derivative_y_limit = 5

# defining arrays where all found peaks wil be stored

peak_y_values = []

peak_x_values = []

peak_i_values = []

# Find all peaks

length_of_data = len(phi_angle)

number_of_steps_for_one_degree = length_of_data / float(360)

#print "number_of_steps_for_one_degree: " + str(number_of_steps_for_one_degree)

i = 0

while i < length_of_data-1:

# if we see a "jump" of more than "derivative_y_limit" units for one step, we assume one peak wil be within the next degree

if(data_firstpeak_t[i+1] - data_firstpeak_t[i] > derivative_y_limit ):

# Found start of peak.

temp_y_max = float(0)

temp_i_max = 0

for i in range(i,i+int(number_of_steps_for_one_degree)):

if i == length_of_data:

# Ignoring that we might get a peak at the end which we don't want

break

# finding the max y-value within one degree and defining that one as the peak

if temp_y_max < data_firstpeak_t[i]:

temp_i_max = i

temp_y_max = data_firstpeak_t[i]

temp_x_max = phi_angle[i]

# print "----------------------------------------------------------------------"

# print str(i) +"x:\t" + str(phi_angle[i]) + ", y:\t" + str(data_firstpeak_t[i])

peak_y_values.append(temp_y_max)

peak_i_values.append(temp_i_max)

peak_x_values.append(temp_x_max)

# printing every x- and y-value, including the index, so we can manualy overlook at the raw-data

#print str(i) +"x:\t" + str(phi_angle[i]) + ", y:\t" + str(data_firstpeak_t[i])

i += 1

#print "-------------------------------------------------------------------------"

#print "peak_y_values: " + str(peak_y_values)

#print "peak_x_values: " + str(peak_x_values)

#print "peak_i_values: " + str(peak_i_values)

#print "number_of_steps_for_one_degree: " + str(number_of_steps_for_one_degree)

#print "Length of data: " + str(length_of_data)

#print "-------------------------------------------------------------------------"

return peak_x_values

peak_diff = np.zeros(len(peak_x_values)-1)

for i in range(len(peak_x_values)-1):

peak_diff[i] = peak_x_values[i+1]-peak_x_values[i]

# This will include differance in angle between last peak and first peak. Remember adjust size of peak_diff on initiateing with zeros

#peak_diff[len(peak_x_values)-1] = 360 - peak_x_values[len(peak_x_values)-1] + peak_x_values[0]

unique_angles = [angles_between_peaks[0]]

isUnique = True

rangeAroundDegree = 0.5

for angle in angles_between_peaks:

for i in range(len(unique_angles)):

if(angle < unique_angles[i] + rangeAroundDegree and angle > unique_angles[i] - rangeAroundDegree):

isUnique = False

break

if(isUnique):

unique_angles.append(angle)

isUnique = True

print "hello MAN"

#first peak [2 2 0]

data = np.loadtxt("../data/DE35214_UMG_treated_U03_firstpeak.xy")

phi_angle = data[:,0]

data_firstpeak_t = data[:,1]

list_first_peaks_found_x = find_phi(phi_angle,data_firstpeak_t)

list_peak_diff_first = find_difference_in_peaks(list_first_peaks_found_x)

#second peak

data = np.loadtxt("../data/DE35214_UMG_treated_U03_secondpeak.xy")

phi_angle = data[:,0]

data_secondpeak_t = data[:,1]

list_second_peaks_found_x = find_phi(phi_angle,data_secondpeak_t)

list_peak_diff_second = find_difference_in_peaks(list_second_peaks_found_x)

#third peak

data = np.loadtxt("../data/DE35214_UMG_treated_U03_thirdpeak.xy")

phi_angle = data[:,0]

data_thirdpeak_t = data[:,1]

list_third_peaks_found_x = find_phi(phi_angle,data_thirdpeak_t)

list_peak_diff_third = find_difference_in_peaks(list_third_peaks_found_x)

#fourth peak

data = np.loadtxt("../data/DE35214_UMG_treated_U04_02_fourthpeak.xy")

phi_angle = data[:,0]

data_fourthpeak_t = data[:,1]

list_fourth_peaks_found_x = find_phi(phi_angle,data_fourthpeak_t)

list_peak_diff_fourth = find_difference_in_peaks(list_fourth_peaks_found_x)

#plotting phi-rotation of treated fiber

color=iter(cm.rainbow(np.linspace(0,1,6)))

fig2 = plt.figure()

c1=next(color)

plt.plot(phi_angle, data_firstpeak_t, color=c1, label=r'$\langle 220 \rangle$ planes')

c=next(color)

plt.plot(phi_angle, data_secondpeak_t, color=c, label=r'$\langle 400 \rangle$ planes')

c=next(color)

plt.plot(phi_angle, data_thirdpeak_t, color=c, label=r'$\langle 440 \rangle$ planes')

c=next(color)

#plt.plot(phi_angle, data_fourthpeak_t, color=c, label=r'$\langle 440 \rangle$ planes')

#Plot peaks found

for i in range(len(list_first_peaks_found_x)):

plt.axvline(x=list_first_peaks_found_x[i],ymin=0.7, ymax=1, linewidth = 2, color = 'r')

for i in range(len(list_second_peaks_found_x)):

plt.axvline(x=list_second_peaks_found_x[i],ymin=0.7, ymax=1, linewidth = 2, color = 'b')

for i in range(len(list_third_peaks_found_x)):

plt.axvline(x=list_third_peaks_found_x[i],ymin=0.7, ymax=1, linewidth = 2, color = 'g')

#for i in range(len(list_fourth_peaks_found_x)):

#plt.axvline(x=list_fourth_peaks_found_x[i],ymin=0.7, ymax=1, linewidth = 2, color = 'k')

plt.xlabel('$\phi$ rotation angle', fontsize=12)

plt.ylabel('intensity', fontsize=12)

plt.xlim(0,360)

#plt.ylim(0,4500)

plt.xticks(fontsize = 8)

plt.yticks(fontsize = 8)

plt.grid()

plt.legend(loc='upper right', prop={'size':10})

fig2.savefig("./U3_phi.pdf")