Bug fixes

eventSegment.py

@@ -428,6 +428,7 @@ def __checkdrift(self, curr):
 		self.windowOpenCurrentSD=sd 
 		self.windowOpenCurrentSlope=sl
 
+	#@profile
 	def __eventsegment(self):
 		"""
 			Cut up a trajectory into individual events. This algorithm uses

stepResponseAnalysis.py

@@ -11,6 +11,7 @@
 import metaEventProcessor
 import util
 import sys
+import math
 
 import numpy as np
 import scipy.optimize
@@ -131,7 +132,8 @@ def formatsettings(self):
 		fmtstr+='Algorithm = {0}\n\n'.format(self.__class__.__name__)
 
 		fmtstr+='\t\tMax. iterations  = {0}\n'.format(self.FitIters)
-		fmtstr+='\t\tFit tolerance (rel. err in leastsq)  = {0}\n\n'.format(self.FitTol)
+		fmtstr+='\t\tFit tolerance (rel. err in leastsq)  = {0}\n'.format(self.FitTol)
+		fmtstr+='\t\tBlockade Depth Rejection = {0}\n\n'.format(self.BlockRejectRatio)
 
 
 		return fmtstr
@@ -186,9 +188,13 @@ def __FitEvent(self):
 
 					self.mdRedChiSq			= optfit.chisqr/( np.var(optfit.residual) * (len(self.eventData) - optfit.nvarys -1) )
 
-					if self.mdBlockDepth > self.BlockRejectRatio:
-						# print 'eBlockDepthHigh', optfit.params['b'].value, optfit.params['b'].value - optfit.params['a'].value, optfit.params['mu1'].value, optfit.params['mu2'].value
-						self.rejectEvent('eBlockDepthHigh')
+					# if self.mdBlockDepth > self.BlockRejectRatio:
+					# 	# print 'eBlockDepthHigh', optfit.params['b'].value, optfit.params['b'].value - optfit.params['a'].value, optfit.params['mu1'].value, optfit.params['mu2'].value
+					# 	self.rejectEvent('eBlockDepthHigh')
+
+					if math.isnan(self.mdRedChiSq):
+						self.rejectEvent('eInvalidFitParams')
+
 					#print i0, i0sig, [optfit.params['a'].value, optfit.params['b'].value, optfit.params['mu1'].value, optfit.params['mu2'].value, optfit.params['tau'].value]
 			else:
 				#print optfit.message, optfit.lmdif_message

test.py

@@ -37,12 +37,12 @@
 
 
 # raw_input("Enter to continue")
-
-# SingleChannelAnalysis.SingleChannelAnalysis(
-# 			abfTrajIO(fnames=['/Volumes/DATA/tetheredPEG/13712018_peg2k.abf']), 
-# 			es.eventSegment,
-# 			sra.stepResponseAnalysis
-# 		).Run()
+# dirname='/Volumes/DATA/tetheredPEG/20130716/',filter='*abf'
+SingleChannelAnalysis.SingleChannelAnalysis(
+ 			abfTrajIO(fnames=['/Users/balijepalliak/Desktop/peg2k/first hour/13730039_001.abf', '/Users/balijepalliak/Desktop/peg2k/first hour/13730039_002.abf']),
+			es.eventSegment,
+			sra.stepResponseAnalysis
+		).Run()
 
 #'set3','set4','set5',
 # [ SingleChannelAnalysis.SingleChannelAnalysis(
@@ -66,21 +66,22 @@ def analysisiter(dir, filt, i):
 			).Run() 
 
 		os.rename(dir+'/eventMD.tsv', dir+'/eventMD_'+str(i).zfill(2)+'.tsv')
-		#os.rename(dir+'/eventTS.csv', dir+'/eventTS_'+str(i).zfill(2)+'.csv')
+		os.rename(dir+'/eventTS.csv', dir+'/eventTS_'+str(i).zfill(2)+'.csv')
 		os.rename(dir+'/eventProcessing.log', dir+'/eventProcessing'+str(i).zfill(2)+'.log')
 	except MemoryError, e:
 		print "memory exceeded: ", e
 		pass
 
 
 
-#[ analysisiter('/Volumes/DATA/PRL Data/EBSPEG600/20130627/m40mV2/', '*-'+str(i).zfill(2)+'??.qdf', i)	for i in range(10, 11) ]
+#[ analysisiter('/Volumes/DATA/PRL Data/EBSPEG600/20130722/m40mV8/', '*-'+str(i).zfill(2)+'??.qdf', i)	for i in range(100, 101) ]
+# [ analysisiter('/Volumes/DATA/PRL Data/EBSPEG600/20130723/m40mV2/', '*-'+str(i).zfill(2)+'??.qdf', i)	for i in range(10, 11) ]
 
-SingleChannelAnalysis.SingleChannelAnalysis(
-			qdfTrajIO(dirname='/Volumes/DATA/PRL Data/EBSPEG600/20130715/m40mV/', filter='*qdf', nfiles=150, Rfb=9.1E+9, Cfb=1.07E-12),
-			es.eventSegment,
-			sra.stepResponseAnalysis
-		).Run() 
+# SingleChannelAnalysis.SingleChannelAnalysis(
+# 			qdfTrajIO(dirname='/Volumes/DATA/PRL Data/EBSPEG600/20130717/m40mV2/', filter='*qdf', nfiles=325, Rfb=9.1E+9, Cfb=1.07E-12),
+# 			es.eventSegment,
+# 			sra.stepResponseAnalysis
+# 		).Run() 
 
 # print ['*-'+str(i).zfill(2)+'??.qdf' for i in range(1,15)]