diff --git a/scripts/analyze_lightcurve.py b/scripts/analyze_lightcurve.py
index add33f7..9934cce 100644
--- a/scripts/analyze_lightcurve.py
+++ b/scripts/analyze_lightcurve.py
@@ -1,53 +1,57 @@
 # -*- coding: utf-8 -*-
 from __future__ import unicode_literals
 import numpy as np
-import clag
 import sys
+import getopt
 
+sys.path.insert(1,"/usr/local/science/clag/")
+import clag
+
+# psd1_output = open("psd1.tmp")
+# psd2_output = open("psd2.tmp")
+# lag_output = open("lag.tmp")
 
 # For jupyter notebook
 # %pylab inline
 
 try:
-    opts,args = getopt.getopt(args, "")
+    opts,args = getopt.getopt(sys.argv[1:], "")
 except getopt.GetoptError:
     print 'analyze_lightcure.py <reference curve> <compared curve>'
     sys.exit(2)
 
 ## load the first light curve
-lc1 = np.loadtxt(args[0])
+lc1_table = np.loadtxt(args[0],skiprows=1)
 
 # works if first two entries represent minimum spacing, from example
-# dt = lc1[1,0] - lc1[0, 0]
+# dt = lc1_table[1,0] - lc1_table[0, 0]
 
 # Time resolution determined from inspection and testing. This script
 # does not expect evenly spaced data in time.
 dt = 0.1
 
 
-_ = plot(lc1[:,0], lc1[:,1])
-_ = plot(lc1[:,0], lc1[:,3])
+# _ = plot(lc1_table[:,0], lc1_table[:,1])
+# _ = plot(lc1_table[:,0], lc1_table[:,3])
+
 
 # Split the light curve into segments #
-seg_length = 256
-index = np.arange(len(lc1)).reshape((-1, seg_length))
+#seg_length = 256
+#index = np.arange(len(data)).reshape((-1, seg_length))
 
-lc1_time = [lc1[i, 0] for i in index]
-lc1_strength  = [lc1[i, 1] for i in index]
-lc1_strength_err = [lc1[i, 2] for i in index]
+# For now, instead of splitting up the curves, the program will assume 
+# that the data list is shorter than 256 elemements. so,
 
-# This would work if both curves are in same file
-# lc2  = [lc1[i, 3] for i in index]
-#Lc2e = [lc1[i, 4] for i in index]
+index = np.arange(len(lc1_table)).reshape(-1,len(lc1_table))
 
-
-# Load second light curve
-lc2 = np.loadtxt(args[1])
+lc1_time = [lc1_table[i, 0] for i in index]
+lc1_strength  = [lc1_table[i, 1] for i in index]
+lc1_strength_err = [lc1_table[i, 2] for i in index]
 
 #### Get the psd for the first light curve ####
 
-# These bin values determined summer 2015 for STORM III optical/UV lightcurves
-fqL = [0.0049999999, 0.018619375, 0.044733049, 0.069336227, 0.10747115, 0.16658029, 0.25819945, 0.40020915, 0.62032418]
+# These bin values determined summer 2016 for STORM III optical/UV lightcurves
+fqL = np.array([0.0049999999, 0.018619375, 0.044733049, 0.069336227, 0.10747115, 0.16658029, 0.25819945, 0.40020915, 0.62032418])
 
 # using utilities to set up frequency bins #
 # fqL = np.logspace(np.log10(1.1/seg_length),np.log10(.5/dt),7)
@@ -56,7 +60,6 @@ fqL = [0.0049999999, 0.018619375, 0.044733049, 0.069336227, 0.10747115, 0.166580
 nfq = len(fqL) - 1
 
 
-
 ## initialize the psd class for multiple light curves ##
 P1  = clag.clag('psd', lc1_time, lc1_strength, lc1_strength_err, dt, fqL)
 
@@ -68,7 +71,7 @@ P1  = clag.clag('psd', lc1_time, lc1_strength, lc1_strength_err, dt, fqL)
 inpars = np.ones(nfq)
 
 ## print the loglikelihood for the input values ##
-print P1.logLikelihood(inpars)
+P1.logLikelihood(inpars)
 
 
 
@@ -81,15 +84,31 @@ psd1, psd1e = clag.optimize(P1, inpars)
 ## plot ##
 fqd = 10**(np.log10( (fqL[:-1]*fqL[1:]) )/2.)
 
-loglog(fqd, 0.1*fqd**(-1.5), label='input psd')
-errorbar(fqd[1:-1], psd1[1:-1], yerr=psd1e[1:-1], fmt='o', ms=10, label='fit')
+#loglog(fqd, 0.1*fqd**(-1.5), label='input psd')
+#errorbar(fqd[1:-1], psd1[1:-1], yerr=psd1e[1:-1], fmt='o', ms=10, label='fit')
 
+# load second lightcurve
+
+# This would work if both curves are in same file
+# lc2_strength  = [lc1_table[i, 3] for i in index]
+# lc2_strength_err = [lc1_table[i, 4] for i in index]
+
+# But, they aren't, so,
+
+# Load second light curve
+lc2_table = np.loadtxt(args[1],skiprows=1)
+
+index = np.arange(len(lc2_table)).reshape(-1,len(lc2_table))
+
+lc2_time = [lc2_table[i, 0] for i in index]
+lc2_strength  = [lc2_table[i, 1] for i in index]
+lc2_strength_err = [lc2_table[i, 2] for i in index]
 
 
 
 ## Now do the second light curve
 
-P2  = clag.clag('psd', lc1_time, lc2, Lc2e, dt, fqL)
+P2  = clag.clag('psd', lc2_time, lc2_strength, lc2_strength_err, dt, fqL)
 
 psd2, psd2e = clag.optimize(P2, inpars)
 
@@ -102,8 +121,8 @@ psd2, psd2e = clag.optimize(P2, inpars)
 ### We also give it the calculated psd values as input ###
 Cx = clag.clag('cxd', 
                [list(i) for i in zip(lc1_time,lc1_time)], 
-               [list(i) for i in zip(lc1_strength,lc2)],
-               [list(i) for i in zip(lc1_strength_err,Lc2e)], 
+               [list(i) for i in zip(lc1_strength,lc2_strength)],
+               [list(i) for i in zip(lc1_strength_err,lc2_strength_err)], 
                dt, fqL, psd1, psd2)
 
 inpars = np.concatenate( (0.3*(psd1*psd2)**0.5, psd1*0+1.) )
@@ -112,6 +131,8 @@ phi, phie = p[nfq:], pe[nfq:]
 lag, lage = phi/(2*np.pi*fqd), phie/(2*np.pi*fqd)
 cx, cxe   = p[:nfq], pe[:nfq]
 
+np.savetxt("lag.out",lag)
+
 
 
 
@@ -121,7 +142,7 @@ cx, cxe   = p[:nfq], pe[:nfq]
 
 ## plot ##
 
-semilogx(fqd, fqd*0+1.0, label='input phase lag')
-ylim([0.8, 1.2])
-errorbar(fqd[1:-1], phi[1:-1], yerr=phie[1:-1], fmt='o', ms=10, label='fit')
+#semilogx(fqd, fqd*0+1.0, label='input phase lag')
+#ylim([0.8, 1.2])
+#errorbar(fqd[1:-1], phi[1:-1], yerr=phie[1:-1], fmt='o', ms=10, label='fit')