharex=True)
fig, ax = plt.subplots(
1, 2, figsize=(14 * ps.cm, 7 * ps.cm), sharey=True, sharex=True
)
# Iterate over all recordings and save chirp- and event-timestamps
good_recs = np.asarray([0, 15])
for i, folder in tqdm(enumerate(foldernames[good_recs])):
foldername = folder.split('/')[-2]
foldername = folder.split("/")[-2]
# logger.info('Loading data from folder: {}'.format(foldername))
broken_folders = ['../data/mount_data/2020-05-12-10_00/']
broken_folders = ["../data/mount_data/2020-05-12-10_00/"]
if folder in broken_folders:
continue
@ -168,27 +181,33 @@ def main(dataroot):
# winner_count += len(winner)
# loser_count += len(loser)
onsets = (timestamps[category == 0])
offsets = (timestamps[category == 1])
physicals = (timestamps[category == 2])
onsets = timestamps[category == 0]
offsets = timestamps[category == 1]
physicals = timestamps[category == 2]
onset_count += len(onsets)
offset_count += len(offsets)
physical_count += len(physicals)
winner_onsets.append(center_chirps(
winner, onsets, time_before, time_after))
winner_offsets.append(center_chirps(
winner, offsets, time_before, time_after))
winner_physicals.append(center_chirps(
winner, physicals, time_before, time_after))
loser_onsets.append(center_chirps(
loser, onsets, time_before, time_after))
loser_offsets.append(center_chirps(
loser, offsets, time_before, time_after))
loser_physicals.append(center_chirps(
loser, physicals, time_before, time_after))
winner_onsets.append(
center_chirps(winner, onsets, time_before, time_after)
)
winner_offsets.append(
center_chirps(winner, offsets, time_before, time_after)
)
winner_physicals.append(
center_chirps(winner, physicals, time_before, time_after)
)
loser_onsets.append(
center_chirps(loser, onsets, time_before, time_after)
)
loser_offsets.append(
center_chirps(loser, offsets, time_before, time_after)
)
loser_physicals.append(
center_chirps(loser, physicals, time_before, time_after)
)
# winner_onset_chirpcount += len(winner_onsets[-1])
# winner_offset_chirpcount += len(winner_offsets[-1])
@ -232,14 +251,17 @@ def main(dataroot):
# event_times=onsets,
# time_before=time_before,
# time_after=time_after))
loser_offsets_boot.append(bootstrap(
loser_offsets_boot.append(
bootstrap(
loser,
nresamples=nbootstraps,
kde_time=kde_time,
kernel_width=kernel_width,
event_times=offsets,
time_before=time_before,
time_after=time_after))
time_after=time_after,
)
)
# loser_physicals_boot.append(bootstrap(
# loser,
# nresamples=nbootstraps,
@ -260,7 +282,6 @@ def main(dataroot):
# time_after=time_after)
if plot_all:
# winner_onsets_conv = acausal_kde1d(
# winner_onsets[-1], kde_time, kernel_width)
# winner_offsets_conv = acausal_kde1d(
@ -271,24 +292,35 @@ def main(dataroot):
# loser_onsets_conv = acausal_kde1d(
# loser_onsets[-1], kde_time, kernel_width)
loser_offsets_conv = acausal_kde1d(
loser_offsets[-1], kde_time, kernel_width)
loser_offsets[-1], kde_time, kernel_width
)
# loser_physicals_conv = acausal_kde1d(
# loser_physicals[-1], kde_time, kernel_width)
ax[i].plot(kde_time, loser_offsets_conv /
len(offsets), lw=2, zorder=100, c=ps.gblue1)
ax[i].plot(
kde_time,
loser_offsets_conv / len(offsets),
lw=2,
zorder=100,
c=ps.gblue1,
)
ax[i].fill_between(
kde_time,
np.percentile(loser_offsets_boot[-1], 1, axis=0),
np.percentile(loser_offsets_boot[-1], 99, axis=0),
color='gray',
alpha=0.8)
color="gray",
alpha=0.8,
)
ax[i].plot(kde_time, np.median(loser_offsets_boot[-1], axis=0),
color=ps.black, linewidth=2)
ax[i].plot(
kde_time,
np.median(loser_offsets_boot[-1], axis=0),
color=ps.black,
linewidth=2,
)
ax[i].axvline(0, color=ps.gray, linestyle='--')
ax[i].axvline(0, color=ps.gray, linestyle="--")
# ax[i].fill_between(
# kde_time,
@ -300,8 +332,8 @@ def main(dataroot):
# color=ps.white, linewidth=2)
ax[i].set_xlim(-60, 60)
fig.supylabel('Chirp rate (a.u.)', fontsize=14)
fig.supxlabel('Time (s)', fontsize=14)
fig.supylabel("Chirp rate (a.u.)", fontsize=14)
fig.supxlabel("Time (s)", fontsize=14)
# fig, ax = plt.subplots(2, 3, figsize=(
# 21*ps.cm, 10*ps.cm), sharey=True, sharex=True)
@ -521,9 +553,9 @@ def main(dataroot):
# color=ps.gray,
# alpha=0.5)
plt.subplots_adjust(bottom=0.21, top=0.93)
plt.savefig('../poster/figs/kde.pdf')
plt.savefig("../poster/figs/kde.pdf")
plt.show()
if __name__ == '__main__':
main('../data/mount_data/')
if __name__ == "__main__":
main("../data/mount_data/")