eyeBlinkBehaviour/test_threadmill.py at master · ananthamurthy/eyeBlinkBehaviour · GitHub

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"""test_threadmill.py:

Read the data from thread-mill and analyze it.

"""
from __future__ import print_function


__author__           = "Dilawar Singh"
__copyright__        = "Copyright 2017-, Dilawar Singh"
__version__          = "1.0.0"
__maintainer__       = "Dilawar Singh"
__email__            = "dilawars@ncbs.res.in"
__status__           = "Development"

import sys
import logging
import os
import numpy as np
import time
import datetime
import scipy.signal as sig
import gnuplotlib as gpl
sys.path.append( 'pyblink' )
import arduino

res_file_ = '__results__tmp__.csv'


def stamp( ):
    return datetime.datetime.now().isoformat( )

def line_to_data(line):
    """First element is timestamp, rest the data etc.
    """
    if '>' in line:
        return [ ]

    line = filter(None, line.split(',') )
    data = [ ]
    for x in line:
        try:
            data.append( int(x) )
        except ValueError as e:
            data.append( x )
    return data

def _readline( ser ):
    eol = b'\n'
    leneol = len(eol)
    line = bytearray()
    while True:
        c = ser.read(1)
        if c:
            line += c
            if line[-leneol:] == eol:
                break
        else:
            break

        if( len(line) > 100 ):
            break

    return bytes(line)

def compute_speed( tvec, yvec ):
    """Compute speed """
    ydiff = np.diff( yvec )
    minus1Ps = np.where( ydiff == -1 )
    minus1Ts = tvec[ minus1Ps ]
    tps = np.diff( minus1Ts )
    velocity = np.mean( 4.1 / tps )    # m / sec
    if np.isnan( velocity ):
        velocity = 0.0
    return velocity


def calculate_motion( t, dx, dy ):
    """Caculate speed and direction of motion """
    t, dx, dy = [ np.array( x ) for x in [ t, dx, dy] ]
    s = np.sqrt( dx ** 2.0 + dy ** 2.0 )
    ds = np.mean( s )
    if np.mean( dx ) < 0:
        ds = -ds

    dt = t[-1] - t[0]
    return ds / dt, 1.0

def calculate_direction( s1, s2 ):
    d = -1
    if s1 > s2:
        d = 1
    else:
        d = -1
    return d

def main( port, baud ):
    print( '[INFO] Using port %s baudrate %d' % (port, baud ) )
    tvec, motion1, motion2 = [ ], [ ], [ ]
    ar = arduino.ArduinoPort( port )
    ar.open( )
    speed, direction = 0.0, 0
    with open( res_file_, 'w' ) as f:
        f.write( "time s1 s2 v1 v2 dir\n" )

    speedVec = [ ]
    while True:
        line = ar.read_line( )
        data = line_to_data( line )
        if len( data ) < 7:
            continue

        tvec.append( data[0] )
        motion1.append( data[5] )
        motion2.append( data[6] )
        try:
            N = 20
            speed,direction = calculate_motion( tvec[-N:], motion1[-N:], motion2[-N:] )
            speedVec.append( speed )
            gpl.plot(
                    np.array( tvec[-1000:] ), np.array( speedVec[-1000:])
                    , set = ( 'yrange [-0.01:0.01]' )
                    )
        except Exception as e:
            speed = 0.0
            direction = 0
            print( e )
        print( '%.5f %s' % (speed, direction))

if __name__ == '__main__':
    port = sys.argv[1]
    baud = 38400
    main( port, baud )