Index: fact/tools/pyscripts/sandbox/dneise/spikes/ananew.py
===================================================================
--- fact/tools/pyscripts/sandbox/dneise/spikes/ananew.py	(revision 14180)
+++ fact/tools/pyscripts/sandbox/dneise/spikes/ananew.py	(revision 14180)
@@ -0,0 +1,154 @@
+#!/usr/bin/python -tt
+
+from pyfact import RawData
+from drs_spikes import DRSSpikes
+import sys
+import numpy as np
+from ctypes import *
+import os
+import os.path as path
+from ROOT import TFile, TCanvas, TH2F, TTree, TStyle, TObject
+import time
+
+dfn = sys.argv[1]
+cfn = sys.argv[2]
+run = RawData( dfn, cfn) 
+
+
+file_base_name = path.splitext(path.basename(dfn))[0]
+root_filename = '/home_nfs/isdc/neise/' + file_base_name + '_' + time.strftime('%Y%m%d_%H%M%S') +'_spikeana.root'
+
+rootfile = TFile(root_filename, "RECREATE")
+
+fbn = path.splitext(file_base_name)[0]
+fbn = fbn[0:8]+fbn[9:12]
+
+
+baum = TTree('spiketree', 'spike ana tree')
+
+# prepare some vars for the tree
+chid               =  c_int(0)
+startcell          =  c_int(0)
+number_of_singles  =  c_int(0)
+position_of_spikes_in_logical_pipeline   =  np.zeros(100, np.int32)
+position_of_spikes_in_physical_pipeline  =  np.zeros(100, np.int32)
+time_to_previous   =  c_int(0)
+event_id           =  c_int(0)
+file_id            =  c_long(long(fbn))
+
+baum.Branch('file',file_id,'file/L')
+baum.Branch('event',event_id,'event/I')
+baum.Branch('chid',chid,'chid/I')
+baum.Branch('sc',startcell,'sc/I')
+baum.Branch('n',number_of_singles,'n/I')
+baum.Branch('logpos',position_of_spikes_in_logical_pipeline,'logpos[n]/I')
+baum.Branch('physpos',position_of_spikes_in_physical_pipeline,'physpos[n]/I')
+baum.Branch('time',time_to_previous,'time/I')
+
+
+def spikecallback(candidates, singles, doubles, data, ind):
+    if len(singles) >0 :
+        for s in singles:
+            s = np.unravel_index(s, data.shape)
+            hs.Fill( s[0], s[1])
+    if len(doubles) >0 :
+        for d in doubles:
+            d = np.unravel_index(d, data.shape)
+            hd.Fill( d[0], d[1])
+            
+            
+    
+despike = DRSSpikes(user_action = spikecallback)
+
+def mars_spikes( data ):
+    """
+    should search for spikes, just as it is implemented in 
+    mcore/DrsCalib.h in DrsCalib::RemoveSpikes
+    static void RemoveSpikes(float *vec, uint32_t roi)
+    {
+        if (roi<4)
+            return;
+
+        for (size_t ch=0; ch<1440; ch++)
+        {
+            float *p = vec + ch*roi;
+
+            for (size_t i=1; i<roi-2; i++)
+            {
+                if (p[i]-p[i-1]>25 && p[i]-p[i+1]>25)
+                {
+                    p[i] = (p[i-1]+p[i+1])/2;
+                }
+
+                if (p[i]-p[i-1]>22 && fabs(p[i]-p[i+1])<4 && p[i+1]-p[i+2]>22)
+                {
+                    p[i] = (p[i-1]+p[i+2])/2;
+                    p[i+1] = p[i];
+                }
+            }
+        }
+    }    
+        
+    """
+
+    #: list, conaining the (chid,slice) tuple of the single spike positions
+    singles = []
+    #: list, conaining the (chid,slice) tuple of the 1st double spike positions
+    doubles = []
+    
+    for chid, pdata in enumerate(data):
+        single_cand = np.where( np.diff(pdata[:-1]) > 25)[0]
+        for cand in single_cand:
+            if -np.diff(pdata[1:])[cand] > 25:
+                singles.append( (chid, cand) )
+        
+        double_cand = np.where( np.diff(pdata[:-1]) > 22 )[0]
+        for cand in double_cand:
+            if cand+1 < len(np.diff(pdata[1:])):
+                if abs(-np.diff(pdata[1:])[cand])<4 and -np.diff(pdata[1:])[cand+1] > 22:
+                    doubles.append( (chid, cand) )
+                
+    
+    return singles, doubles        
+
+
+
+
+
+event = run.next()
+board_time = event['board_times'].copy()
+
+for event in run:
+    event_id.value = event['event_id']
+
+
+    data = event['data']
+    singles, doubles = mars_spikes(data)
+    sc = event['start_cells']
+    bt_old = board_time.copy()
+    board_time = event['board_times'].copy()
+  #  print fbn, event['event_id'] 
+
+    ss = []
+    for i in range(1440):
+        ss.append([])
+    for s in singles:
+        ss[s[0]].append(s[1])
+        
+    for pixel_id,pixel in enumerate(ss):
+        if len(pixel) >0 :
+            chid.value  = pixel_id
+            startcell.value = sc[ chid.value ]
+            number_of_singles.value = len(pixel)
+            time_to_previous.value = board_time[pixel_id/36]-bt_old[pixel_id/36]
+            for num,s in enumerate(pixel):
+                log = s
+                phys  = (startcell.value+log)%1024
+                position_of_spikes_in_logical_pipeline[num] = log
+                position_of_spikes_in_physical_pipeline[num] = phys
+            baum.Fill()
+
+
+baum.Write()
+
+rootfile.Close()