#!/usr/bin/env python

# -*- coding: utf-8 -*-

"""

process_data.py: Python script that processes fiber photometry data. It truncates

the signal, filters it, labels events, processes trials, and groups trials by epoch.

"""

__author__ = "DM Brady"

__datewritten__ = "07 Mar 2018"

__lastmodified__ = "06 Feb 2019"

import sys

from imaging_analysis.event_processing import LoadEventParams, ProcessEvents, ProcessTrials, GroupTrialsByEpoch, GenerateManualEventParamsJson

from imaging_analysis.segment_processing import TruncateSegments, AppendDataframesToSegment, AlignEventsAndSignals

from imaging_analysis.utils import ReadNeoTdt, PrintNoNewLine

from imaging_analysis.signal_processing import ProcessSignalData, SmoothSignalWithPeriod, ZScoreCalculator, SmoothSignalWithPeriod, Downsample

import numpy as np

import pandas as pd

import seaborn as sns

import matplotlib.pyplot as plt

from scipy import stats

import json

import click

import os

from typing import List, Dict, Tuple, Any

def process_data(file: str='./params.json') -> Tuple[pd.DataFrame, List[Any], Dict[str, pd.DataFrame]]:

return trials, seglist, all_signals

@click.command()

@click.option(

'-f',

'--file',

default="params.json",

type=str,

show_default=True,

help=("Parameter file with channel info, events of interest, etc."))

def main(file: str) -> None:

"""Runs imaging analysis based on inputs from a parameter file"""

process_data(file)

if __name__ == '__main__':

main()