KIAPBCI/kiap_bci/analytics/lfp_analysis_exploration.py

'''
description: offline analysis of kiap data
author: Ioannis Vlachos
date:   02.04.2019

Copyright (c) 2019 Ioannis Vlachos.
All rights reserved.'''

import re
import os
import glob
import importlib
import urllib
import time

import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
from scipy import signal
from scipy import stats
from cachetools import cached, LRUCache, TTLCache
from neo.io.blackrockio import BlackrockIO

import aux
from aux import log
from analytics import analytics1
importlib.reload(analytics1)



# @cached(cache={})
def read_data():
    '''returns first array1 and then array2 channels'''

    data = reader.get_analogsignal_chunk(i_stop=eval(str(params.lfp.i_stop)),
                                channel_indexes=list(set(params.lfp.array1) | set(params.lfp.array2)))

    return data


def get_triggers(n_triggers=10, verbose=True):
    '''get triggers from corresponding nev files'''

    try:
        triggers_ts = [tt[0] for tt in reader.nev_data['Comments'][0]]
        triggers_txt = [tt[5].decode('utf-8') for tt in reader.nev_data['Comments'][0]]
    except:
        log.error('Triggers could not be loaded. Does Nev file exist?')
        return None, None

    if verbose:
        print(reader.nev_data['Comments'])

    triggers= [list() for ii in range(8)]

    for ii in range(len(triggers_txt)):
        if 'SchliesseHand, response, start' in triggers_txt[ii]:
            triggers[0].append(triggers_ts[ii]// params.lfp.sampling_ratio)
        elif 'BeugeRechtenMittelfinger, response, start' in triggers_txt[ii]:
            triggers[1].append(triggers_ts[ii]// params.lfp.sampling_ratio)
        elif 'BeugeRechtenZeigefinger, response, start' in triggers_txt[ii]:
            triggers[2].append(triggers_ts[ii]// params.lfp.sampling_ratio)
        elif 'BeugeRechtenDaumen, response, start' in triggers_txt[ii]:
            triggers[3].append(triggers_ts[ii]// params.lfp.sampling_ratio)
        elif 'OeffneHand, response, start' in triggers_txt[ii]:
            triggers[4].append(triggers_ts[ii]// params.lfp.sampling_ratio)
        elif 'StreckeRechtenMittelfinger, response, start' in triggers_txt[ii]:
            triggers[5].append(triggers_ts[ii]// params.lfp.sampling_ratio)
        elif 'StreckeRechtenZeigefinger, response, start' in triggers_txt[ii]:
            triggers[6].append(triggers_ts[ii]// params.lfp.sampling_ratio)
        elif 'StreckeRechtenDaumen, response, start' in triggers_txt[ii]:
            triggers[7].append(triggers_ts[ii]// params.lfp.sampling_ratio)        

    for ii in range(8):
        triggers[ii] = np.array(triggers[ii])
    # triggers = np.array(triggers_yes)
    # triggers_no = np.array(triggers_no)

    # get timestamps for ns2
    # triggers = triggers_yes // params.lfp.sampling_ratio
    # triggers_no_ns2 = triggers_no // params.lfp.sampling_ratio

    return triggers


def get_valid_trials(triggers_no_ns2, triggers_yes_ns2):
    trials_msk = np.ones((10, 2), dtype=bool)
    for ii, tt in enumerate(triggers_no_ns2):
        tmp = data1[tt + psth_win[0]:tt + psth_win[1], :]
        if (np.any(tmp > params.lfp.artifact_thr) or np.any(tmp < -params.lfp.artifact_thr)):
            trials_msk[ii, 0] = False

    for ii, tt in enumerate(triggers_yes_ns2):
        tmp = data1[tt + psth_win[0]:tt + psth_win[1], :]
        if (np.any(tmp > params.lfp.artifact_thr) or np.any(tmp < -params.lfp.artifact_thr)):
            trials_msk[ii, 1] = False
            print(ii)

    print('\nTrials excluded', np.where(trials_msk[:, 0] == False)[0], np.where(trials_msk[:, 1] == False)[0])
    return trials_msk


def calc_cc():
    '''calculate time resolved correlation coefficients betweech channels of each array'''
    
    cc_step = 5000
    rng = range(0, data1.shape[0], cc_step)
    cc1 = np.zeros((len(rng), 3))
    cc2 = np.zeros((len(rng), 3))
    hist1 = np.zeros((len(rng), 100))
    hist2 = np.zeros((len(rng), 100))
    for ii, idx in enumerate(rng):
        # cc1[ii, 0] = np.min(np.abs(np.triu(np.corrcoef(data01[idx:idx + cc_step, :].T), k=1)))
        # cc1[ii, 1] = np.max(np.abs(np.triu(np.corrcoef(data01[idx:idx + cc_step, :].T), k=1)))
        # cc1[ii, 2] = np.mean(np.abs(np.triu(np.corrcoef(data01[idx:idx + cc_step, :].T), k=1)))
        cc1[ii, 0] = np.min(np.triu(np.corrcoef(data01[idx:idx + cc_step, :].T), k=1))
        cc1[ii, 1] = np.max(np.triu(np.corrcoef(data01[idx:idx + cc_step, :].T), k=1))
        cc1[ii, 2] = np.mean(np.triu(np.corrcoef(data01[idx:idx + cc_step, :].T), k=1))
        # hist1[ii, :] = np.histogram(np.triu(np.corrcoef(data0[idx:idx + cc_step, array1].T)).flatten(), 100)[1][:-1]

        # cc2[ii, 0] = np.min(np.abs(np.triu(np.corrcoef(data02[idx:idx + cc_step, :].T), k=1)))
        # cc2[ii, 1] = np.max(np.abs(np.triu(np.corrcoef(data02[idx:idx + cc_step, :].T), k=1)))
        # cc2[ii, 2] = np.mean(np.abs(np.triu(np.corrcoef(data02[idx:idx + cc_step, :].T), k=1)))
        cc2[ii, 0] = np.min(np.triu(np.corrcoef(data02[idx:idx + cc_step, :].T), k=1))
        cc2[ii, 1] = np.max(np.triu(np.corrcoef(data02[idx:idx + cc_step, :].T), k=1))
        cc2[ii, 2] = np.mean(np.triu(np.corrcoef(data02[idx:idx + cc_step, :].T), k=1))
        # hist2[ii, :] = np.histogram(np.triu(np.corrcoef(data0[idx:idx + cc_step, array2].T)), 100)[1][:-1]

        # print(ii)

    if params.lfp.plot.general:
        plt.figure()
        plt.plot(cc1)
        plt.gca().set_prop_cycle(None)
        plt.plot(c2, '-.')
        plt.show()
    return None


def compute_psth(triggers, arr_nr=1, sub_band=-1):
    '''compute the psth for no and yes questions'''

    psth_len = np.diff(psth_win)[0]

    if arr_nr == 1:
        ch_nr = ch_nr1
        if sub_band == -1:
            data_tmp = data01                   # raw data
        else:
            data_tmp = data1[:, :, sub_band]    # sub_band

    elif arr_nr == 2:
        ch_nr = ch_nr2
        if sub_band == -1:
            data_tmp = data02                  # raw data
        else:
            data_tmp = data2[:, :, sub_band]   # sub_band

    psth = [list() for ii in range(8)]
    for ii in range(8):
        psth[ii] = np.zeros((len(triggers[ii]), psth_len, ch_nr))

    for jj in range(8):
        for ii in range(len(triggers[jj])):
            if (triggers[jj][ii] + psth_win[0] > 0) & (triggers[jj][ii] + psth_win[1] < len(data2)):
                tmp = data_tmp[(triggers[jj][ii] + psth_win[0]):(triggers[jj][ii] + psth_win[1]), :]
                psth[jj][ii, :, :] = tmp

    # psth_yes, psth_no = remove_trials(psth_yes, psth_no)

    return psth


def remove_channels(data01, data02):
    '''remove channels for which variance lies outside 25-75 percentiles'''

    var1 = np.var(data01, axis=0)
    var2 = np.var(data02, axis=0)

    L1 = np.percentile(var1, 25, axis=0, keepdims=True)
    L2 = np.percentile(var2, 25, axis=0, keepdims=True)
    U1 = np.percentile(var1, 75, axis=0, keepdims=True)
    U2 = np.percentile(var2, 75, axis=0, keepdims=True)

    w = 1  # manual parameter that affects the valid range
    valid1 = [L1 - w * (U1 - L1), U1 + w * (U1 - L1)]
    valid2 = [L2 - w * (U2 - L2), U2 + w * (U2 - L2)]

    # plt.plot(var1, 'C0')
    # plt.plot(var2, 'C1')

    # array1_msk = (np.where(var1 < valid1[0]) and np.where(var1 > valid1[1]))[0]
    # array1_msk = (np.where(var1 < valid1[0]) and np.where(var1 > valid1[1]))[0]
    array1_msk = np.unique(((var1 < valid1[0]) | (var1 > valid1[1])).nonzero()[0])
    array2_msk = np.unique(((var2 < valid2[0]) | (var2 > valid2[1])).nonzero()[0])

    array1_msk = np.hstack((array1_msk, params.lfp.array1_exclude)).astype(int)
    array2_msk = np.hstack((array2_msk, params.lfp.array2_exclude)).astype(int)
    array1_msk.sort()
    array2_msk.sort()

    print(f'excluded channels, array1: {array1_msk}')
    print(f'excluded channels, array2: {array2_msk}')

    plot_channels(data01, [], arr_id=1, fs=params.lfp.fs, array_msk=array1_msk, i_stop=1000, step=1, color='C0')
    plot_channels(data02, [], arr_id=2, fs=params.lfp.fs, array_msk=array2_msk, i_stop=1000, step=1, color='C1')

    data01 = np.delete(data01, array1_msk, axis=1)
    data02 = np.delete(data02, array2_msk, axis=1)

    return data01, data02, array1_msk, array2_msk


def remove_trials(psth_yes, psth_no):
    '''remove trials for which variance lies outside 25-75 percentiles'''

    var1 = np.var(psth_yes, axis=1)
    var2 = np.var(psth_no, axis=1)

    L1 = np.percentile(var1, 25, axis=0, keepdims=True)
    L2 = np.percentile(var2, 25, axis=0, keepdims=True)
    U1 = np.percentile(var1, 75, axis=0, keepdims=True)
    U2 = np.percentile(var2, 75, axis=0, keepdims=True)

    w = 10
    valid1 = [L1 - w * (U1 - L1), U1 + w * (U1 - L1)]
    valid2 = [L2 - w * (U2 - L2), U2 + w * (U2 - L2)]

    # array1_msk = np.unique((np.where(var1 < valid1[0])[0] or np.where(var1 > valid1[1])[0]))
    # array2_msk = np.unique((np.where(var2 < valid2[0])[0] or np.where(var2 > valid2[1])[0]))
    array1_msk = ((var1 < valid1[0]) | (var1 > valid1[1])).nonzero()[0]
    array2_msk = ((var2 < valid2[0]) | (var2 > valid2[1])).nonzero()[0]

    print(f'excluded yes-trials: {array1_msk}')
    print(f'excluded no-trials: {array2_msk}')


    psth_yes = np.delete(psth_yes, array1_msk, axis=0)
    psth_no = np.delete(psth_no, array2_msk, axis=0)

    return psth_yes, psth_no


def plot_channels(data, ch_ids, fs, array_msk=[], arr_id=1, i_start=0, i_stop=10000, step=5, color='C0'):
    '''plot all data from array1 or array2 in the time domain'''


    if not params.lfp.zscore:           # z-score only for visualization
        data = stats.zscore(data)

    if ch_ids == []:
        ch_ids = range(data.shape[1])
    if i_stop == -1:
        i_stop = data.shape[0]

    offset = np.cumsum(4 * np.var(data[:, ch_ids], axis=0)[:, np.newaxis]).T

    plt.figure()
    plt.plot(np.arange(i_start, i_stop) / fs, data[i_start:i_stop, ch_ids] + offset, color=color, lw=1)
    if array_msk.size > 0:  # highlight excluded channels
        plt.plot(np.arange(i_start, i_stop) / fs, data[i_start:i_stop, array_msk] + offset[array_msk], color='C3', lw=1)

    plt.xlabel('Time (sec)')
    plt.yticks(offset[::step], range(0, len(ch_ids), step))
    plt.ylim(0, offset[-1] + 4)
    plt.title(f'raw data from array {arr_id}')
    plt.tight_layout()

    return None


def plot_spectra(ch_ids=[0]):
    '''plot spectra of raw data and sub_bands, single channels from ch_ids and averages'''

    mpl.rcParams['axes.formatter.limits'] = (-2, 2)

    yy = data01.std() * 2
    xx = np.arange(data1.shape[0]) / params.lfp.fs              # plot raw and filtered traces for visual inspection
    xmax = 150

    plt.figure(1, figsize=(10, 10))
    plt.clf()

    # column 1: first array
    plt.subplot(521)        # plot raw
    plt.plot(ff1, Y01[:, ch_ids[0]], 'C0', label=f'channel: {array1[ch_ids[0]]}')
    plt.plot(ff1, Y01.mean(1), 'C3', alpha=0.2, label='average')
    plt.xlim(xmin=0, xmax=xmax)
    plt.title('array1 raw')

    # plt.legend()
    plt.gca().set_xticklabels([])
    plt.legend()
    
    plt.subplot(523)
    plt.plot(ff1, Y1[:, ch_ids[0], 0], 'C0', label='array1')
    plt.plot(ff1, Y1[:, :, 0].mean(1), 'C3', alpha=0.2)
    # plt.xlim(xmin=0, xmax=params.lfp.filter_fc_lb[1] * 2)
    plt.xlim(xmin=0, xmax=xmax)
    plt.gca().set_xticklabels([])
    plt.title('sub_band 0')
    
    plt.subplot(525)
    plt.plot(ff1, Y1[:, ch_ids[0], 1], 'C0', label='array1')
    plt.plot(ff1, Y1[:, :, 1].mean(1), 'C3', alpha=0.2)
    # plt.xlim(xmin=0, xmax=params.lfp.filter_fc_mb[1] * 2)
    plt.xlim(xmin=0, xmax=xmax)
    plt.gca().set_xticklabels([])
    plt.title('sub_band 1')

    plt.subplot(527)
    plt.plot(ff1, Y1[:, ch_ids[0], 2], 'C0', label='array1')
    plt.plot(ff1, Y1[:, :, 2].mean(1), 'C3', alpha=0.2)
    # plt.xlim(xmin=0, xmax=params.lfp.filter_fc_hb[1] * 2)
    plt.xlim(xmin=0, xmax=xmax)
    plt.title('sub_band 2')

    plt.subplot(529)
    plt.loglog(ff1, Y01[:, ch_ids[0]], 'C0')
    plt.loglog(ff1, Y01.mean(1), 'C3', alpha=0.2)
    plt.title('array1 raw loglog')


    plt.xlabel('Frequency (Hz)')
    # plt.legend()

    # column 2: second array
    plt.subplot(522)
    plt.plot(ff02, Y02[:, ch_ids[0]], 'C0', label=f'channel: {array2[ch_ids[0]]}')
    plt.plot(ff02, Y02.mean(1), 'C3', alpha=0.2, label='average')
    plt.xlim(xmin=0, xmax=xmax)
    # plt.gca().set_yticklabels([])
    plt.title('array2 raw')

    # xxx
    # plt.legend()
    plt.gca().set_xticklabels([])
    plt.legend()
    
    plt.subplot(524)
    plt.plot(ff2, Y2[:, ch_ids[0], 0], 'C0', label='array1')
    plt.plot(ff2, Y2[:, :, 0].mean(1), 'C3', alpha=0.2)
    # plt.xlim(xmin=0, xmax=params.lfp.filter_fc_lb[1] * 2)
    plt.xlim(xmin=0, xmax=xmax)
    plt.gca().set_xticklabels([])
    plt.title('sub_band 0')
    
    plt.subplot(526)
    plt.plot(ff2, Y2[:, ch_ids[0], 1], 'C0', label='array1')
    plt.plot(ff2, Y2[:, :, 1].mean(1), 'C3', alpha=0.2)
    # plt.xlim(xmin=0, xmax=params.lfp.filter_fc_mb[1] * 2)
    plt.xlim(xmin=0, xmax=xmax)
    plt.gca().set_xticklabels([])
    # plt.gca().set_yticklabels([])
    plt.title('sub_band 1')

    plt.subplot(528)
    plt.plot(ff2, Y2[:, ch_ids[0], 2], 'C0', label='array1')
    plt.plot(ff2, Y2[:, :, 2].mean(1), 'C3', alpha=0.2)
    # plt.xlim(xmin=0, xmax=params.lfp.filter_fc_hb[1] * 2)
    plt.xlim(xmin=0, xmax=xmax)
    plt.title('sub_band 2')
    # plt.gca().set_yticklabels([])

    plt.subplot(5, 2, 10)
    plt.loglog(ff01, Y02[:, ch_ids[0]], 'C0')
    plt.loglog(ff01, Y02.mean(1), 'C3', alpha=0.2)
    # plt.gca().set_yticklabels([])
    plt.title('raw loglog')


    plt.xlabel('Frequency (Hz)')

    plt.tight_layout()

    plt.draw()
    plt.show()

    return None


def plot_spectra2(arr_nr=1):
    '''plot spectra of raw data for all channels of arr_nr, compare with spectrum of white noise'''

    mpl.rcParams['axes.formatter.limits'] = (-2, 2)


    if arr_nr == 1:
        YY = Y01
        d0,d1 = data01.shape
    elif arr_nr == 2:
        YY = Y02
        d0,d1 = data02.shape

    Y_GWN, _ = analytics1.calc_fft(np.random.randn(d0, d1), params.lfp.fs, i_stop=1e5, axis=0)

    plt.figure(1, figsize=(10, 10))
    plt.clf()

    for ii in range(YY.shape[1]):
        ax = plt.subplot(8,8,ii+1)
        plt.loglog(ff1, YY[:, ii], 'C0')
        plt.loglog(ff1, Y_GWN[:, ii], 'C1', alpha=0.5)
        plt.ylim(10e-16, 10e2)


        # if ii<56:
        if (ii // 8) < (d1 // 8):
            ax.set_xticks([])
        if np.mod(ii, 8) != 0:
            ax.set_yticks([])

    plt.draw()

    return None


def plot_psth(ff=[], sub_band=0, ch_id=0, trial_id=0, step=10):
    ''' plot psth for no and yes responses separately'''

    yy = max(data01.std(), data1[:, ch_id, sub_band].std()) * 2

    xx1 = np.arange(data1.shape[0]) / params.lfp.fs
    xx2 = np.arange(psth_win[0], psth_win[1]) / params.lfp.fs
    f_idx = ff < 150

    plt.figure(figsize=(10, 10))
    plt.clf()

    log.info(f'Selected sub-band: {sub_band}')
    plt.subplot(411)
    plt.plot(xx1[::step], data01[::step, ch_id], label='raw ns2')       # plot raw
    plt.plot(xx1[::step], data1[::step, ch_id, sub_band], 'C1', alpha=0.5, label=f'sub-band: {sub_band}')   # plot sub_band (low, middle, high)
    for ii in range(8):
        plt.stem(triggers[ii] / params.lfp.fs, triggers[ii] * 0 + yy * 0.8, markerfmt='C3o')  # red
    # plt.stem(triggers_yes_ns2 / params.lfp.fs, triggers_yes_ns2 * 0 + yy * 0.8, markerfmt='C2o', label='yes')  # green
    plt.ylim(-yy, yy)
    plt.xlabel('sec')
    plt.legend(loc=1)

    plt.subplot(423)                                                         # plot psth no-questions
    plt.plot(xx2, psth_no.mean(0)[:, ch_id], label='trial av. no')           # average accross trials, plot 1 channel
    plt.plot(xx2, psth_no.mean(0).mean(1), 'C3', alpha=0.4, label='trial-ch av. no')   # average accross trials and channels
    plt.xlabel('sec')
    plt.legend()

    plt.subplot(424)                                                         # plot psth yes-questions
    plt.plot(xx2, psth_yes.mean(0)[:, ch_id], label='trial av. yes')         # average accross trials, plot 1 channel
    plt.plot(xx2, psth_yes.mean(0).mean(1), 'C3', alpha=0.4, label='trial-ch av. yes')  # average accross trials and channels
    plt.xlabel('sec')
    plt.legend()

    plt.subplot(425)                                               # plot spectrogram no-question, single channel and trial
    # plt.pcolormesh(tt, ff[f_idx], Sxx1[f_idx, ch_id, :])
    if params.lfp.normalize:
        plt.pcolormesh(tt, ff[f_idx], Sxx1[trial_id, f_idx, ch_id, :] / Sxx1_norm[f_idx, :, ch_id])
    else:
        plt.pcolormesh(tt, ff[f_idx], Sxx1[trial_id, f_idx, ch_id, :])
        vmax = max(Sxx1[trial_id, f_idx, ch_id, :].max(), Sxx2[trial_id, f_idx, ch_id, :].max())
        plt.clim(vmax=vmax)
    plt.xlabel('sec')
    plt.colorbar(orientation='horizontal', fraction=0.05, aspect=50)

    plt.subplot(426)                                               # plot spectrogram yes-question, single channel and trial
    if params.lfp.normalize:
        plt.pcolormesh(tt, ff[f_idx], Sxx2[trial_id, f_idx, ch_id, :] / Sxx2_norm[f_idx, :, ch_id])
    else:
        plt.pcolormesh(tt, ff[f_idx], Sxx2[trial_id, f_idx, ch_id, :])
        plt.clim(vmax=vmax)
    plt.xlabel('sec')
    plt.colorbar(orientation='horizontal', fraction=0.05, aspect=50)


    plt.subplot(427)                                               # plot spectrogram no-question, averaged
    # plt.pcolormesh(tt, ff[f_idx], Sxx1[f_idx, ch_id, :])
    if params.lfp.normalize:
        plt.pcolormesh(tt, ff[f_idx], Sxx1[:, f_idx, ch_id, :].mean(0) / Sxx1_norm[f_idx, :, ch_id])
    else:
        plt.pcolormesh(tt, ff[f_idx], Sxx1[:, f_idx, ch_id, :].mean(0))
        vmax = max(Sxx1[trial_id, f_idx, ch_id, :].max(), Sxx2[trial_id, f_idx, ch_id, :].max())
        plt.clim(vmax=vmax)
    plt.xlabel('sec')
    plt.colorbar(orientation='horizontal', fraction=0.05, aspect=50)

    plt.subplot(428)                                               # plot spectrogram yes-question, averaged
    if params.lfp.normalize:
        plt.pcolormesh(tt, ff[f_idx], Sxx2[:, f_idx, ch_id, :].mean(0) / Sxx2_norm[f_idx, :, ch_id])
    else:
        plt.pcolormesh(tt, ff[f_idx], Sxx2[:, f_idx, ch_id, :].mean(0))
        plt.clim(vmax=vmax)
    plt.xlabel('sec')
    plt.colorbar(orientation='horizontal', fraction=0.05, aspect=50)

    plt.tight_layout()
    plt.show()

    return None




def plot_psth(ff=[], sub_band=0, ch_id=0, trial_id=0, step=10):
    ''' plot psth for no and yes responses separately'''

    xx1 = np.arange(data1.shape[0]) / params.lfp.fs
    xx2 = np.arange(psth_win[0], psth_win[1]) / params.lfp.fs
    f_idx = ff < 150

    plt.figure(figsize=(10, 10))
    plt.clf()

    for ii in range(8):
        plt.subplot(4,4,ii+1)
        plt.pcolormesh(tt, ff[f_idx], Sxx1[ii][trial_id, f_idx, ch_id, :])


    if params.lfp.sub_band<1:
        fct = 10
    if params.lfp.sub_band==1:
        fct = 10
    elif params.lfp.sub_band==2:
        fct = 5

    cmax = np.array([Sxx1[ii][:,f_idx, ch_id,:].mean() for ii in range(8)]).max()*fct

    for ii in range(8):
        plt.subplot(4,4,8+ii+1)
        plt.pcolormesh(tt, ff[f_idx], np.mean(Sxx1[ii][:, f_idx, ch_id, :], axis=0))    

        plt.clim(0,cmax)

    plt.tight_layout()
    # plt.show()

    return None


params = aux.load_config()
# params.lfp.array1 = np.delete(params.lfp.array1, params.lfp.array1_exclude)
# params.lfp.array2 = np.delete(params.lfp.array2, params.lfp.array2_exclude)
psth_win = params.lfp.psth_win

# file_name = '/home/vlachos/data_kiap/20190321-135311/20190321-135311-001'
# path = '/home/kiap/Documents/kiap/k01/20190414-123429/'
# path = '/media/vlachos/kiap_backup/Recordings/K01/Recordings/20190415-145905/'
path = '/media/kiap/kiap_backup/Recordings/K01/Recordings/20190326-160445/'
# file_name = path + '20190415-145905-004.ns2'
file_name = path + '20190326-160445-001.ns2'
# file_name = '/media/vlachos/kiap_backup/Recordings/K01/bci_sessions/20190321-140130/20190321-140130-003'
# file_name = path + '20190414-123429-001.ns2'


array1 = params.lfp.array1
array2 = params.lfp.array2


if not 'data0' in locals():                     # load data if not already loaded by previous call

    # READ DATA
    # ----------------------------------
    reader = BlackrockIO(filename=file_name)
    data0 = read_data()  # (samples, channels)
    data0 = data0.copy().astype(np.float64)

    # IMPORT TRIGGERS FROM NEV FILE
    # ----------------------------------
    triggers = get_triggers(n_triggers=20)
    # trials_msk = get_valid_trials(triggers_no_ns2, triggers_yes_ns2)

    # data1[data1 > params.lfp.artifact_thr] = 0
    # data1[data1 < -params.lfp.artifact_thr] = 0
    # data0 = data0 - np.mean(data0, 1)[:, np.newaxis]

    # reader.nev_data['Comments'][0]

    # Z-SCORE DATA
    # ----------------------------------
    if params.lfp.zscore:
        data0 = stats.zscore(data0)        

    # SEPARATE DATA INTO CHANNELS FROM ARRAY-1 AND ARRAY-2
    # ----------------------------------
    data01 = data0[:, :len(array1)]                                 # array-1 electrodes
    data02 = data0[:, len(array1):len(array1) + len(array2)]        # array-2 electrodes

    # EXCLUDE CHANNELS IF VARIANCE IS OUTSIDE PERCENTILES
    # ----------------------------------------------------------------------
    if params.lfp.exclude:
        data01, data02, array1_msk, array2_msk = remove_channels(data01, data02)
        ch_nr1 = len(params.lfp.array1) - len(array1_msk)
        ch_nr2 = len(params.lfp.array2) - len(array2_msk)
    else:
        ch_nr1 = len(params.lfp.array1)
        ch_nr2 = len(params.lfp.array2)

    # PERFORM COMMON AVERAGE REFERENCING
    # ----------------------------------------------------------------------
    if params.lfp.car:
        data01 = data01 - np.repeat(np.mean(data01, axis=1)[:, np.newaxis], data01.shape[1], 1)
        data02 = data02 - np.repeat(np.mean(data02, axis=1)[:, np.newaxis], data02.shape[1], 1)

    # DEVIDE DATA INTO 3 SUB-BANDS
    # ----------------------------------
    data1 = np.zeros((data01.shape[0], data01.shape[1], 3))     # (samples, channels, 3)
    data2 = np.zeros((data02.shape[0], data02.shape[1], 3))     # (samples, channels, 3)
    # Y1 = np.zeros((data01.shape[0], data01.shape[1], 3))

    # FILTER IN THE THREE DIFFERENT BANDS
    # ----------------------------------
    data1[:, :, 0], _, _ = analytics1.bw_filter(data01.T, params.lfp.filter_fc_lb, params.lfp.fs, params.lfp.filter_order_lb, plot=params.lfp.plot.filters)
    data1[:, :, 1], _, _ = analytics1.bw_filter(data01.T, params.lfp.filter_fc_mb, params.lfp.fs, params.lfp.filter_order_mb, plot=params.lfp.plot.filters)
    data1[:, :, 2], _, _ = analytics1.bw_filter(data01.T, params.lfp.filter_fc_hb, params.lfp.fs, params.lfp.filter_order_hb, plot=params.lfp.plot.filters)

    data2[:, :, 0], _, _ = analytics1.bw_filter(data02.T, params.lfp.filter_fc_lb, params.lfp.fs, params.lfp.filter_order_lb, plot=params.lfp.plot.filters)
    data2[:, :, 1], _, _ = analytics1.bw_filter(data02.T, params.lfp.filter_fc_mb, params.lfp.fs, params.lfp.filter_order_mb, plot=params.lfp.plot.filters)
    data2[:, :, 2], _, _ = analytics1.bw_filter(data02.T, params.lfp.filter_fc_hb, params.lfp.fs, params.lfp.filter_order_hb, plot=params.lfp.plot.filters)

    # PERFORM STFT USING FFT
    # ----------------------------------
    Y01, ff01 = analytics1.calc_fft(data01, params.lfp.fs, i_stop=1e5, axis=0)
    Y02, ff02 = analytics1.calc_fft(data02, params.lfp.fs, i_stop=1e5, axis=0)
    Y1, ff1 = analytics1.calc_fft(data1, params.lfp.fs, i_stop=1e5, axis=0)
    Y2, ff2 = analytics1.calc_fft(data2, params.lfp.fs, i_stop=1e5, axis=0)



# COMPUTE PSTH
# ----------------------------------

# psth shape: (trials, time, channels)
# offset = 600 * params.lfp.fs  # offset in sec to get data for normalization
# triggers_yes_norm = np.hstack((triggers_yes_ns2 + offset, triggers_yes_ns2 + offset + 10))
# triggers_no_norm = np.hstack((triggers_yes_ns2 + offset, triggers_yes_ns2 + offset + 10))
# if np.any(triggers_yes_norm > data01.shape[1]):
#     log.error('triggers_norm outside imported data')
psth = compute_psth(triggers, arr_nr=1, sub_band=params.lfp.sub_band)
# psth_norm1, psth_norm2 = compute_psth(triggers_yes_norm, triggers_no_norm, arr_nr=1, sub_band=params.lfp.sub_band)


# COMPUTE PSTH SPECTROGRAMS
# ----------------------------------

nperseg = params.lfp.spectra.spgr_len
nperseg = min(nperseg, psth[0].shape[1])
# ff, tt, Sxx1 = signal.spectrogram(psth_no.mean(0), params.lfp.fs, axis=0, nperseg=nperseg, noverlap=int(nperseg * 0.9))
# ff, tt, Sxx2 = signal.spectrogram(psth_yes.mean(0), params.lfp.fs, axis=0, nperseg=nperseg, noverlap=int(nperseg * 0.9))

# Sxx1.shape = (trials, ff, channels, time)
# Sxx1_norm.shape = (ff,time, channels)
Sxx1 = [list() for ii in range(8)]
for ii in range(8):
    ff, tt, Sxx1_tmp = signal.spectrogram(psth[ii], params.lfp.fs, axis=1, nperseg=nperseg, noverlap=int(nperseg * 0.9))
    Sxx1[ii] = Sxx1_tmp

# ff, tt, Sxx1_norm = signal.spectrogram(psth_norm1.mean(0), params.lfp.fs, axis=0, nperseg=nperseg, noverlap=int(nperseg * 0.9))
# ff, tt, Sxx2_norm = signal.spectrogram(psth_norm2.mean(0), params.lfp.fs, axis=0, nperseg=nperseg, noverlap=int(nperseg * 0.9))


# Sxx1 = Sxx1.mean(1)
# Sxx2 = Sxx2.mean(1)
# Sxx1_norm = Sxx1_norm.mean(2)
# Sxx2_norm = Sxx2_norm.mean(2)

tt = tt + psth_win[0] / params.lfp.fs


t_idx = tt < 1

# Sxx1_norm = Sxx1_norm[:, np.newaxis].repeat(len(tt), 1)
# Sxx2_norm = Sxx2_norm[:, np.newaxis].repeat(len(tt), 1)


# if params.lfp.normalize:
    # Sxx1 = Sxx1 / Sxx1_norm
    # Sxx2 = Sxx2 / Sxx2_norm

# 11. PLOT RESULTS
# ----------------------------------

if params.lfp.plot.general:
    # plot_spectra()
    plot_psth(ff=ff, sub_band=params.lfp.sub_band, ch_id=0, trial_id=0, step=100)
    pass

# xxx
plt.ioff()

for trial_id in range(0, 1):
    # for ch_id in range(ch_nr1 - 1, ch_nr1):
    for ch_id in range(ch_nr1):
        
        plot_psth(ff=ff, sub_band=params.lfp.sub_band, ch_id=ch_id, trial_id=0, step=100)
        fig2 = plt.gcf()
        fname = path + f'results/trial_{trial_id}_ch_{ch_id}_sband_{params.lfp.sub_band}.png'
        fig2.savefig(fname)
        print(ch_id)