Index: fact/tools/pyscripts/examples/CalFactFitsPerformance.py
===================================================================
--- fact/tools/pyscripts/examples/CalFactFitsPerformance.py	(revision 13515)
+++ fact/tools/pyscripts/examples/CalFactFitsPerformance.py	(revision 13515)
@@ -0,0 +1,78 @@
+#!/usr/bin/python -tt
+# ********************************
+# Test script for the CalFactFits class
+# 
+# written by Thomas Kraehenbuehl, ETH Zurich
+# tpk@phys.ethz.ch, +41 44 633 3973
+# April 2012
+# ********************************
+
+datafilename = '/fact/raw/2012/04/17/20120417_004.fits.gz'
+calibfilename = '/fact/raw/2012/04/17/20120417_003.drs.fits.gz'
+
+import numpy as np
+import itertools
+
+from ROOT import gSystem
+gSystem.Load("calfactfits_h.so")
+from ROOT import *
+print "Testing object creation: "
+caltest = CalFactFits(datafilename,calibfilename)
+npcalevent  = np.empty( caltest.npix * caltest.nroi, np.float64) #.reshape(caltest.npix ,caltest.nroi)
+caltest.SetNpcaldataPtr(npcalevent)
+
+print "Common variables:"
+print "ROI: ", caltest.nroi
+print "#Pix: ", caltest.npix
+print "Number of events: ", caltest.nevents
+print
+
+print "Information per Event:"
+caltest.GetCalEvent()
+print "Event ID: ", caltest.event_id
+print "Trigger type: ", caltest.event_triggertype
+print "Uncalibrated data: ", caltest.event_data
+print "Calibrated data: ", caltest.npcaldata
+print "Board times: ", caltest.event_boardtimes
+print "Trigger offsets: ", caltest.event_offset
+print
+
+print "Examples of other information"
+print "Calibfile ROI: ", caltest.calib_nroi
+print "Column size BaselineMean: ", caltest.calibfile.GetN("BaselineMean")
+print "Datafile ROI: ", caltest.data_nroi
+print "Data: ", caltest.datafile.GetN("Data")
+print "StartCellData: ", caltest.datafile.GetN("StartCellData")
+print "Direct datafile access: ", caltest.datafile.GetN("StartCellData")
+print
+print "Columns of the datafile: "
+caltest.datafile.PrintColumns()
+
+def offsum(x,y):
+    return np.sum(npcalevent[x,y+5:y+15])
+vecoffsum = np.vectorize(offsum) #specifying otypes=[np.float/double] does not improve speed
+
+while caltest.GetCalEvent():
+    if caltest.event_id>30:
+        break
+    npcalevent = npcalevent.reshape((caltest.npix, caltest.nroi))
+    npthr = npcalevent>2.5 #true if above threshold
+    npthr = npthr[:,1:-14] * np.logical_not(npthr[:,:-15]) #only true for the zero crossings, shape (1400,285) [smaller due to necessary integration range]
+#    print [(x,y) for x,y in zip(npthr.nonzero()[0],npthr.nonzero()[1])] #print the coordinates, range 0-1399,0-284
+    
+    integrals = []
+    #Various versions to get the integral, all with approximately the same miserable speed (3 Hz), except for the last one (vectorized function) with ~4.3 Hz
+    #Missing: add deadtime after an integration, remove start & end of the array
+#    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in np.transpose(npthr.nonzero())]
+#    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in zip(npthr.nonzero()[0],npthr.nonzero()[1])]
+#    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in itertools.izip(npthr.nonzero()[0],npthr.nonzero()[1])]
+#    integrals = map((lambda index_a,index_b: np.sum(npcalevent[index_a,index_b+5:index_b+15])),npthr.nonzero()[0],npthr.nonzero()[1])
+    integrals = vecoffsum(npthr.nonzero()[0],npthr.nonzero()[1])
+    
+#    print len(integrals)
+#    for i in range(10):
+#        print i, npcalevent[0,i], integrals[i]
+#    print caltest.event_id, caltest.event_triggertype, caltest.event_caldata[10]
+#    pass
+
+del caltest
Index: fact/tools/pyscripts/examples/CalFactFitsPerformanceWeave.py
===================================================================
--- fact/tools/pyscripts/examples/CalFactFitsPerformanceWeave.py	(revision 13515)
+++ fact/tools/pyscripts/examples/CalFactFitsPerformanceWeave.py	(revision 13515)
@@ -0,0 +1,114 @@
+#!/usr/bin/python -tt
+# ********************************
+# Test script for the CalFactFits class
+# 
+# written by Thomas Kraehenbuehl, ETH Zurich
+# tpk@phys.ethz.ch, +41 44 633 3973
+# April 2012
+# ********************************
+
+datafilename = '/fact/raw/2012/04/17/20120417_004.fits.gz'
+calibfilename = '/fact/raw/2012/04/17/20120417_003.drs.fits.gz'
+
+import numpy as np
+from scipy import weave
+from scipy.weave import converters
+
+from ROOT import gSystem
+gSystem.Load("calfactfits_h.so")
+from ROOT import *
+print "Testing object creation: "
+caltest = CalFactFits(datafilename,calibfilename)
+npcalevent  = np.empty( caltest.npix * caltest.nroi, np.float64) #.reshape(caltest.npix ,caltest.nroi)
+caltest.SetNpcaldataPtr(npcalevent)
+
+print "Common variables:"
+print "ROI: ", caltest.nroi
+print "#Pix: ", caltest.npix
+print "Number of events: ", caltest.nevents
+print
+
+print "Information per Event:"
+caltest.GetCalEvent()
+print "Event ID: ", caltest.event_id
+print "Trigger type: ", caltest.event_triggertype
+print "Uncalibrated data: ", caltest.event_data
+print "Calibrated data: ", caltest.npcaldata
+print "Board times: ", caltest.event_boardtimes
+print "Trigger offsets: ", caltest.event_offset
+print
+
+print "Examples of other information"
+print "Calibfile ROI: ", caltest.calib_nroi
+print "Column size BaselineMean: ", caltest.calibfile.GetN("BaselineMean")
+print "Datafile ROI: ", caltest.data_nroi
+print "Data: ", caltest.datafile.GetN("Data")
+print "StartCellData: ", caltest.datafile.GetN("StartCellData")
+print "Direct datafile access: ", caltest.datafile.GetN("StartCellData")
+print
+print "Columns of the datafile: "
+caltest.datafile.PrintColumns()
+
+#AND WE HAVE A WINNER: 43 Hz with scipy.weave!
+while caltest.GetCalEvent():
+    c_integrals = np.zeros(40000, np.float64) #Allocate the memory for about 40000 singles
+    if caltest.event_id>300:
+        break
+    
+    cppcode = """
+    //ToDo: get nroi and npix, check singles<40000
+    double slice, lastslice, integral;
+    int singles = 0;
+    double threshold = 2.5;
+    for(int px=0; px<npix; px++) {
+        lastslice = npcalevent(px*nroi);
+        for(int sl=1; sl<nroi-14; sl++) {
+            slice = npcalevent(px*nroi+sl);
+            if((lastslice<threshold)&&(slice>threshold)) {
+                integral = 0;
+                for(int l=5; l<15; l++) {
+                    integral += npcalevent(px*nroi+sl+l);
+                }
+                c_integrals(singles) = integral;
+                ++singles;
+//                std::cout << sl << " ";
+            }
+            lastslice = slice;
+        }
+    }
+//    std::cout << std::endl << singles << std::endl;
+    """
+    
+    #Passing the caltest object to weave is not possible
+    #The int() statement is necessary to add additional data type information to the variable (ie. otherwise some things would work in the C-code, other would not)
+    nroi = int(caltest.nroi)
+    npix = int(caltest.npix)
+    
+    weave.inline(cppcode, ['c_integrals', 'npcalevent','nroi','npix'], type_converters=converters.blitz)
+    
+#    print "CalFactFitsPerformanceWeave"
+#    for i in range(10):
+#        print i, npcalevent[i], c_integrals[i]
+#    for x in c_integrals:
+#        if x:
+#            print x,
+
+#    #Old attempts using numpy functions
+#    npcalevent = npcalevent.reshape((caltest.npix, caltest.nroi))
+#    npthr = npcalevent>2.5 #true if above threshold
+#    npthr = npthr[:,1:-14] * np.logical_not(npthr[:,:-15]) #only true for the zero crossings, shape (1400,285) [smaller due to necessary integration range]
+##    print [(x,y) for x,y in zip(npthr.nonzero()[0],npthr.nonzero()[1])] #print the coordinates, range 0-1399,0-284
+#    
+#    #Various versions to get the integral, all with approximately the same miserable speed (3 Hz), except for the last one (vectorized function) with ~4.3 Hz
+#    #Missing: add deadtime after an integration, remove start & end of the array
+##    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in np.transpose(npthr.nonzero())]
+##    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in zip(npthr.nonzero()[0],npthr.nonzero()[1])]
+##    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in itertools.izip(npthr.nonzero()[0],npthr.nonzero()[1])]
+##    integrals = map((lambda index_a,index_b: np.sum(npcalevent[index_a,index_b+5:index_b+15])),npthr.nonzero()[0],npthr.nonzero()[1])
+#    integrals = vecoffsum(npthr.nonzero()[0],npthr.nonzero()[1])
+#    print len(integrals)
+
+#    print caltest.event_id, caltest.event_triggertype, caltest.event_caldata[10]
+#    pass
+
+del caltest
Index: fact/tools/pyscripts/examples/CalFactFitsTest.py
===================================================================
--- fact/tools/pyscripts/examples/CalFactFitsTest.py	(revision 13515)
+++ fact/tools/pyscripts/examples/CalFactFitsTest.py	(revision 13515)
@@ -0,0 +1,58 @@
+#!/usr/bin/python -tt
+# ********************************
+# Test script for the CalFactFits class
+# 
+# written by Thomas Kraehenbuehl, ETH Zurich
+# tpk@phys.ethz.ch, +41 44 633 3973
+# April 2012
+# ********************************
+
+datafilename = '/fact/raw/2012/04/17/20120417_004.fits.gz'
+calibfilename = '/fact/raw/2012/04/17/20120417_003.drs.fits.gz'
+
+import numpy as np
+
+from ROOT import gSystem
+gSystem.Load("calfactfits_h.so")
+from ROOT import *
+print "Testing object creation: "
+caltest = CalFactFits(datafilename,calibfilename)
+npcalevent  = np.empty( caltest.npix * caltest.nroi, np.float64) #.reshape(caltest.npix ,caltest.nroi)
+caltest.SetNpcaldataPtr(npcalevent)
+
+print "Common variables:"
+print "ROI: ", caltest.nroi
+print "#Pix: ", caltest.npix
+print "Number of events: ", caltest.nevents
+print
+
+print "Information per Event:"
+caltest.GetCalEvent()
+print "Calibrated data in numpy array: ", npcalevent
+print "Event ID: ", caltest.event_id
+print "Trigger type: ", caltest.event_triggertype
+print "Uncalibrated data: ", caltest.event_data
+print "Calibrated data: ", caltest.npcaldata
+print "Board times: ", caltest.event_boardtimes
+print "Trigger offsets: ", caltest.event_offset
+print
+
+print "Examples of other information"
+print "Calibfile ROI: ", caltest.calib_nroi
+print "Column size BaselineMean: ", caltest.calibfile.GetN("BaselineMean")
+print "Datafile ROI: ", caltest.data_nroi
+print "Data: ", caltest.datafile.GetN("Data")
+print "StartCellData: ", caltest.datafile.GetN("StartCellData")
+print "Direct datafile access: ", caltest.datafile.GetN("StartCellData")
+print
+print "Columns of the datafile: "
+caltest.datafile.PrintColumns()
+
+#while caltest.GetCalEvent():
+#    if caltest.event_id>10:
+#        break
+#    print caltest.event_id, caltest.event_triggertype, caltest.event_caldata[10]
+#    pass
+#print
+
+del caltest
Index: fact/tools/pyscripts/examples/CalFitsPerformance.py
===================================================================
--- fact/tools/pyscripts/examples/CalFitsPerformance.py	(revision 13503)
+++ 	(revision )
@@ -1,78 +1,0 @@
-#!/usr/bin/python -tt
-# ********************************
-# Test script for the CalFits class
-# 
-# written by Thomas Kraehenbuehl, ETH Zurich
-# tpk@phys.ethz.ch, +41 44 633 3973
-# April 2012
-# ********************************
-
-datafilename = '/fact/raw/2012/04/17/20120417_004.fits.gz'
-calibfilename = '/fact/raw/2012/04/17/20120417_003.drs.fits.gz'
-
-import numpy as np
-import itertools
-
-from ROOT import gSystem
-gSystem.Load("calfits_h.so")
-from ROOT import *
-print "Testing object creation: "
-caltest = CalFits(datafilename,calibfilename)
-npcalevent  = np.empty( caltest.npix * caltest.nroi, np.float64) #.reshape(caltest.npix ,caltest.nroi)
-caltest.SetNpcaldataPtr(npcalevent)
-
-print "Common variables:"
-print "ROI: ", caltest.nroi
-print "#Pix: ", caltest.npix
-print "Number of events: ", caltest.nevents
-print
-
-print "Information per Event:"
-caltest.GetCalEvent()
-print "Event ID: ", caltest.event_id
-print "Trigger type: ", caltest.event_triggertype
-print "Uncalibrated data: ", caltest.event_data
-print "Calibrated data: ", caltest.npcaldata
-print "Board times: ", caltest.event_boardtimes
-print "Trigger offsets: ", caltest.event_offset
-print
-
-print "Examples of other information"
-print "Calibfile ROI: ", caltest.calib_nroi
-print "Column size BaselineMean: ", caltest.calibfile.GetN("BaselineMean")
-print "Datafile ROI: ", caltest.data_nroi
-print "Data: ", caltest.datafile.GetN("Data")
-print "StartCellData: ", caltest.datafile.GetN("StartCellData")
-print "Direct datafile access: ", caltest.datafile.GetN("StartCellData")
-print
-print "Columns of the datafile: "
-caltest.datafile.PrintColumns()
-
-def offsum(x,y):
-    return np.sum(npcalevent[x,y+5:y+15])
-vecoffsum = np.vectorize(offsum) #specifying otypes=[np.float/double] does not improve speed
-
-while caltest.GetCalEvent():
-    if caltest.event_id>30:
-        break
-    npcalevent = npcalevent.reshape((caltest.npix, caltest.nroi))
-    npthr = npcalevent>2.5 #true if above threshold
-    npthr = npthr[:,1:-14] * np.logical_not(npthr[:,:-15]) #only true for the zero crossings, shape (1400,285) [smaller due to necessary integration range]
-#    print [(x,y) for x,y in zip(npthr.nonzero()[0],npthr.nonzero()[1])] #print the coordinates, range 0-1399,0-284
-    
-    integrals = []
-    #Various versions to get the integral, all with approximately the same miserable speed (3 Hz), except for the last one (vectorized function) with ~4.3 Hz
-    #Missing: add deadtime after an integration, remove start & end of the array
-#    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in np.transpose(npthr.nonzero())]
-#    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in zip(npthr.nonzero()[0],npthr.nonzero()[1])]
-#    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in itertools.izip(npthr.nonzero()[0],npthr.nonzero()[1])]
-#    integrals = map((lambda index_a,index_b: np.sum(npcalevent[index_a,index_b+5:index_b+15])),npthr.nonzero()[0],npthr.nonzero()[1])
-    integrals = vecoffsum(npthr.nonzero()[0],npthr.nonzero()[1])
-    
-#    print len(integrals)
-#    for i in range(10):
-#        print i, npcalevent[0,i], integrals[i]
-#    print caltest.event_id, caltest.event_triggertype, caltest.event_caldata[10]
-#    pass
-
-del caltest
Index: fact/tools/pyscripts/examples/CalFitsPerformanceWeave.py
===================================================================
--- fact/tools/pyscripts/examples/CalFitsPerformanceWeave.py	(revision 13503)
+++ 	(revision )
@@ -1,114 +1,0 @@
-#!/usr/bin/python -tt
-# ********************************
-# Test script for the CalFits class
-# 
-# written by Thomas Kraehenbuehl, ETH Zurich
-# tpk@phys.ethz.ch, +41 44 633 3973
-# April 2012
-# ********************************
-
-datafilename = '/fact/raw/2012/04/17/20120417_004.fits.gz'
-calibfilename = '/fact/raw/2012/04/17/20120417_003.drs.fits.gz'
-
-import numpy as np
-from scipy import weave
-from scipy.weave import converters
-
-from ROOT import gSystem
-gSystem.Load("calfits_h.so")
-from ROOT import *
-print "Testing object creation: "
-caltest = CalFits(datafilename,calibfilename)
-npcalevent  = np.empty( caltest.npix * caltest.nroi, np.float64) #.reshape(caltest.npix ,caltest.nroi)
-caltest.SetNpcaldataPtr(npcalevent)
-
-print "Common variables:"
-print "ROI: ", caltest.nroi
-print "#Pix: ", caltest.npix
-print "Number of events: ", caltest.nevents
-print
-
-print "Information per Event:"
-caltest.GetCalEvent()
-print "Event ID: ", caltest.event_id
-print "Trigger type: ", caltest.event_triggertype
-print "Uncalibrated data: ", caltest.event_data
-print "Calibrated data: ", caltest.npcaldata
-print "Board times: ", caltest.event_boardtimes
-print "Trigger offsets: ", caltest.event_offset
-print
-
-print "Examples of other information"
-print "Calibfile ROI: ", caltest.calib_nroi
-print "Column size BaselineMean: ", caltest.calibfile.GetN("BaselineMean")
-print "Datafile ROI: ", caltest.data_nroi
-print "Data: ", caltest.datafile.GetN("Data")
-print "StartCellData: ", caltest.datafile.GetN("StartCellData")
-print "Direct datafile access: ", caltest.datafile.GetN("StartCellData")
-print
-print "Columns of the datafile: "
-caltest.datafile.PrintColumns()
-
-#AND WE HAVE A WINNER: 43 Hz with scipy.weave!
-while caltest.GetCalEvent():
-    c_integrals = np.zeros(40000, np.float64) #Allocate the memory for about 40000 singles
-    if caltest.event_id>300:
-        break
-    
-    cppcode = """
-    //ToDo: get nroi and npix, check singles<40000
-    double slice, lastslice, integral;
-    int singles = 0;
-    double threshold = 2.5;
-    for(int px=0; px<npix; px++) {
-        lastslice = npcalevent(px*nroi);
-        for(int sl=1; sl<nroi-14; sl++) {
-            slice = npcalevent(px*nroi+sl);
-            if((lastslice<threshold)&&(slice>threshold)) {
-                integral = 0;
-                for(int l=5; l<15; l++) {
-                    integral += npcalevent(px*nroi+sl+l);
-                }
-                c_integrals(singles) = integral;
-                ++singles;
-//                std::cout << sl << " ";
-            }
-            lastslice = slice;
-        }
-    }
-//    std::cout << std::endl << singles << std::endl;
-    """
-    
-    #Passing the caltest object to weave is not possible
-    #The int() statement is necessary to add additional data type information to the variable (ie. otherwise some things would work in the C-code, other would not)
-    nroi = int(caltest.nroi)
-    npix = int(caltest.npix)
-    
-    weave.inline(cppcode, ['c_integrals', 'npcalevent','nroi','npix'], type_converters=converters.blitz)
-    
-#    print "CalFitsPerformanceWeave"
-#    for i in range(10):
-#        print i, npcalevent[i], c_integrals[i]
-#    for x in c_integrals:
-#        if x:
-#            print x,
-
-#    #Old attempts using numpy functions
-#    npcalevent = npcalevent.reshape((caltest.npix, caltest.nroi))
-#    npthr = npcalevent>2.5 #true if above threshold
-#    npthr = npthr[:,1:-14] * np.logical_not(npthr[:,:-15]) #only true for the zero crossings, shape (1400,285) [smaller due to necessary integration range]
-##    print [(x,y) for x,y in zip(npthr.nonzero()[0],npthr.nonzero()[1])] #print the coordinates, range 0-1399,0-284
-#    
-#    #Various versions to get the integral, all with approximately the same miserable speed (3 Hz), except for the last one (vectorized function) with ~4.3 Hz
-#    #Missing: add deadtime after an integration, remove start & end of the array
-##    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in np.transpose(npthr.nonzero())]
-##    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in zip(npthr.nonzero()[0],npthr.nonzero()[1])]
-##    integrals = [np.sum(npcalevent[x,y+5:y+15]) for x,y in itertools.izip(npthr.nonzero()[0],npthr.nonzero()[1])]
-##    integrals = map((lambda index_a,index_b: np.sum(npcalevent[index_a,index_b+5:index_b+15])),npthr.nonzero()[0],npthr.nonzero()[1])
-#    integrals = vecoffsum(npthr.nonzero()[0],npthr.nonzero()[1])
-#    print len(integrals)
-
-#    print caltest.event_id, caltest.event_triggertype, caltest.event_caldata[10]
-#    pass
-
-del caltest
Index: fact/tools/pyscripts/examples/CalFitsTest.py
===================================================================
--- fact/tools/pyscripts/examples/CalFitsTest.py	(revision 13503)
+++ 	(revision )
@@ -1,58 +1,0 @@
-#!/usr/bin/python -tt
-# ********************************
-# Test script for the CalFits class
-# 
-# written by Thomas Kraehenbuehl, ETH Zurich
-# tpk@phys.ethz.ch, +41 44 633 3973
-# April 2012
-# ********************************
-
-datafilename = '/fact/raw/2012/04/17/20120417_004.fits.gz'
-calibfilename = '/fact/raw/2012/04/17/20120417_003.drs.fits.gz'
-
-import numpy as np
-
-from ROOT import gSystem
-gSystem.Load("calfits_h.so")
-from ROOT import *
-print "Testing object creation: "
-caltest = CalFits(datafilename,calibfilename)
-npcalevent  = np.empty( caltest.npix * caltest.nroi, np.float64) #.reshape(caltest.npix ,caltest.nroi)
-caltest.SetNpcaldataPtr(npcalevent)
-
-print "Common variables:"
-print "ROI: ", caltest.nroi
-print "#Pix: ", caltest.npix
-print "Number of events: ", caltest.nevents
-print
-
-print "Information per Event:"
-caltest.GetCalEvent()
-print "Calibrated data in numpy array: ", npcalevent
-print "Event ID: ", caltest.event_id
-print "Trigger type: ", caltest.event_triggertype
-print "Uncalibrated data: ", caltest.event_data
-print "Calibrated data: ", caltest.npcaldata
-print "Board times: ", caltest.event_boardtimes
-print "Trigger offsets: ", caltest.event_offset
-print
-
-print "Examples of other information"
-print "Calibfile ROI: ", caltest.calib_nroi
-print "Column size BaselineMean: ", caltest.calibfile.GetN("BaselineMean")
-print "Datafile ROI: ", caltest.data_nroi
-print "Data: ", caltest.datafile.GetN("Data")
-print "StartCellData: ", caltest.datafile.GetN("StartCellData")
-print "Direct datafile access: ", caltest.datafile.GetN("StartCellData")
-print
-print "Columns of the datafile: "
-caltest.datafile.PrintColumns()
-
-#while caltest.GetCalEvent():
-#    if caltest.event_id>10:
-#        break
-#    print caltest.event_id, caltest.event_triggertype, caltest.event_caldata[10]
-#    pass
-#print
-
-del caltest