Ejemplo n.º 1
0
def Nov18():
    a =loadtxt('/home/chris/Dropbox/DataWeiss/151118/Dots with untreated alumina.csv', unpack = True, delimiter = ',', skiprows = 1,usecols = (0,1,7,9,11))
    s = pf(a[0][0:150],a[4][0:150],1)
    a[4]-=polyval(a[0],s)
    for i in a[array([1,3,4])]:#[1:]:
        i-=i[150]
        r = findpeak(a[0],i,(405,420))
        print r
        
        i-=i[150]
        i/=r[1]
        plot(a[0], i)
    
    legend(['as prep', 'alumina 4 mg', 'alumina 5.8 mg'])
    ylabel('absorbance')
    xlabel('wavelength')
    return 0
Ejemplo n.º 2
0
def findderivative(x,y,derivorder=1):

    window_len=25
#    if spectrum.ndim != 1:
#        raise ValueError, "smooth only accepts 1 dimension arrays."
#
#    if spectrum.size < window_len:
#        raise ValueError, "Input vector needs to be bigger than window size."

        
    

    retval = numpy.ndarray(y.shape)
    for i in range(y.size):
        
        i_min = max(0,i-window_len/2)
        i_max = min( i+window_len/2-1, y.size)
        fit = pf(x[i_min:i_max+1],y[i_min:i_max+1],min(5,window_len))
        retval[i] = polyval(x[i],polyder(fit,derivorder),tensor=False) 
        
    return retval
Ejemplo n.º 3
0
def exampleplot():
    figure()
    ax1=subplot(121)
    ax2=subplot(122)
    c = linspace(0,10,1000)
    
    cmaxdot = 0.2
  #  subplot(121)
    for K in [100,1000,10000]:
        K=float(K)
        a = K
        #def b():return -ctot0*K - K*c +K*cmaxdot+1
        #def d():return ctot0+c
        #    
        #def cfree():return (-b()+sqrt(b()**2-4*a*d()))/(2*a)
        a=K
        b=1+K*cmaxdot-K*c
        d=-c
            
        cfree = (-b+sqrt(b**2-4*a*d))/(2*a)
        cfree2= (-b-sqrt(b**2-4*a*d))/(2*a)
        r = pf(c[10:15],cfree[10:15],1)
        
        
        #print r[0], (K+0.5*((1+K*cmaxdot-K*xlarge)**2+4*K*xlarge)**-0.5*(-2*K*(1+K*cmaxdot-K*xlarge)+4*K))/(2*K)
        
        M = (r[0]-0.5)**2
        A = (M-0.5)#*xlarge**2
        B = (2*M-1)#*xlarge
        
        C = M-0.5
        print M,A,B,C,B**2
        
        #print K,'estimated K=',(-B+sqrt(B**2-4*A*C))/(2*A)
        print 'early slope=', cfree[0]/c[1],cfree[0]/c[1]-c[1]*r[1]
       # plot(c[:10],(c[:10]-0.1)*r[1]+cfree[10]/c[10])
        ax1.plot(c,cfree/c)
        ax2.plot(c,cfree/c)
    
       # plot(c,findderivative(c,cfree/c,derivorder=1)/200,'--')
        #plot(c,fd(c,cfree/c),'-.')
        
        #plot(c,K*cfree/(1+K*cfree))
       # plot(c,cfree2)
    legend([1,10,100,1000])
    
    ax1.set_ylabel('$\delta_{observed}$',fontsize=24)
    #ax2.set_ylabel('$\delta$',fontsize=24)
    ax1.set_xlabel('c$_{total}$ (mM)', fontsize=24)
    ax2.set_xlabel('c$_{total}$ (mM)', fontsize=24)
    ax2.set_xlim((0,0.4))
    ax2.set_xticks([0,0.1,0.2,0.3,0.4,0.5])
    ax1.set_yticks([0,1])
    ax2.set_yticks([])
    ax1.set_yticklabels(['$\delta_{bound}$','$\delta_{free}$'],fontsize=24)
    
    figure()
    ax1=subplot(211)
    ax2=subplot(212)
   
    for K in [50]:
        K=float(K)
        a = K
        #def b():return -ctot0*K - K*c +K*cmaxdot+1
        #def d():return ctot0+c
        #    
        #def cfree():return (-b()+sqrt(b()**2-4*a*d()))/(2*a)
        a=K
        b=1+K*cmaxdot-K*c
        d=-c
            
        cfree = (-b+sqrt(b**2-4*a*d))/(2*a)
       
        ax1.plot(c,cfree/c)
        ax2.plot(c,c-cfree)#K*cfree*cmaxdot/(1+K*cfree))
        ax2.plot(c,cfree,'--')
        ax2.plot(c,c)
       
    
    legend(['bound', 'free', 'total'],loc=2)
    
    ax1.set_ylabel('$\delta_{observed}$',fontsize=24)
 
    ax2.set_xlabel('c$_{total}$ (mM)', fontsize=24)
    ax2.set_ylabel('c (mM)',fontsize=24)
    #ax2.set_xticks([0,0.1,0.2,0.3,0.4,0.5])
    ax1.set_yticks([0,1])
    ax1.set_xlim(0,1)
    ax2.set_xlim(0,1)
    
    #ax1.set_ylim(-0.1,1.1)
    ax2.set_ylim(0,1)
    
   
    ax1.set_yticklabels(['$\delta_{bound}$','$\delta_{free}$'],fontsize=24)
    
#    subplot(122)   
#    for cinit in [0,0.1,0.2,0.5,1]:
#        a = K
#        #def b():return -ctot0*K - K*c +K*cmaxdot+1
#        #def d():return ctot0+c
#        #    
#        #def cfree():return (-b()+sqrt(b()**2-4*a*d()))/(2*a)
#        ctot = cinit+c
#        a=K
#        b=1+K*cmaxdot-K*ctot
#        d=-ctot
#            
#        cfree = (-b+sqrt(b**2-4*a*d))/(2*a)
#        
#        plot(c,cfree/ctot)
#       # plot(c,cfree2)
#    legend([0,0.1,0.2,0.5,1])
    
    return 0