def proto_0303(theABF):
    """protocol: repeated IC ramps."""

    abf=ABF(theABF)
    abf.log.info("analyzing as a halorhodopsin (2s pulse)")

    # show average voltage
    proto_avgRange(theABF,0.2,1.2)
    plt.close('all')

    # show stacked sweeps
    plt.figure(figsize=(8,8))
    for sweep in abf.setsweeps():
        color='b'
        if sweep in np.array(abf.comment_sweeps,dtype=int):
            color='r'
        plt.plot(abf.sweepX2,abf.sweepY+100*sweep,color=color,alpha=.5)
    plt.margins(0,.01)
    plt.tight_layout()
    frameAndSave(abf,"IC ramps")
    plt.close('all')

    # do AP event detection
    ap=AP(abf)
    ap.detect_time1=2.3
    ap.detect_time2=8.3
    ap.detect()
    apCount=[]
    apSweepTimes=[]

    for sweepNumber,times in enumerate(ap.get_bySweep("times")):
        apCount.append(len(times))
        if len(times):
            apSweepTimes.append(times[0])
        else:
            apSweepTimes.append(0)

    # plot AP frequency vs time
    plt.figure(figsize=(8,8))

    ax1=plt.subplot(211)
    plt.grid(alpha=.4,ls='--')
    plt.plot(np.arange(len(apCount))*abf.sweepLength/60,apCount,'.-',ms=15)
    comment_lines(abf)
    plt.ylabel("AP Count")

    plt.subplot(212,sharex=ax1)
    plt.grid(alpha=.4,ls='--')
    plt.plot(np.arange(len(apCount))*abf.sweepLength/60,apSweepTimes,'.-',ms=15)
    comment_lines(abf)
    plt.ylabel("First AP Time (s)")
    plt.xlabel("Experiment Duration (minutes)")
    plt.tight_layout()
    frameAndSave(abf,"IC ramp freq")
    plt.close('all')
def proto_0303(theABF):
    """protocol: repeated IC ramps."""

    abf=ABF(theABF)
    abf.log.info("analyzing as a halorhodopsin (2s pulse)")

    # show average voltage
    proto_avgRange(theABF,0.2,1.2)
    plt.close('all')

    # show stacked sweeps
    plt.figure(figsize=(8,8))
    for sweep in abf.setsweeps():
        color='b'
        if sweep in np.array(abf.comment_sweeps,dtype=int):
            color='r'
        plt.plot(abf.sweepX2,abf.sweepY+100*sweep,color=color,alpha=.5)
    plt.margins(0,.01)
    plt.tight_layout()
    frameAndSave(abf,"IC ramps")
    plt.close('all')

    # do AP event detection
    ap=AP(abf)
    ap.detect_time1=2.3
    ap.detect_time2=8.3
    ap.detect()
    apCount=[]
    apSweepTimes=[]

    for sweepNumber,times in enumerate(ap.get_bySweep("times")):
        apCount.append(len(times))
        if len(times):
            apSweepTimes.append(times[0])
        else:
            apSweepTimes.append(0)

    # plot AP frequency vs time
    plt.figure(figsize=(8,8))

    ax1=plt.subplot(211)
    plt.grid(alpha=.4,ls='--')
    plt.plot(np.arange(len(apCount))*abf.sweepLength/60,apCount,'.-',ms=15)
    comment_lines(abf)
    plt.ylabel("AP Count")

    plt.subplot(212,sharex=ax1)
    plt.grid(alpha=.4,ls='--')
    plt.plot(np.arange(len(apCount))*abf.sweepLength/60,apSweepTimes,'.-',ms=15)
    comment_lines(abf)
    plt.ylabel("First AP Time (s)")
    plt.xlabel("Experiment Duration (minutes)")
    plt.tight_layout()
    frameAndSave(abf,"IC ramp freq")
    plt.close('all')
def proto_0303 ( theABF ) : abf = ABF ( theABF ) abf . log . info ( "analyzing as a halorhodopsin (2s pulse)" ) # show average voltage proto_avgRange ( theABF , 0.2 , 1.2 ) plt . close ( 'all' ) # show stacked sweeps plt . figure ( figsize = ( 8 , 8 ) ) for sweep in abf . setsweeps ( ) : color = 'b' if sweep in np . array ( abf . comment_sweeps , dtype = int ) : color = 'r' plt . plot ( abf . sweepX2 , abf . sweepY + 100 * sweep , color = color , alpha = .5 ) plt . margins ( 0 , .01 ) plt . tight_layout ( ) frameAndSave ( abf , "IC ramps" ) plt . close ( 'all' ) # do AP event detection ap = AP ( abf ) ap . detect_time1 = 2.3 ap . detect_time2 = 8.3 ap . detect ( ) apCount = [ ] apSweepTimes = [ ] for sweepNumber , times in enumerate ( ap . get_bySweep ( "times" ) ) : apCount . append ( len ( times ) ) if len ( times ) : apSweepTimes . append ( times [ 0 ] ) else : apSweepTimes . append ( 0 ) # plot AP frequency vs time plt . figure ( figsize = ( 8 , 8 ) ) ax1 = plt . subplot ( 211 ) plt . grid ( alpha = .4 , ls = '--' ) plt . plot ( np . arange ( len ( apCount ) ) * abf . sweepLength / 60 , apCount , '.-' , ms = 15 ) comment_lines ( abf ) plt . ylabel ( "AP Count" ) plt . subplot ( 212 , sharex = ax1 ) plt . grid ( alpha = .4 , ls = '--' ) plt . plot ( np . arange ( len ( apCount ) ) * abf . sweepLength / 60 , apSweepTimes , '.-' , ms = 15 ) comment_lines ( abf ) plt . ylabel ( "First AP Time (s)" ) plt . xlabel ( "Experiment Duration (minutes)" ) plt . tight_layout ( ) frameAndSave ( abf , "IC ramp freq" ) plt . close ( 'all' )
protocol: repeated IC ramps.
protocol : repeated IC ramps .