diff --git a/FinalTimepixDocumentation.pdf b/FinalTimepixDocumentation.pdf
index 6c22110..4862f56 100644
Binary files a/FinalTimepixDocumentation.pdf and b/FinalTimepixDocumentation.pdf differ
diff --git a/FinalTimepixDocumentation_orig.pdf b/FinalTimepixDocumentation_orig.pdf
new file mode 100644
index 0000000..6c22110
Binary files /dev/null and b/FinalTimepixDocumentation_orig.pdf differ
diff --git a/dataAnalysis/hough1D.py b/dataAnalysis/hough1D.py
index dae2adb..918e3ed 100644
--- a/dataAnalysis/hough1D.py
+++ b/dataAnalysis/hough1D.py
@@ -1,12 +1,8 @@
-#!/usr/bin/python
-import math
+#!/usr/bin/python3
+
 import sys
 import numpy as np
-from scipy import linspace, polyval, polyfit, sqrt, stats, randn
-#from ROOT import gROOT, TCanvas,TH1D,TH2D,TFile,TStyle,TLegend,TPave,TPaveStats,TPad,TPaveLabel,gStyle,gPad,TPaletteAxis,TLine
-#gROOT.Reset()
-from ROOT import gROOT,TCanvas,TH1D,TH2D,TFile,TStyle,TLegend,TPave,TPaveStats,TPad,TPaveLabel,gStyle,TPaletteAxis,TLine
-#gROOT.Reset()
+from ROOT import TCanvas,TH1D,TFile,gStyle,TLine
 
 
 def printCanvas(histogram,title):
@@ -37,13 +33,13 @@ def linearRegression(histogram):
             if histogram.GetBinContent(i,k)!=0:
                 x.append(i)
                 y.append(k)
-    (ar,br)=polyfit(x,y,1)
-    xr=polyval([ar,br],x)
-    err=sqrt(sum((xr-y)**2)/len(y))
+    (ar,br)=np.polyfit(x,y,1)
+    xr=np.polyval([ar,br],x)
+    err=np.sqrt(sum((xr-y)**2)/len(y))
     if abs(ar)>1.0:
-        (ar,br)=polyfit(y,x,1)
-        xr=polyval([ar,br],y)
-        err=sqrt(sum((xr-x)**2)/len(y))
+        (ar,br)=np.polyfit(y,x,1)
+        xr=np.polyval([ar,br],y)
+        err=np.sqrt(sum((xr-x)**2)/len(y))
     return err
 
 
@@ -263,6 +259,8 @@ def hough(inputfile,pattern,folder,eventNumber):
         del accumulator
     meta.close()
     return eventNumber
-#if __name__ == '__main__':
+
+if __name__ == '__main__':
 #    hough1D(inputfile,pattern,folder):
+    print("This file is to be imported as a module")
     
diff --git a/dataAnalysis/hough1D.pyc b/dataAnalysis/hough1D.pyc
deleted file mode 100644
index 65653ed..0000000
Binary files a/dataAnalysis/hough1D.pyc and /dev/null differ
diff --git a/dataAnalysis/loopClusters.py b/dataAnalysis/loopClusters.py
old mode 100644
new mode 100755
index 950fc3c..66a2b1f
--- a/dataAnalysis/loopClusters.py
+++ b/dataAnalysis/loopClusters.py
@@ -1,8 +1,10 @@
+#!/usr/bin/env python3
+
 from ROOT import gROOT, TCanvas, TH1D,TH2D,TFile
 gROOT.Reset()
 import numpy as np
 import sys
-print sys.argv
+print (sys.argv)
 import os
 import os.path
 import re
@@ -29,7 +31,7 @@ def plotClusters(filepath):
     totalTime=0
     numberOfPixels=0
     fileS.write("new\n")
-    print "working with file ",filepath
+    print ("working with file ",filepath)
     for line in open(filepath):
         columns = line.split()
         if columns[0]=="new":
diff --git a/dataAnalysis/loopHough.py b/dataAnalysis/loopHough.py
old mode 100644
new mode 100755
index 0127249..451e524
--- a/dataAnalysis/loopHough.py
+++ b/dataAnalysis/loopHough.py
@@ -1,8 +1,10 @@
+#!/usr/bin/env python3
+
 from ROOT import gROOT, TCanvas, TH1D,TH2D,TFile
 #gROOT.Reset()
 import numpy as np
 import sys
-print sys.argv
+print (sys.argv)
 import os
 import os.path
 import re
diff --git a/dataAnalysis/preprocess.py b/dataAnalysis/preprocess.py
old mode 100644
new mode 100755
index c37540d..5ed3d01
--- a/dataAnalysis/preprocess.py
+++ b/dataAnalysis/preprocess.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 from ROOT import gROOT, TCanvas, TH1D,TH2D,TFile
 gROOT.Reset()
 import numpy