doc/oldcode/swhlab/core/plot.py
def IV(abf,T1,T2,plotToo=True,color='b'):
    """
    Given two time points (seconds) return IV data.
    Optionally plots a fancy graph (with errorbars)
    Returns [[AV],[SD]] for the given range.
    """
    rangeData=abf.average_data([[T1,T2]]) #get the average data per sweep
    AV,SD=rangeData[:,0,0],rangeData[:,0,1] #separate by average and SD
    Xs=abf.clampValues(T1) #get clamp values at time point T1
    if plotToo:
        new(abf) #do this so it's the right shape and size

        # plot the original sweep
        pylab.subplot(221)
        pylab.title("sweep data")
        pylab.xlabel("time (s)")
        pylab.ylabel("Measurement (%s)"%abf.units)
        sweep(abf,'all',protocol=False)
        pylab.axis([None,None,np.min(rangeData)-50,np.max(rangeData)+50])
        pylab.axvspan(T1,T2,alpha=.1,color=color) #share measurement region
        pylab.margins(0,.1)

        # plot the data zoomed in
        pylab.subplot(223)
        pylab.title("measurement region")
        pylab.xlabel("time (s)")
        pylab.ylabel("Measurement (%s)"%abf.units)
        sweep(abf,'all',protocol=False)
        pylab.axis([T1-.05,T2+.05,np.min(rangeData)-50,np.max(rangeData)+50])
        pylab.axvspan(T1,T2,alpha=.1,color=color) #share measurement region
        pylab.margins(0,.1)

        # plot the protocol
        pylab.subplot(222)
        pylab.title("protocol")
        pylab.xlabel("time (s)")
        pylab.ylabel("Command (%s)"%abf.unitsCommand)
        sweep(abf,'all',protocol=True)
        pylab.axvspan(T1,T2,alpha=.1,color=color) #share measurement region
        pylab.margins(0,.1)

        # plot the I/V
        pylab.subplot(224)
        pylab.grid(alpha=.5)
        pylab.title("command / measure relationship")
        pylab.xlabel("Command (%s)"%abf.unitsCommand)
        pylab.ylabel("Measurement (%s)"%abf.units)
        pylab.errorbar(Xs,AV,SD,capsize=0,marker='.',color=color)
        if abf.units=="pA":
            pylab.axhline(0,alpha=.5,lw=2,color='r',ls="--")
            pylab.axvline(-70,alpha=.5,lw=2,color='r',ls="--")
        else:
            pylab.axhline(-70,alpha=.5,lw=2,color='r',ls="--")
            pylab.axvline(0,alpha=.5,lw=2,color='r',ls="--")
        pylab.margins(.1,.1)
    annotate(abf)
    return AV,SD
def IV(abf,T1,T2,plotToo=True,color='b'):
    """
    Given two time points (seconds) return IV data.
    Optionally plots a fancy graph (with errorbars)
    Returns [[AV],[SD]] for the given range.
    """
    rangeData=abf.average_data([[T1,T2]]) #get the average data per sweep
    AV,SD=rangeData[:,0,0],rangeData[:,0,1] #separate by average and SD
    Xs=abf.clampValues(T1) #get clamp values at time point T1
    if plotToo:
        new(abf) #do this so it's the right shape and size

        # plot the original sweep
        pylab.subplot(221)
        pylab.title("sweep data")
        pylab.xlabel("time (s)")
        pylab.ylabel("Measurement (%s)"%abf.units)
        sweep(abf,'all',protocol=False)
        pylab.axis([None,None,np.min(rangeData)-50,np.max(rangeData)+50])
        pylab.axvspan(T1,T2,alpha=.1,color=color) #share measurement region
        pylab.margins(0,.1)

        # plot the data zoomed in
        pylab.subplot(223)
        pylab.title("measurement region")
        pylab.xlabel("time (s)")
        pylab.ylabel("Measurement (%s)"%abf.units)
        sweep(abf,'all',protocol=False)
        pylab.axis([T1-.05,T2+.05,np.min(rangeData)-50,np.max(rangeData)+50])
        pylab.axvspan(T1,T2,alpha=.1,color=color) #share measurement region
        pylab.margins(0,.1)

        # plot the protocol
        pylab.subplot(222)
        pylab.title("protocol")
        pylab.xlabel("time (s)")
        pylab.ylabel("Command (%s)"%abf.unitsCommand)
        sweep(abf,'all',protocol=True)
        pylab.axvspan(T1,T2,alpha=.1,color=color) #share measurement region
        pylab.margins(0,.1)

        # plot the I/V
        pylab.subplot(224)
        pylab.grid(alpha=.5)
        pylab.title("command / measure relationship")
        pylab.xlabel("Command (%s)"%abf.unitsCommand)
        pylab.ylabel("Measurement (%s)"%abf.units)
        pylab.errorbar(Xs,AV,SD,capsize=0,marker='.',color=color)
        if abf.units=="pA":
            pylab.axhline(0,alpha=.5,lw=2,color='r',ls="--")
            pylab.axvline(-70,alpha=.5,lw=2,color='r',ls="--")
        else:
            pylab.axhline(-70,alpha=.5,lw=2,color='r',ls="--")
            pylab.axvline(0,alpha=.5,lw=2,color='r',ls="--")
        pylab.margins(.1,.1)
    annotate(abf)
    return AV,SD
def IV ( abf , T1 , T2 , plotToo = True , color = 'b' ) : rangeData = abf . average_data ( [ [ T1 , T2 ] ] ) #get the average data per sweep AV , SD = rangeData [ : , 0 , 0 ] , rangeData [ : , 0 , 1 ] #separate by average and SD Xs = abf . clampValues ( T1 ) #get clamp values at time point T1 if plotToo : new ( abf ) #do this so it's the right shape and size # plot the original sweep pylab . subplot ( 221 ) pylab . title ( "sweep data" ) pylab . xlabel ( "time (s)" ) pylab . ylabel ( "Measurement (%s)" % abf . units ) sweep ( abf , 'all' , protocol = False ) pylab . axis ( [ None , None , np . min ( rangeData ) - 50 , np . max ( rangeData ) + 50 ] ) pylab . axvspan ( T1 , T2 , alpha = .1 , color = color ) #share measurement region pylab . margins ( 0 , .1 ) # plot the data zoomed in pylab . subplot ( 223 ) pylab . title ( "measurement region" ) pylab . xlabel ( "time (s)" ) pylab . ylabel ( "Measurement (%s)" % abf . units ) sweep ( abf , 'all' , protocol = False ) pylab . axis ( [ T1 - .05 , T2 + .05 , np . min ( rangeData ) - 50 , np . max ( rangeData ) + 50 ] ) pylab . axvspan ( T1 , T2 , alpha = .1 , color = color ) #share measurement region pylab . margins ( 0 , .1 ) # plot the protocol pylab . subplot ( 222 ) pylab . title ( "protocol" ) pylab . xlabel ( "time (s)" ) pylab . ylabel ( "Command (%s)" % abf . unitsCommand ) sweep ( abf , 'all' , protocol = True ) pylab . axvspan ( T1 , T2 , alpha = .1 , color = color ) #share measurement region pylab . margins ( 0 , .1 ) # plot the I/V pylab . subplot ( 224 ) pylab . grid ( alpha = .5 ) pylab . title ( "command / measure relationship" ) pylab . xlabel ( "Command (%s)" % abf . unitsCommand ) pylab . ylabel ( "Measurement (%s)" % abf . units ) pylab . errorbar ( Xs , AV , SD , capsize = 0 , marker = '.' , color = color ) if abf . units == "pA" : pylab . axhline ( 0 , alpha = .5 , lw = 2 , color = 'r' , ls = "--" ) pylab . axvline ( - 70 , alpha = .5 , lw = 2 , color = 'r' , ls = "--" ) else : pylab . axhline ( - 70 , alpha = .5 , lw = 2 , color = 'r' , ls = "--" ) pylab . axvline ( 0 , alpha = .5 , lw = 2 , color = 'r' , ls = "--" ) pylab . margins ( .1 , .1 ) annotate ( abf ) return AV , SD
Given two time points (seconds) return IV data.
    Optionally plots a fancy graph (with errorbars)
    Returns [[AV],[SD]] for the given range.
Given two time points ( seconds ) return IV data . Optionally plots a fancy graph ( with errorbars ) Returns [[ AV ] [ SD ]] for the given range .