Index: fact/tools/pyscripts/tools/cleaning/area_vs_size.py
===================================================================
--- fact/tools/pyscripts/tools/cleaning/area_vs_size.py	(revision 13102)
+++ fact/tools/pyscripts/tools/cleaning/area_vs_size.py	(revision 13102)
@@ -0,0 +1,92 @@
+#!/usr/bin/python -i
+#
+# Dominik Neise
+#
+# cleaning a small step towards the truth
+from pyfact_rename import *
+import os.path
+import matplotlib.pyplot as plt
+import numpy as np
+from fir_filter import *
+from extractor import *
+from drs_spikes import *
+from plotters import *
+import time as t
+from cleaners import AmplitudeCleaner
+confirm_next_step = False# this is for user interaction
+
+data_file_name = '/media/daten_platte/FACT/data/20120229_144.fits.gz'
+calib_file_name = '/media/daten_platte/FACT/data/20120229_132.drs.fits.gz'
+if not os.path.isfile(data_file_name):
+    print 'not able to find file:', data_file_name
+    sys.exit(-1)
+if not os.path.isfile(calib_file_name ):
+    print 'not able to find file:', calib_file_name 
+    sys.exit(-1)
+
+run = RawData(data_file_name, calib_file_name)
+despike = DRSSpikes()
+smooth = SlidingAverage(8)
+extract = GlobalMaxFinder(40,200)
+cleaner = AmplitudeCleaner(45,18)
+
+#plotA = CamPlotter('amplitudes')
+#plotT = CamPlotter('times')
+#plotCA = CamPlotter('cleaned amplitudes')
+
+#plotArea = HistPlotter('area', 1440, (0,1440) )
+#plotSize = HistPlotter('size', 1000, (0,10000) )
+
+
+areas = []
+sizes = []
+for data,startcell,tt in run:
+    if tt==4:
+        data = despike(data)
+        data = smooth(data)
+        amplitude, time_of_max = extract(data)
+        clean_mask = cleaner(amplitude)
+        #plotA.name='amplitudes EvtID:' + str(run.event_id.value) + ' TT:' + str(tt)
+        #plotA(amplitude)
+        #plotT(time_of_max)
+        #plotCA(data=amplitude, mask=clean_mask)
+        
+        survivors = np.where( clean_mask)[0]
+        size = 0
+        for pixel in survivors:
+            size += amplitude[pixel]
+        
+        if len(survivors) > 0:
+            areas.append( len(survivors) )
+            sizes.append( size )
+        
+        
+        #plotArea(areas, 'areas of ' + str(run.event_id.value) + 'events')
+        #plotSize(sizes, 'sizes of ' + str(run.event_id.value) + 'events')
+        
+        if confirm_next_step:
+            user_input = raw_input("'q'-quit, 'r'-run, anything else goes one step")
+            number=None
+            try:
+                number=int(user_input)
+            except:
+                number=None
+            if user_input.find('q') != -1:
+                sys.exit(0)
+            elif user_input.find('r') != -1:
+                confirm_next_step = False
+            elif number!=None:
+                run += number
+
+
+plt.ion()
+myfig = plt.figure()
+myn = myfig.number
+logsize = np.log10(np.array(sizes))
+areas = np.array(areas)
+
+plt.figure(myn)
+plt.title('area vs. log10(size) of '+ str(run.event_id.value) + 'events')
+plt.xlabel('log10(size/1mV)')
+plt.ylabel('area [#pixel]')
+plt.plot( logsize,areas, '.')