def doCONTIN(self, gamma_min=1, gamma_max=1E6):
'''
run CONTIN program using module pyCONTIN
generate an input file and an output file
pyCONTIN: https://github.com/kanhua/pyCONTIN
'''
# genetate paramTemplate file for pyCONTIN module
content = ''' TEST DATA SET 1 (inverse laplace transform)
LAST,,1
GMNMX,1,{}
GMNMX,2,{}
IWT,,1
NERFIT,,0
NINTT,,-1
NLINF,,1
IFORMY,,(1E11.4)
IFORMT,,(1E11.4)
DOUSNQ,,1
IUSER,10,2
RUSER,10,-1
NONNEG,,1'''.format(str(gamma_min), str(gamma_max))
with open('paramTemplate.txt', 'w') as f:
f.write(content)
self.paramTemplateFile = 'paramTemplate.txt'
if self.testParams['Time Unit'] == 'microsecond':
xdata = self.Ctau[:,
0] * 1e-6 # in CONTIN, unit of delay time is sec
ydata = self.Ctau[:, 1]
runCONTINfit(xdata, ydata, self.paramTemplateFile)
self.CONTINOutputFile = 'CONTINOutput.txt'
def testExperimentFile(templateFile):
filepath='/Users/kanhua/Dropbox/Experiment data drive/TTI data/20140910 GaAsN test DLTS/OMARS1'
filepath2='/Users/kanhua/Dropbox/Experiment data drive/TTI data/20140910 GaAsN test DLTS/'
cp=capTime(join(filepath,'T012.Y1A'))
xdata=cp.time
ydata=-cp.capTrans
plt.plot(xdata,ydata)
plt.show()
alldata=runCONTINfit(xdata,ydata,templateFile)
for i,data in enumerate(alldata):
plt.semilogx(data[1][:,2],data[1][:,0],hold=True)
plt.xlabel("emission rate(s^-1)")
plt.ylabel("amplitude")
plt.title("alpha %s"%data[0][1])
plt.savefig("./tmpoutput/test"+str(i)+".png")
plt.close()
def Contin(g2_tau, contin_pars):
create_contin_parameter_file(contin_pars)
parameterFile = os.path.join(
'contin', "contin_parameter_template.txt"
) #the parameters for the contin program are stored in this file.
# print(parameterFile)
alldata = runCONTINfit(
g2_tau[0, :], g2_tau[1, :],
parameterFile) #, continInputFile=None, continOutputFile=None)
# print('\n\n\n\n contin data', data_temp)
return alldata
def testExperimentFile(templateFile):
filepath = '/Users/kanhua/Dropbox/Experiment data drive/TTI data/20140910 GaAsN test DLTS/OMARS1'
filepath2 = '/Users/kanhua/Dropbox/Experiment data drive/TTI data/20140910 GaAsN test DLTS/'
cp = capTime(join(filepath, 'T012.Y1A'))
xdata = cp.time
ydata = -cp.capTrans
plt.plot(xdata, ydata)
plt.show()
alldata = runCONTINfit(xdata, ydata, templateFile)
for i, data in enumerate(alldata):
plt.semilogx(data[1][:, 2], data[1][:, 0], hold=True)
plt.xlabel("emission rate(s^-1)")
plt.ylabel("amplitude")
plt.title("alpha %s" % data[0][1])
plt.savefig("./tmpoutput/test" + str(i) + ".png")
plt.close()
# ## This example file demonstrates how to use pyCONTIN wrapper
# Load the required packages
import numpy as np
import matplotlib.pyplot as plt
from CONTINWrapper import runCONTINfit
# #### Load example transient file
trans_data = np.loadtxt("demo_input.csv")
# #### Assign template file
template_file = "paramTemplate.txt"
fp = open("paramTemplate.txt", 'r')
alldata = runCONTINfit(trans_data[:, 0], trans_data[:, 1], template_file)
testxdata = alldata[2][1][:, 2]
testydata = alldata[2][1][:, 0]
plt.plot(testxdata, testydata)
plt.show()