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

@@ -24,11 +24,11 @@ from datetime import datetime
 
 import km3pipe as kp
 
-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. D_ORCA005)')
-parser.add_argument('-o', dest='plot_dir', type=str, nargs=1, required=True,
-                    help='Directory in which the plot is saved')
+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. D_ORCA005)')
+parser.add_argument('-o', dest = 'plot_dir', type = str, nargs = 1, required = True,
+                    help = 'Directory in which the plot is saved')
 
 args = parser.parse_args()
 detid = args.det_id[0]
@@ -40,7 +40,7 @@ def diff(first, second):
 
 db = kp.db.DBManager()
 sds = kp.db.StreamDS()
-table=db.run_table(detid)
+table = db.run_table(detid)
 
 
 
@@ -54,7 +54,7 @@ TIT = 600 # Time Interval between Trains of acoustic pulses)
 SSW = 160 # Signal Security Window (Window size with signal)
 
 check = True
-while check == True:
+while check:
     
     minrun = table["RUN"][len(table["RUN"]) - 1]	
     ind, = np.where((table["RUN"] == minrun))
@@ -62,7 +62,7 @@ while check == True:
     mintime = mintime1.values
     maxrun = table["RUN"][len(table["RUN"]) - 1]
     now = time.time()
-    if (now-mintime/1000) < TIT:
+    if (now - mintime/1000) < TIT:
         minrun = table["RUN"][len(table["RUN"]) - 1] - 1 
     print(now)
 
@@ -73,7 +73,7 @@ while check == True:
             for dom in DOMS:
                 try:
                     domID = db.doms.via_omkey((du, dom), detid).dom_id
-                    toas_all = sds.toashort(detid=detid, minrun=minrun, maxrun=maxrun, domid=domID, emitterid=ab) 
+                    toas_all = sds.toashort(detid = detid, minrun = minrun, maxrun = maxrun, domid = domID, emitterid = ab) 
                 
                     QF_abdom = toas_all["QUALITYFACTOR"]
                     UTB_abdom = toas_all["UNIXTIMEBASE"]
@@ -124,7 +124,7 @@ while check == True:
                     
                     if len(QF_second) > 11:
                         QF_second = np.array(QF_second)
-                        QF_third = [k for k in QF_second if (np.where(QF_second == k)[0][0]<11)]
+                        QF_third = [k for k in QF_second if (np.where(QF_second == k)[0][0] < 11)]
                     else:
                         QF_third = QF_second
                     
@@ -139,11 +139,11 @@ while check == True:
                         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()
-                    D=[]
+                    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)):
                            D.append(g)
-                    for d in sorted(D, reverse=True):
+                    for d in sorted(D, reverse = True):
                         del QF_fourth[d]  
                     QF_fifth = QF_fourth
                     QF_OK = QF_fifth
@@ -160,8 +160,7 @@ while check == True:
                         N_Pulses_Indicator_DU.append(-1.5)
 
                         
-                except:
-                    stop = []
+                except (TypeError, ValueError): # TypeError if no data found for a certain piezo, ValueError if there are zero data for a certain piezo
                     N_Pulses_Indicator_DU.append(-1.5)
                     
         N_Pulses_Indicator.append(N_Pulses_Indicator_DU)
@@ -172,23 +171,24 @@ while check == True:
     
     fig = plt.figure()
     ax = fig.add_subplot(111)
-    dom = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ,11, 12, 13, 14, 15, 16, 17, 18]
-    l = len(dom)
-    du1AB1 = 0.9*np.ones(l)
-    du1AB2 = 1*np.ones(l)
-    du1AB3 = 1.1*np.ones(l)
-    du2AB1 = 1.9*np.ones(l)
-    du2AB2 = 2*np.ones(l)
-    du2AB3 = 2.1*np.ones(l)
-    du3AB1 = 2.9*np.ones(l)
-    du3AB2 = 3*np.ones(l)
-    du3AB3 = 3.1*np.ones(l)
-    du4AB1 = 3.9*np.ones(l)
-    du4AB2 = 4*np.ones(l)
-    du4AB3 = 4.1*np.ones(l)
-    du5AB1 = 4.9*np.ones(l)
-    du5AB2 = 5*np.ones(l)
-    du5AB3 = 5.1*np.ones(l)
+    N_doms = 18
+    doms = range(N_doms + 1)
+    L = len(doms)
+    du1AB1 = 0.9*np.ones(L)
+    du1AB2 = 1*np.ones(L)
+    du1AB3 = 1.1*np.ones(L)
+    du2AB1 = 1.9*np.ones(L)
+    du2AB2 = 2*np.ones(L)
+    du2AB3 = 2.1*np.ones(L)
+    du3AB1 = 2.9*np.ones(L)
+    du3AB2 = 3*np.ones(L)
+    du3AB3 = 3.1*np.ones(L)
+    du4AB1 = 3.9*np.ones(L)
+    du4AB2 = 4*np.ones(L)
+    du4AB3 = 4.1*np.ones(L)
+    du5AB1 = 4.9*np.ones(L)
+    du5AB2 = 5*np.ones(L)
+    du5AB3 = 5.1*np.ones(L)
     
     
     
@@ -199,47 +199,47 @@ while check == True:
     DU5 = np.array(N_Pulses_Indicator[4])
     
     ind = np.where(DU2 < 1000)
-    iAB1 = np.where(ind[0] < l)
-    iAB2_up = np.where(ind[0] > (l - 1))
-    iAB2_down = np.where(ind[0] < 2*l)
+    iAB1 = np.where(ind[0] < L)
+    iAB2_up = np.where(ind[0] > (L - 1))
+    iAB2_down = np.where(ind[0] < 2*L)
     iAB2 = np.intersect1d(iAB2_up, iAB2_down)
-    iAB3 = np.where(ind[0] > (2*l - 1))
+    iAB3 = np.where(ind[0] > (2*L - 1))
     
     colorsList = [(0, 0, 0),(1, 0.3, 0),(1, 1, 0),(0.2, 0.9, 0)]
     CustomCmap = matplotlib.colors.ListedColormap(colorsList)
     bounds=[-2, -1, 0, 1, 2]
     norma = colors.BoundaryNorm(bounds, CustomCmap.N)
-    color = ax.scatter(du1AB1, dom, s = 20, c = DU1[iAB1], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du1AB2, dom, s = 20, c = DU1[iAB2], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du1AB3, dom, s = 20, c = DU1[iAB3], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du2AB1, dom, s = 20, c = DU2[iAB1], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du2AB2, dom, s = 20, c = DU2[iAB2], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du2AB3, dom, s = 20, c = DU2[iAB3], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du3AB1, dom, s = 20, c = DU3[iAB1], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du3AB2, dom, s = 20, c = DU3[iAB2], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du3AB3, dom, s = 20, c = DU3[iAB3], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du4AB1, dom, s = 20, c = DU4[iAB1], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du4AB2, dom, s = 20, c = DU4[iAB2], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du4AB3, dom, s = 20, c = DU4[iAB3], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du5AB1, dom, s = 20, c = DU5[iAB1], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du5AB2, dom, s = 20, c = DU5[iAB2], norm=norma, marker = 's', cmap = CustomCmap);
-    color = ax.scatter(du5AB3, dom, s = 20, c = DU5[iAB3], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du1AB1, doms, s = 20, c = DU1[iAB1], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du1AB2, doms, s = 20, c = DU1[iAB2], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du1AB3, doms, s = 20, c = DU1[iAB3], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du2AB1, doms, s = 20, c = DU2[iAB1], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du2AB2, doms, s = 20, c = DU2[iAB2], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du2AB3, doms, s = 20, c = DU2[iAB3], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du3AB1, doms, s = 20, c = DU3[iAB1], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du3AB2, doms, s = 20, c = DU3[iAB2], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du3AB3, doms, s = 20, c = DU3[iAB3], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du4AB1, doms, s = 20, c = DU4[iAB1], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du4AB2, doms, s = 20, c = DU4[iAB2], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du4AB3, doms, s = 20, c = DU4[iAB3], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du5AB1, doms, s = 20, c = DU5[iAB1], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du5AB2, doms, s = 20, c = DU5[iAB2], norm=norma, marker = 's', cmap = CustomCmap);
+    color = ax.scatter(du5AB3, doms, s = 20, c = DU5[iAB3], norm=norma, marker = 's', cmap = CustomCmap);
     
     
     cbar = plt.colorbar(color)
     cbar.ax.get_yaxis().set_ticks([])
     for j, lab in enumerate(['$0. pings$', '$1-3 pings$', '$4-7 pings$', '$>7. pings$']):
-        cbar.ax.text(3.5, (2 * j + 1)/8.0, lab, ha='center', va='center')
+        cbar.ax.text(3.5, (2 * j + 1)/8.0, lab, ha = 'center', va = 'center')
     cbar.ax.get_yaxis().labelpad = 18
     
-    matplotlib.pyplot.xticks(np.arange(1, 6, step=1))
-    matplotlib.pyplot.yticks(np.arange(0, 19, step=1))
-    matplotlib.pyplot.grid(color='k', linestyle='-', linewidth=0.2)
-    ax.set_xlabel('DUs', fontsize=18)
-    ax.set_ylabel('Floors', fontsize=18)
-    ts = now+3600
+    matplotlib.pyplot.xticks(np.arange(1, 6, step = 1))
+    matplotlib.pyplot.yticks(np.arange(0, 19, step = 1))
+    matplotlib.pyplot.grid(color='k', linestyle='-', linewidth = 0.2)
+    ax.set_xlabel('DUs', fontsize = 18)
+    ax.set_ylabel('Floors', fontsize = 18)
+    ts = now + 3600
     DATE = datetime.utcfromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S')
-    ax.set_title(r' %.16s Detection of the pings emitted by autonomous beacons' %DATE, fontsize=10)
+    ax.set_title(r' %.16s Detection of the pings emitted by autonomous beacons' %DATE, fontsize = 10)
 #    plt.show()                   
     
     
@@ -252,32 +252,10 @@ while check == True:
     print(time.time())
                 
                
-    check=False
+    check = False
     check_time=time.time() - now
     print(check_time)
     
     
     time.sleep(abs(TIT - check_time))
-    check=True               
-                
-
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
-                
+    check = True