def ripple_minima(chi_file, background_file, background_level, composition,
qmin, qmaxinst):
pwd = os.getcwd()
if os.path.exists(os.path.join(pwd, 'ripple_minima_test')) is False:
os.mkdir(os.path.join(pwd, 'ripple_minima_test'))
ripple_list = []
gr_list = []
qmax_min = 18.5
qmax_max = qmaxinst
qmax_step = .01
print 'Start qmax refinement'
for qmax in np.arange(qmax_min, qmax_max, qmax_step):
print qmax
gr_file, bg, q=Calculate.pdfgetx3(
chi_file,
background_file,
background_level,
composition,
qmax,
qmin,
qmax,
'QA',
os.path.join(pwd, 'ripple_minima_test', '@b_ripple_test_'+str(
qmax).ljust(5,'0')+'.@o'))
gr_file = os.path.join(pwd, 'ripple_minima_test', os.path.split(
os.path.splitext(chi_file)[0])[1]+'_ripple_test_'+str(qmax).ljust(5,'0')+'.gr')
x, y = IO.load_gr_file(gr_file)
w = y - np.convolve(y, np.ones(3)/3, 'same')
ripple_sum = np.sum(abs(w))
ripple_list.append(ripple_sum)
gr_list.append(gr_file)
t = np.arange(qmax_min, qmax_max, qmax_step)
ripple_array=np.array(ripple_list)
minima_index = signal.argrelextrema(ripple_array, np.greater_equal,
order=2*len(ripple_array)/100)[0]
minima = ripple_array[minima_index]
minima_q = t[minima_index]
maxima_index = signal.argrelextrema(ripple_array, np.less_equal,
order=2*len(ripple_array)/100)[0]
maxima = ripple_array[maxima_index]
maxima_q = t[maxima_index]
plt.plot(t, ripple_array, 'g')
plt.plot(minima_q, minima, 'o', markerfacecolor='none', mec='r')
plt.plot(maxima_q, maxima, 'o', markerfacecolor='none', mec='b')
plt.title('Ripples in PDF')
plt.xlabel('Qmax (1/A)')
plt.ylabel('Ripple Cumulative Sum')
plt.show()
plt.cla()
# data_list = []
# key_list = []
# for minima_q_point in minima_q:
# data = IO.load_gr_file([x for x in gr_list if str(qmax) in x] [0])
# data_list_element = data
# key_list_element = minima_q_point
# data_list.append(data_list_element)
# key_list.append(key_list_element)
# plot_stack(data_list, key_list)
ziped_minima = zip(minima_q, minima)
while True:
for q, value in ziped_minima:
print 'q= ', q,'rippleness= ', value
qmax= float(raw_input('Please pick a qmax. qmax= '))
gr_file = [x for x in gr_list if str(qmax) in x] [0]
print gr_file
x, y = IO.load_gr_file(gr_file)
plt.plot(x, y)
plt.show()
if raw_input('Is this the file you wanted? y/[n] ') == 'y':
break
return qmax
background_file, background_level,
composition, qmax, qmin, qmaxinst, pdf_format, output)
return gr_file, background_level, qmax, bg_refine_qmin_index, bg_refine_qmax_index
# MODELS
if __name__ == "__main__":
plt.ioff()
chi_name = tif_to_iq(
poni_file=None,
image_path=None,
mask_file=None,
plot_verbose=True,
)
print 'Start PDF'
gr_file, bg, calculated_qmax, bg_refine_qmin_index, bg_refine_qmax_index = \
write_pdf(
chi_file=None,
background_file=None,
composition='Ni.3Pd.7',
plot_verbose=True,
qmax='ripple',
qmaxinst=27.1,
bg_refine_qmin_index=None,
bg_refine_qmax_index=None)
radius, gr = IO.load_gr_file(gr_file)
plt.plot(radius, gr)
plt.show()
