trying to resolve a merge issue...

autoCombFindLHO.sh

 #!/bin/bash
-source /home/aneunzert/test/bin/activate
+#source /home/aneunzert/test/bin/activate
 
 TEMP_DIR=~/public_html/latest/
 CONSEC=4
@@ -10,6 +10,7 @@ rm $TEMP_DIR/*
 
 echo "Finding latest spectrum file and copying to temp directory..."
 RECENTSPECT=$(ls -tr ~/public_html/comb_plots/combCheck*_cumulsince_2016-09-18/* | grep dat_ | tail -n1)
+echo $RECENTSPECT
 echo $RECENTSPECT > $TEMP_DIR/foundcombs.txt
 cp $RECENTSPECT $TEMP_DIR
 RECENTSPECT=$(ls -t $TEMP_DIR/* | head -n1)
@@ -44,7 +45,11 @@ echo "$SUMMARY" > $TEMP_DIR/summary.txt
 
 echo "Plotting..."
 
+<<<<<<< HEAD:autoCombFindLHO.sh
 python chplot.py --truefcutoff=True --fmin 0 --fmax 200 --consecutive 3 --checkrange 1 --overwrite=True --scalerange=0 $TAGCOMBS --inputfolder $TEMP_DIR --knowncombfile="preER10combnotes.txt"
+=======
+python chplot.py --truefcutoff=True --fmin 0 --fmax 100 --consecutive $CONSEC --checkrange 1 --overwrite=True --scalerange=0 $TAGCOMBS --inputfolder $TEMP_DIR --knowncombfile="preER10combnotes.txt"
+>>>>>>> 659cbf2df0a80a2c8bf081d7c704ef964300b239:autoCombFind.sh
 
 HTMLFILE=$(ls $TEMP_DIR/*.html)
 

combfinder.py

@@ -14,6 +14,7 @@ def bootstrap_reject(data,sigma=100,nmax=5):
 		if nmax<len(data):
 			avg=np.average(data[descendInds[nmax:]])
 			std=np.std(data[descendInds[nmax:]])
+			print(std,std+avg,np.log10(std*sigma+avg))
 			if data[descendInds[nmax-1]]>avg+std*sigma:
 				return descendInds[0:nmax]
 		nmax-=1
@@ -171,7 +172,7 @@ def get_peaks_threshold(vData,iConsider,nCheckAdj,spectBg=None,spectStd=None,thr
 			iiMarkComb=np.intersect1d(iiMarkComb,np.where(vData[(iConsider+i)%(len(vData))]<vData[iConsider])[0])
 	return iiMarkComb
 
-def mark_comb(vData,iOnComb,nCheckAdj,nReqConsec,spectBg=None,spectStd=None,threshold=0,rejectOutlierOnStdDevs=5):
+def mark_comb(vData,iOnComb,nCheckAdj,nReqConsec,spectBg=None,spectStd=None,threshold=0,rejectOutlierOnStdDevs=2):
 	''' Return the indices of points which are likely to actually be on a comb
 
 	Parameters
@@ -205,8 +206,12 @@ def mark_comb(vData,iOnComb,nCheckAdj,nReqConsec,spectBg=None,spectStd=None,thre
 	iiMarkComb2=iiMarkComb2.astype(int)
 	iMarkComb=iOnComb[iiMarkComb2]
 	if rejectOutlierOnStdDevs>0:
-		std=np.std(vData[iMarkComb])
-		iMarkComb=iMarkComb[vData[iMarkComb]<=1+std*rejectOutlierOnStdDevs]
+		rejectinds=bootstrap_reject(vData[iMarkComb],sigma=1000)
+		if len(rejectinds)<.3*len(iMarkComb):
+			iMarkComb=np.delete(iMarkComb,rejectinds)
+		#std=np.std(vData[iMarkComb])
+		#print(np.log10(1+std*rejectOutlierOnStdDevs))
+		#iMarkComb=iMarkComb[vData[iMarkComb]<=1+std*rejectOutlierOnStdDevs]
 	return iMarkComb
 
 def get_background(vData,inds,scalerange,calcStd=False):