Add acoustics monitoring

I do not know if I'm doing the right thing. I tried to upload the script "acoustic.py" and I am asked to send a merge request. Is this the correct procedure? @tgal Thank you

scripts/acoustics.py

 #!/usr/bin/env python
 # coding=utf-8
+"""
+Online Acoustic Monitoring
+
+Usage:
+    acoustics.py [options]
+    acoustics.py (-h | --help)
+
+Options:
+    -d DET_ID       Detector ID 
+    -o PLOT_DIR     The directory to save the plot 
+    -h --help       Show this screen.
+
+"""
 import numpy as np
 import matplotlib.pyplot as plt
 import matplotlib
@@ -12,7 +25,7 @@ import argparse
 
 parser = argparse.ArgumentParser(description='Online_monitoring')
 parser.add_argument('-d', dest='det_id', type=str, nargs=1, required=True,
-                    help='The detector ID (e.g. D0ARCA001)')
+                    help='The detector ID (e.g. D_ORCA005)')
 parser.add_argument('-o', dest='plot_dir', type=str, nargs=1, required=True,
                     help='Directory in which the plot is saved')
 
@@ -24,22 +37,20 @@ def diff(first, second):
     second = set(second)
     return [item for item in first if item not in second]
 
-#detid='D_ORCA005'
-#print(time.time())
-
 db = kp.db.DBManager()
 sds = kp.db.StreamDS()
 table=db.run_table(detid)
 
 
 
-AB=[12,14,16] # Acoustic Beacons
-DOM=[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18] # DOMs
-DU=[1,2,3,4,5] # DUs
+ACOUSTIC_BEACONS = [12, 14, 16]
+N_DOMS = 18
+DOMS = range(N_DOMS + 1)
+N_DUS = 5
+DUS = range(1, N_DUS + 1)
 
-#AB=[16] # Acoustic Beacons
-#DOM=[7] #
-#DU=[3] # DUs
+TIT=600 # Time Interval between Trains of acoustic pulses)
+SSW=160 # Signal Security Window (Window size with signal)
 
 check=True
 while check==True:
@@ -50,24 +61,24 @@ while check==True:
     mintime=mintime1.values
     maxrun=table["RUN"][len(table["RUN"])-1]
     now=time.time()
-    if (now-mintime/1000)<600:
+    if (now-mintime/1000)<TIT:
         minrun=table["RUN"][len(table["RUN"])-1]-1 
     print(now)
 
-    COL=[]
-    for i in DU:
-        DUx=[]
-        for j in AB:
-            for k in DOM:
+    N_Pulses_Indicator=[] # Matrix indicating how many pulses each piezo reveals
+    for du in DUS:
+        N_Pulses_Indicator_DU=[] # Array indicating for each DU how many pulses each piezo reveals.
+        for ab in ACOUSTIC_BEACONS:
+            for dom in DOMS:
                 try:
-                    macaddress = db.doms.via_omkey((i,k), detid).dom_id
-                    toas_all = sds.toashort(detid=detid, minrun=minrun, maxrun=maxrun, domid=macaddress, emitterid=j) # Prendere i dati basandosi sul tempo e non sul run????
+                    domID = db.doms.via_omkey((du,dom), detid).dom_id
+                    toas_all = sds.toashort(detid=detid, minrun=minrun, maxrun=maxrun, domid=domID, emitterid=ab) 
                 
                     QF_abdom=toas_all["QUALITYFACTOR"]
                     UTB_abdom=toas_all["UNIXTIMEBASE"]
                     TOAS_abdom=toas_all["TOA_S"]
                     UTB_abdom=UTB_abdom.values
-                    up=np.where(UTB_abdom>(now-600))
+                    up=np.where(UTB_abdom>(now-TIT))
                     down=np.where(UTB_abdom<(now))
                     intr=np.intersect1d(up,down)
                     UTB_abdom=UTB_abdom[intr]
@@ -77,8 +88,8 @@ while check==True:
                     QFlist.sort(reverse=True)
                     QF_max=max(QF_abdom)
                     QF_max_index=np.where(QF_abdom==QF_max)
-                    UTB_signal_min=UTB_abdom[QF_max_index]-80
-                    UTB_signal_max=UTB_abdom[QF_max_index]+80
+                    UTB_signal_min=UTB_abdom[QF_max_index]-SSW/2
+                    UTB_signal_max=UTB_abdom[QF_max_index]+SSW/2
                     temp1=np.where(UTB_abdom>(UTB_signal_min[0]))
                     temp2=np.where(UTB_abdom<(UTB_signal_max[0]))
                     inter=np.intersect1d(temp1,temp2)
@@ -95,11 +106,12 @@ while check==True:
                     noise_threshold=max(NOISE) 
                     
                     # First filter: 22 greatest
+                    Security_Number=22 # To be sure to take all the pulses
                         
                     SIGNAL=SIGNAL.tolist()
                     SIGNAL_OLD=np.array(SIGNAL)
                     SIGNAL.sort(reverse=True)
-                    QF_first=SIGNAL[0:22]
+                    QF_first=SIGNAL[0:Security_Number]
                     
                     # Second filter: delete duplicates
                     
@@ -121,13 +133,11 @@ while check==True:
                     
                     # Fifth filter: Check if the clicks are interspersed in the right way
                     
-    #                    QF_fifth=[k for k in QF_fourth if (abs(k-max(QF_fourth))<abs(k-noise_threshold))]
                     Q=[]
                     for q in np.arange(len(QF_fourth)):
                         Q.append(np.where(SIGNAL_OLD==QF_fourth[q])[0][0])
                     UTB_fourth=np.array(UTB_SIGNAL.tolist())[Q]
                     UTB_fourth_l=UTB_fourth.tolist()
-    #                    UTB_fourth_l.sort()
                     D=[]
                     for g in np.arange(len(UTB_fourth_l)):
                         if ((np.mod((UTB_fourth_l[g]-UTB_fourth_l[0]),5)>0.5 and np.mod((UTB_fourth_l[g]-UTB_fourth_l[0]),5)<4.5) or (np.mod((UTB_fourth_l[g]-UTB_fourth_l[0]),5)>5)):
@@ -137,24 +147,24 @@ while check==True:
                     QF_fifth=QF_fourth
                     QF_OK=QF_fifth
     #                print(QF_OK)
-                    NUM=len(QF_OK)
+                    NUM=len(QF_OK) # Number of pulses
                     print(NUM)
                     
                     if (NUM>7):
-                        DUx.append(1.5)
+                        N_Pulses_Indicator_DU.append(1.5)
                     elif (NUM<8 and NUM>3):
-                        DUx.append(0.5)
+                        N_Pulses_Indicator_DU.append(0.5)
                     elif (NUM<4 and NUM>0):
-                        DUx.append(-0.5)
+                        N_Pulses_Indicator_DU.append(-0.5)
                     elif (NUM==0):
-                        DUx.append(-1.5)
+                        N_Pulses_Indicator_DU.append(-1.5)
 
                         
                 except:
                     stop=[]
-                    DUx.append(-1.5)
+                    N_Pulses_Indicator_DU.append(-1.5)
                     
-        COL.append(DUx)
+        N_Pulses_Indicator.append(N_Pulses_Indicator_DU)
         
     
     
@@ -182,11 +192,11 @@ while check==True:
     
     
     
-    DU1=np.array(COL[0])
-    DU2=np.array(COL[1])
-    DU3=np.array(COL[2])
-    DU4=np.array(COL[3])
-    DU5=np.array(COL[4])
+    DU1=np.array(N_Pulses_Indicator[0])
+    DU2=np.array(N_Pulses_Indicator[1])
+    DU3=np.array(N_Pulses_Indicator[2])
+    DU4=np.array(N_Pulses_Indicator[3])
+    DU5=np.array(N_Pulses_Indicator[4])
     
     ind=np.where(DU2<1000)
     iAB1=np.where(ind[0]<l)
@@ -247,7 +257,7 @@ while check==True:
     print(check_time)
     
     
-    time.sleep(abs(600-check_time))
+    time.sleep(abs(TIT-check_time))
     check=True