In [23]:
#Graham Jordan Prog with parts by Caspar Lant
import sys
import numpy as np
import matplotlib.pyplot as plt
import math
from datetime import datetime
import os
#naming conventions
np.set_printoptions(precision=3)
Dict = {"y":1,"Y":1,"n":0,"N":0,"":0,"g":1,"G":1,"l":0,"L":0,'1':1}
Term = {1:'Increasing Field, Increasing Resistance',2:'Increasing Field, Decreasing Resistance',3:'Decreasing Field, Decreasing Resistance',4:'Decreasing Field, Decreasing Resistance'}
color = {1:'red',2:'green',3:'blue',4:'orange',5:'black'}
color2 = {1:'red',2:'blue'}
evens = {"1":1,"2":1,"3":2,"4":2}
direction = {1:'Up',2:'Down'}
Local = Dict[raw_input("Graham's Computer or Lab: G/L? ")]
ResTitle = {1:"Log of Resistance (ln[ohms])",0:"Resistance (Ohms)"}
if Local == 1:
Location = "C:\Users\Graham\OneDrive\LabData\KentLab\data"
elif Local == 0:
Location = "C:\Users\KentLab\Desktop\caspar\data"
sample = 1
while sample == 1:
title = "Magnetoresistance in F5 Nanopillar Sample "
cont = 1
DyeX = raw_input("X coordinate of sample ")
DyeY = raw_input("Y coordinate of sample ")
Current = raw_input("Current through sample (mA) ")
while cont == 1:
compare = 0
print("enter: 1 for single graph, 2 for two comparative trial graphs, 3 for range of trials ")
print("4 for separated single graph, 5 for Quad Split")
compare = int(raw_input("Which option listed above? ")) #compare is the variable used to determine the process for the data
#if compare == 5 or compare == 4:
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#option 1: Single Graph Print
if compare == 1:
#Data Grab
j = raw_input("trial # ")
field, resistance = np.loadtxt((Location+"\Sample_F5_"+DyeX+"_"+DyeY+"_"+Current+"mA_trial"+j+".txt"), skiprows=0 , unpack=True, delimiter=' ')
#separator and plotter (written by Caspar)
color = []
array = []
i = 0
while (i < len(field) - 1):
if (float(field[i]) >= float(field[i+1])):
color = 'blue'
else:
color = 'red'
fig = plt.plot(field[i], (resistance[i] + math.fabs(float(i)/75000.00)), '.', color = color)
i = i+1
#plot title
plt.ylabel("Resistance (Ohms)");
plt.xlabel("Magnetic Field Strength (Tesla)");
plt.title((title+DyeX+' by '+DyeY+', Trial '+str(j)+', '+str(Current)+'mA'))
plt.show ()
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#option 2: Comparative Graph Print For 2 Trials
elif compare == 2 :
#data grab
j = int(raw_input("first trial # "))
a = int(raw_input("second trial # "))
field, resistance = np.loadtxt((Location+"\Sample_F5_"+DyeX+"_"+DyeY+"_"+Current+"mA_trial"+str(j)+".txt"), skiprows=0 , unpack=True, delimiter=' ')
plt.subplot(2,1,1)
#separator and plotter for 1st trial (written by Caspar)
color = []
array = []
i = 0
while (i < len(field) - 1):
if (float(field[i]) >= float(field[i+1])):
color = 'blue'
else:
color = 'red'
fig = plt.plot(field[i], (resistance[i] + math.fabs(float(i)/75000.00)), '.', color = color)
i = i+1
#Plot titles
plt.ylabel("Resistance (Ohms)");
plt.xlabel("Magnetic Field Strength (Tesla)");
plt.title((title+DyeX+' by '+DyeY+', Trial '+str(j)+', '+str(Current)+'mA'))
field, resistance = np.loadtxt((Location+"\Sample_F5_"+DyeX+"_"+DyeY+"_"+Current+"mA_trial"+str(a)+".txt"), skiprows=0 , unpack=True, delimiter=' ')
plt.subplot(2,1,2)
#Separator and plotter for 2nd trial (written by Caspar)
color = []
array = []
i = 0
while (i < len(field) - 1):
if (float(field[i]) >= float(field[i+1])):
color = 'blue'
else:
color = 'red'
fig = plt.plot(field[i], (resistance[i] + math.fabs(float(i)/75000.00)), '.', color = color)
i = i+1
#Plot titles
plt.ylabel("Resistance (Ohms)");
plt.xlabel("Magnetic Field Strength (Tesla)");
plt.title((title+DyeX+' by '+DyeY+', Trial '+str(a)+', '+str(Current)+'mA'))
plt.show ()
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#option 3: Print Range of Trials (from _ to _)
elif compare == 3:
j = int(raw_input("starting trial #"))
first = j
last = int(raw_input("Last Trial #"))
while j <= last:
# Data grab
Trial = str(j);
field, resistance = np.loadtxt((Location+"\Sample_F5_"+DyeX+"_"+DyeY+"_"+Current+"mA_trial"+str(j)+".txt"), skiprows=0 , unpack=True, delimiter=' ');
PlotNum = 2*(j-first)+1
PlotH = 2*(last-first)+1
plt.subplot(PlotH,1,PlotNum)
#Separator and plotter (writen by Caspar)
color = []
array = []
i = 0
while (i < len(field) - 1):
if (float(field[i]) >= float(field[i+1])):
color = 'blue'
else:
color = 'red'
fig = plt.plot(field[i], (resistance[i] + math.fabs(float(i)/75000.00)), '.', color = color)
i = i+1
#Plot titles
plt.ylabel("Resistance (Ohms)");
plt.xlabel("Magnetic Field Strength (Tesla)");
plt.title((title+DyeX+' by '+DyeY+', Trial '+str(j)+', '+str(Current)+'mA'));
j = j+1
plt.show()
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#option 4: Separate Plot into Increasing Field and Decreasing Field
elif compare == 4 or compare == 5:
philter = Dict[raw_input("Apply filter, Y/N? ")]
#Data Grab
j = raw_input("trial # ")
field, resistance = np.loadtxt((Location+"\Sample_F5_"+DyeX+"_"+DyeY+"_"+Current+"mA_trial"+j+".txt"), skiprows=0 , unpack=True, delimiter=' ')
i = 0
UpField = []
DownField = []
UpRes = []
DownRes = []
while (i < len(field)-1):
#Seperator and filter (written by Graham)
sig = np.std(resistance[(i-10):(i+10)])
if philter == 1 and float(Current) < 1 and (abs(resistance[i]-resistance[i+1]) > (0.5*sig)):#Due to the lower currents having more variable data points (i.e. more noise) a stricter filter is applied of half a standard deviation
i=i+1
elif philter == 1 and float(Current) < 1 and (abs(resistance[i]-resistance[i-1]) > (0.5*sig)):#Due to the lower currents having more variable data points (i.e. more noise) a stricter filter is applied of half a standard deviation
i=i+1
elif philter == 1 and (abs(resistance[i]-resistance[i+1]) > (sig)): #should exclude any data point that is of a distance larger than the standard deviation from the next point
i=i+1
elif philter == 1 and (abs(resistance[i]-resistance[i-1]) > (sig)): #should exclude any data point that is of a distance larger than the standard deviation from the next point
i=i+1
elif (field[i] < field[i+1] ): # While the magnetic field is increasing the prog will place the values in the separate arrays
UpField.extend([field[i]])
UpRes.extend([resistance[i]])
i = i + 1
else : #Will place all remaining data points (the decreasing mag field side) in a separate array
DownField.extend([field[i]])
DownRes.extend([resistance[i]])
i = i +1
#Plots and plot titles
if compare == 4:
#Does an nth degree polynomial fit of the data (Still under construction, has trouble with very large n and with some samples that were not filtered by kiethly)
Poly = Dict[raw_input("do a polynomial fit, Y/N? ")]
if Poly == 1:
n = int(raw_input("What degree polynomial? "))
a=1
UpCoeff = np.polyfit(UpField,UpRes,n)
DownCoeff = np.polyfit(DownField,DownRes,n)
while a <= 2:
x = eval(direction[a]+'Field')
y = eval(direction[a]+'Res')
firstx = x[0]
lastx = x[-1]
step = 0.001
if firstx > lastx:
xfit = np.arange(lastx,firstx,step)
else:
xfit = np.arange(firstx,lastx,step)
i = 0
yfit = 0
while i <= n:
yfit = yfit+(xfit**(n-i))*eval(direction[a]+'Coeff')[i]
i = i+1
plt.subplot(2,1,a)
if a == 1:
plt.title((title+DyeX+' by '+DyeY+', Trial '+str(j)+', '+str(Current)+'mA increasing field'))
else:
plt.title((title+DyeX+' by '+DyeY+', Trial '+str(j)+', '+str(Current)+'mA decreasing field'))
plt.plot(xfit,yfit,'b-',color = color[5], label=('Polynomial fit '+str(a)+ ' degree '+str(n)))
plt.plot(x,y, '.', color = color2[a])
a = a+1
plt.legend()
print('Note: coefficients go in the order of C1x^n + C2x^(n-1) + ...')
print('Increasing Field Polynomial fit Coefficients: '+str(UpCoeff))
print('Decreasing Field Polynomial fit Coefficients: '+str(DownCoeff))
plt.show()
else:
plt.subplot(2,1,1)
plt.plot(UpField, UpRes, '.', color='red')
plt.ylabel("Resistance (Ohms)");
plt.xlabel("Magnetic Field Strength (Tesla)");
plt.title((title+DyeX+' by '+DyeY+', Trial '+str(j)+', '+str(Current)+'mA increasing field'));
plt.subplot(2,1,2)
plt.plot(DownField, DownRes, '.', color='blue')
plt.ylabel("Resistance (Ohms)");
plt.xlabel("Magnetic Field Strength (Tesla)");
plt.title((title+DyeX+' by '+DyeY+', Trial '+str(j)+', '+str(Current)+'mA decreasing field'));
plt.show()
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Option 5: Splits data into 4 quadrants as listed below
elif compare == 5:
s = max(UpRes)
s = UpRes.index(s)
Quad1 = [] #increasing field part 1
Res1 = []
Quad2 = [] #increasing field part 2
Res2 = []
Quad3 = [] #decreasing field part 1
Res3 = []
Quad4 = [] #decreasing field part 2
Res4 = []
#divides the increasing magnetic field plot into increasing resistance and decreasing resistance
i = 0
while (i < s ):
Quad1.extend([UpField[i]])
Res1.extend([UpRes[i]])
i = i + 1
while (i < len(UpRes)-1):
Quad2.extend([UpField[i]])
Res2.extend([UpRes[i]])
i = i +1
g = max(DownRes)
g = DownRes.index(g)
#divides decreasing magnetic field into increasing resistance and decreasing resistance
i = 0
while (i < g ):
Quad4.extend([DownField[i]])
Res4.extend([DownRes[i]])
i = i + 1
while (i < len(DownRes)-1):
Quad3.extend([DownField[i]])
Res3.extend([DownRes[i]])
i = i +1
a = 1
STOP = 1
#Horizontal filter (under construction)
while a<= 4:
i=0
X,Y = 0,0
X,Y = [],[]
while i < (len(eval("Quad"+str(a)))-1):
sig = np.std(resistance)
if abs(eval("Quad"+str(a))[i]-eval("Quad"+str(a))[i+1]) > (0.5*sig) and philter == 1 and STOP == 0:
i = i+1
elif abs(eval("Quad"+str(a))[i]-eval("Quad"+str(a))[i-1]) > (0.5*sig) and philter == 1 and STOP == 0:
i = i+1
else:
X.append(eval("Quad"+str(a))[i])
Y.append(eval("Res"+str(a))[i])
i = i+1
if a ==1:
Quad1 = np.array(X)
Res1 = np.array(Y)
elif a ==2:
Quad2 = np.array(X)
Res2 = np.array(Y)
elif a ==3:
Quad3 = np.array(X)
Res3 = np.array(Y)
elif a ==4:
Quad4 = np.array(X)
Res4 = np.array(Y)
a = a+1
a = 1
x = []
y = []
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#Fitter (under construction-Linear works)
Fit = Dict[raw_input("do a fit of the data, Y/N? ")]
Log = 0
if Fit == 1:
Log = Dict[raw_input("Logrithmic Fit, Y/N? (default is Linear) ")]
if Log == 1:
Res1 = np.log(Res1)
Res2 = np.log(Res2)
Res3 = np.log(Res3)
Res4 = np.log(Res4)
def LineFit(x, y):
#Returns slope and y-intercept of linear fit to (x,y) data set
xavg = x.mean()
B = np.array((y*(x-xavg)).sum()/(x*(x-xavg)).sum()) # slope
A = np.array(y.mean()-B*xavg) # intercept
return B, A
while a <= 4:
x = eval("Quad"+str(a))
y = eval("Res"+str(a))
B,A = LineFit(x,y)
Coeff = np.around([B, A], decimals=3)
firstx = x[0]
lastx = x[-1]
step = 0.001
if firstx > lastx:
xfit = np.arange(lastx,firstx,step)
else:
xfit = np.arange(firstx,lastx,step)
yfit = A + B*xfit
Loc = evens[str(a)]
plt.subplot(2,1,Loc)
plt.plot(xfit,yfit,'b-',color = color[a], label=('Linear fit '+str(a)))
print(Term[a]+" equation: Resistance = "+str(Coeff[0])+"(Ohms/mTesla)*Magnetic Field + "+str(Coeff[1])+" Ohms")
plt.plot(x,y, '.', color = color[a])
a = a+1
plt.legend()
plt.subplot(2,1,1)
plt.plot(Quad1,Res1, '.', color = 'red', label='increasing resistance')
plt.ylabel(ResTitle[Log]);
plt.xlabel("Magnetic Field Strength (Tesla)");
plt.title((title+DyeX+' by '+DyeY+', Trial '+str(j)+', '+str(Current)+'mA increasing field'));
plt.plot(Quad2,Res2, '.', color = 'green', label='decreasing resistance')
plt.legend()
plt.subplot(2,1,2)
plt.plot(Quad3,Res3, '.', color = 'blue', label='decreasing resistance')
plt.ylabel(ResTitle[Log]);
plt.xlabel("Magnetic Field Strength (Tesla)");
plt.title((title+DyeX+' by '+DyeY+', Trial '+str(j)+', '+str(Current)+'mA decreasing field'));
plt.plot(Quad4,Res4, '.', color = 'orange', label='increasing resistance')
plt.legend()
plt.show()
cont = Dict[raw_input("Continue with this sample, Y/N? ")]
sample = Dict[raw_input("Change sample, Y/N? ")]
print("Good bye")
In [ ]: