316 lines
13 KiB
Python
316 lines
13 KiB
Python
import os
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import sys
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import argparse
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import time
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import numpy as np
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try:
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import cupy as cp
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except ImportError:
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import numpy as cp
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import matplotlib.pyplot as plt
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import matplotlib.gridspec as gridspec
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import pandas as pd
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from IPython import embed
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from tqdm import tqdm
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def load_and_converete_boris_events(trial_path, recording, sr):
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def converte_video_frames_to_grid_idx(event_frames, led_frames, led_idx):
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event_idx_grid = (event_frames - led_frames[0]) / (led_frames[-1] - led_frames[0]) * (led_idx[-1] - led_idx[0]) + led_idx[0]
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return event_idx_grid
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# idx in grid-recording
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led_idx = pd.read_csv(os.path.join(trial_path, 'led_idxs.csv'), header=None).iloc[:, 0].to_numpy()
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# frames where LED gets switched on
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led_frames = np.load(os.path.join(trial_path, 'LED_frames.npy'))
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times, behavior, t_ag_on_off, t_contact, video_FPS = load_boris(trial_path, recording)
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contact_frame = np.array(np.round(t_contact * video_FPS), dtype=int)
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ag_on_off_frame = np.array(np.round(t_ag_on_off * video_FPS), dtype=int)
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# led_t_GRID = led_idx / sr
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contact_t_GRID = converte_video_frames_to_grid_idx(contact_frame, led_frames, led_idx) / sr
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ag_on_off_t_GRID = converte_video_frames_to_grid_idx(ag_on_off_frame, led_frames, led_idx) / sr
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return contact_t_GRID, ag_on_off_t_GRID, led_idx, led_frames
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def load_boris(trial_path, recording):
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boris_file = '-'.join(recording.split('-')[:3]) + '.csv'
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data = pd.read_csv(os.path.join(trial_path, boris_file))
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times = data['Start (s)']
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behavior = data['Behavior']
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t_ag_on = times[behavior == 0]
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t_ag_off = times[behavior == 1]
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t_ag_on_off = []
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for t in t_ag_on:
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t1 = np.array(t_ag_off)[t_ag_off > t]
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if len(t1) >= 1:
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t_ag_on_off.append(np.array([t, t1[0]]))
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t_contact = times[behavior == 2]
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return times, behavior, np.array(t_ag_on_off), t_contact.to_numpy(), data['FPS'][0]
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def gauss(t, shift, sigma, size, norm = False):
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if not hasattr(shift, '__len__'):
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g = np.exp(-((t - shift) / sigma) ** 2 / 2) * size
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if norm:
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g /= np.sum(g)
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return g
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else:
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t = np.array([t, ] * len(shift))
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res = np.exp(-((t.transpose() - shift).transpose() / sigma) ** 2 / 2) * size
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return res
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def event_centered_times(centered_event_times, surrounding_event_times, max_dt = np.inf):
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event_dt = []
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for Cevent_t in centered_event_times:
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Cdt = np.array(surrounding_event_times - Cevent_t)
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event_dt.extend(Cdt[np.abs(Cdt) <= max_dt])
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return np.array(event_dt)
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def kde(event_dt, conv_t, kernal_w = 1, kernal_h = 0.2):
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conv_array = np.zeros(len(conv_t))
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for e in event_dt:
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conv_array += gauss(conv_t, e, kernal_w, kernal_h)
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return conv_array
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def permulation_kde(event_dt, repetitions = 2000, max_dt = 60, max_mem_use_GB = 4, kernal_w = 1, kernal_h = 0.2):
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def chunk_permutation(select_event_dt, conv_tt, n_chuck, max_jitter, kernal_w, kernal_h):
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# array.shape = (120, 100, 15486) = (len(conv_t), repetitions, len(event_dt))
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# event_dt_perm = cp.tile(event_dt, (len(conv_t), repetitions, 1))
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event_dt_perm = cp.tile(select_event_dt, (len(conv_tt), n_chuck, 1))
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jitter = cp.random.uniform(-max_jitter, max_jitter, size=(event_dt_perm.shape[1], event_dt_perm.shape[2]))
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jitter = cp.expand_dims(jitter, axis=0)
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event_dt_perm += jitter
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# conv_t_perm = cp.tile(conv_tt, (1, repetitions, len(event_dt)))
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gauss_3d = cp.exp(-((conv_tt - event_dt_perm) / kernal_w) ** 2 / 2) * kernal_h
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kde_3d = cp.sum(gauss_3d, axis = 2).transpose()
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try:
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kde_3d_numpy = cp.asnumpy(kde_3d)
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del event_dt_perm, gauss_3d, kde_3d
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return kde_3d_numpy
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except AttributeError:
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del event_dt_perm, gauss_3d
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return kde_3d
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t0 = time.time()
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max_jitter = 2*max_dt
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select_event_dt = event_dt[np.abs(event_dt) <= max_dt + max_jitter*2]
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conv_t = cp.arange(-max_dt, max_dt, 1)
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conv_tt = cp.reshape(conv_t, (len(conv_t), 1, 1))
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chunk_size = int(np.floor(max_mem_use_GB / (select_event_dt.nbytes * conv_t.size / 1e9)))
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chunk_collector =[]
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for _ in range(repetitions // chunk_size):
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chunk_boot_KDE = chunk_permutation(select_event_dt, conv_tt, chunk_size, max_jitter, kernal_w, kernal_h)
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chunk_collector.extend(chunk_boot_KDE)
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# # array.shape = (120, 100, 15486) = (len(conv_t), repetitions, len(event_dt))
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# # event_dt_perm = cp.tile(event_dt, (len(conv_t), repetitions, 1))
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# event_dt_perm = cp.tile(event_dt, (len(conv_t), chunk_size, 1))
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# jitter = np.random.uniform(-max_jitter, max_jitter, size=(event_dt_perm.shape[1], event_dt_perm.shape[2]))
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# jitter = np.expand_dims(jitter, axis=0)
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#
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# event_dt_perm += jitter
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# # conv_t_perm = cp.tile(conv_tt, (1, repetitions, len(event_dt)))
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#
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# gauss_3d = cp.exp(-((conv_tt - event_dt_perm) / kernal_w) ** 2 / 2) * kernal_h
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# kde_3d = cp.sum(gauss_3d, axis = 2).transpose()
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# try:
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# kde_3d_numpy = cp.asnumpy(kde_3d)
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# chunk_collector.extend(kde_3d_numpy)
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# except AttributeError:
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# chunk_collector.extend(kde_3d)
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# del event_dt_perm, gauss_3d, kde_3d
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chunk_boot_KDE = chunk_permutation(select_event_dt, conv_tt, repetitions % chunk_size, max_jitter, kernal_w, kernal_h)
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chunk_collector.extend(chunk_boot_KDE)
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chunk_collector = np.array(chunk_collector)
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# ToDo: this works but is incorrect i think
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# chunk_collector /= np.sum(chunk_collector, axis=1).reshape(chunk_collector.shape[0], 1)
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print(f'bootstrap with {repetitions:.0f} repetitions took {time.time() - t0:.2f}s.')
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# fig, ax = plt.subplots()
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# for i in range(len(chunk_collector)):
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# ax.plot(cp.asnumpy(conv_t), chunk_collector[i])
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return chunk_collector
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def jackknife_kde(event_dt, repetitions = 2000, max_dt = 60, max_mem_use_GB = 2, jack_pct = 0.9, kernal_w = 1, kernal_h = 0.2):
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def chunk_jackknife(select_event_dt, conv_tt, n_chuck, jack_pct, kernal_w, kernal_h):
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event_dt_rep = cp.tile(select_event_dt, (n_chuck, 1))
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idx = cp.random.rand(*event_dt_rep.shape).argsort(1)[:, :int(event_dt_rep.shape[-1]*jack_pct)]
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event_dt_jk = event_dt_rep[cp.arange(event_dt_rep.shape[0])[:, None], idx]
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event_dt_jk_full = cp.tile(event_dt_jk, (len(conv_tt), 1, 1))
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# event_dt_perm = cp.tile(select_event_dt, (len(conv_tt), n_chuck, 1))
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# jitter = cp.random.uniform(-max_jitter, max_jitter, size=(event_dt_perm.shape[1], event_dt_perm.shape[2]))
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# jitter = cp.expand_dims(jitter, axis=0)
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# event_dt_perm += jitter
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# conv_t_perm = cp.tile(conv_tt, (1, repetitions, len(event_dt)))
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gauss_3d = cp.exp(-((conv_tt - event_dt_jk_full) / kernal_w) ** 2 / 2) * kernal_h
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kde_3d = cp.sum(gauss_3d, axis = 2).transpose()
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try:
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kde_3d_numpy = cp.asnumpy(kde_3d)
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del event_dt_rep, idx, event_dt_jk, event_dt_jk_full, gauss_3d, kde_3d
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return kde_3d_numpy
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except AttributeError:
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del event_dt_rep, idx, event_dt_jk, event_dt_jk_full, gauss_3d
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return kde_3d
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t0 = time.time()
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# max_jitter = 2*max_dt
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select_event_dt = event_dt[np.abs(event_dt) <= max_dt * 2]
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conv_t = cp.arange(-max_dt, max_dt, 1)
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conv_tt = cp.reshape(conv_t, (len(conv_t), 1, 1))
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chunk_size = int(np.floor(max_mem_use_GB / (select_event_dt.nbytes * jack_pct * conv_t.size / 1e9)))
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chunk_collector =[]
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for _ in range(repetitions // chunk_size):
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chunk_jackknife_KDE = chunk_jackknife(select_event_dt, conv_tt, chunk_size, jack_pct, kernal_w, kernal_h)
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chunk_collector.extend(chunk_jackknife_KDE)
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del chunk_jackknife_KDE
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# # array.shape = (120, 100, 15486) = (len(conv_t), repetitions, len(event_dt))
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# # event_dt_perm = cp.tile(event_dt, (len(conv_t), repetitions, 1))
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# event_dt_perm = cp.tile(event_dt, (len(conv_t), chunk_size, 1))
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# jitter = np.random.uniform(-max_jitter, max_jitter, size=(event_dt_perm.shape[1], event_dt_perm.shape[2]))
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# jitter = np.expand_dims(jitter, axis=0)
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#
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# event_dt_perm += jitter
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# # conv_t_perm = cp.tile(conv_tt, (1, repetitions, len(event_dt)))
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#
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# gauss_3d = cp.exp(-((conv_tt - event_dt_perm) / kernal_w) ** 2 / 2) * kernal_h
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# kde_3d = cp.sum(gauss_3d, axis = 2).transpose()
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# try:
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# kde_3d_numpy = cp.asnumpy(kde_3d)
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# chunk_collector.extend(kde_3d_numpy)
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# except AttributeError:
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# chunk_collector.extend(kde_3d)
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# del event_dt_perm, gauss_3d, kde_3d
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chunk_jackknife_KDE = chunk_jackknife(select_event_dt, conv_tt, repetitions % chunk_size, jack_pct, kernal_w, kernal_h)
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chunk_collector.extend(chunk_jackknife_KDE)
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del chunk_jackknife_KDE
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chunk_collector = np.array(chunk_collector)
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print(f'jackknife with {repetitions:.0f} repetitions took {time.time() - t0:.2f}s.')
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return chunk_collector
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def main(base_path):
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trial_summary = pd.read_csv('trial_summary.csv', index_col=0)
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lose_chrips_centered_on_ag_off_t = []
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lose_chirp_count = []
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for index, trial in tqdm(trial_summary.iterrows()):
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trial_path = os.path.join(base_path, trial['recording'])
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if trial['group'] < 5:
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continue
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if not os.path.exists(os.path.join(trial_path, 'led_idxs.csv')):
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continue
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if not os.path.exists(os.path.join(trial_path, 'LED_frames.npy')):
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continue
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ids = np.load(os.path.join(trial_path, 'analysis', 'ids.npy'))
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times = np.load(os.path.join(trial_path, 'times.npy'))
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sorter = -1 if trial['win_ID'] != ids[0] else 1
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### event times --> BORIS behavior
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contact_t_GRID, ag_on_off_t_GRID, led_idx, led_frames = \
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load_and_converete_boris_events(trial_path, trial['recording'], sr=20_000)
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### communication
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if not os.path.exists(os.path.join(trial_path, 'chirp_times_cnn.npy')):
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continue
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chirp_t = np.load(os.path.join(trial_path, 'chirp_times_cnn.npy'))
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chirp_ids = np.load(os.path.join(trial_path, 'chirp_ids_cnn.npy'))
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chirp_times = [chirp_t[chirp_ids == trial['win_ID']], chirp_t[chirp_ids == trial['lose_ID']]]
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rise_idx = np.load(os.path.join(trial_path, 'analysis', 'rise_idx.npy'))[::sorter]
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rise_idx_int = [np.array(rise_idx[i][~np.isnan(rise_idx[i])], dtype=int) for i in range(len(rise_idx))]
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rise_times = [times[rise_idx_int[0]], times[rise_idx_int[1]]]
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lose_chrips_centered_on_ag_off_t.append(event_centered_times(ag_on_off_t_GRID[:, 1], chirp_times[1]))
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lose_chirp_count.append(len(chirp_times[1]))
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max_dt = 30
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conv_t = np.arange(-max_dt, max_dt, 1)
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kde_array = kde(np.hstack(lose_chrips_centered_on_ag_off_t), conv_t, kernal_w = 1, kernal_h = 1)
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boot_kde = permulation_kde(np.hstack(lose_chrips_centered_on_ag_off_t), max_dt=max_dt, kernal_w=1, kernal_h=1)
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jack_pct = 0.9
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jk_kde = jackknife_kde(np.hstack(lose_chrips_centered_on_ag_off_t), max_dt=max_dt, jack_pct = jack_pct, kernal_w=1, kernal_h=1)
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perm_p1, perm_p50, perm_p99 = np.percentile(boot_kde, (1, 50, 99), axis=0)
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jk_p1, jk_p50, jk_p99 = np.percentile(jk_kde, (1, 50, 99), axis=0)
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embed()
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quit()
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fig = plt.figure(figsize=(20/2.54, 12/2.54))
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gs = gridspec.GridSpec(1, 1, left=0.1, bottom=0.1, right=0.95, top=0.95)
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ax = fig.add_subplot(gs[0, 0])
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ax.fill_between(conv_t, perm_p1/np.sum(lose_chirp_count), perm_p99/np.sum(lose_chirp_count), color='cornflowerblue', alpha=.8)
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ax.plot(conv_t, perm_p50/np.sum(lose_chirp_count), color='dodgerblue', alpha=1, lw=3)
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ax.fill_between(conv_t, jk_p1/np.sum(lose_chirp_count)/jack_pct, jk_p99/np.sum(lose_chirp_count)/jack_pct, color='tab:red', alpha=.8)
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ax.plot(conv_t, jk_p50/np.sum(lose_chirp_count)/jack_pct, color='firebrick', alpha=1, lw=3)
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ax_m = ax.twinx()
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for enu, centered_events in enumerate(lose_chrips_centered_on_ag_off_t):
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Cevents = centered_events[np.abs(centered_events) <= max_dt]
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ax_m.plot(Cevents, np.ones(len(Cevents)) * enu, '|', markersize=8, color='k', alpha=.1)
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ax_m.set_yticks([])
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ax.set_xlabel('time [s]', fontsize=12)
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ax.set_ylabel('event rate [Hz]', fontsize=12)
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ax.set_xlim(-max_dt, max_dt)
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ax.tick_params(labelsize=10)
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# for i in range(len(boot_kde)):
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# ax.plot(conv_t, boot_kde[i] / np.sum(lose_chirp_count), color='tab:blue')
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#
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# for i in range(len(boot_kde)):
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# ax.plot(conv_t, jk_kde[i] / np.sum(lose_chirp_count) / jack_pct, color='tab:red')
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# ax.plot(conv_t, kde_array/np.sum(lose_chirp_count), color='k', lw=3)
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plt.show()
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pass
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if __name__ == '__main__':
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main(sys.argv[1])
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