Update example.py

example.py

-
 import os
 import sys
 import numpy as np
@@ -7,6 +6,24 @@ from PeakOTron import PeakOTron
 from joblib import dump
 import time
 
+
+C_tau = lambda V, V_bd, V_0: (V - V_bd)/V_0
+f_tau = lambda V, V_bd, V_0: -1/np.log((1-np.exp(C_tau(V, V_bd, V_0)*np.exp(-1)))/(1 - np.exp(C_tau(V, V_bd, V_0))))  
+
+V_bd_hmt = 51.570574 + 0.307
+V_0_hmt = 2.906
+
+tau = 21.953 ##SLOW COMPONENT OF SIPM PULSE
+t_0 = 100.0  ## PRE-INTEGRATION TIME
+t_gate = 104.0 ## GATE LENGTH
+bin_0=-100.0  ## SELECT FIRST BIN OF SPECTRUM (CAN BE AUTOMATIC)
+truncate_nsigma0_up = 2.0 ## SCAN SPECTRUM FROM Q < Q_0 - 4 sigma_0
+truncate_nsigma0_do = 2.0 ## EVALUATE SPECTRUM CHI2 IN Q_0 - x*sigma_0  < Q < Q_0 + 2*sigma_0
+prefit_only=False  ## FIT THE WHOLE SPECTRUM
+
+
+
+
 print("--------------------")
 print('EXAMPLE SIPM CALIBRATION RUN')
 print("--------------------")
@@ -16,7 +33,7 @@ out_dict = {}
 files_to_fit = []
 
 ## Find all histograms in directory 
-for root, dirs, files in os.walk("./data/hamamatsu_pcb6/Light"):
+for root, dirs, files in os.walk("./data_paper/hamamatsu_pcb6/Light"):
      
         for file in files:
             
@@ -40,6 +57,9 @@ for i, (file, path) in enumerate(files_to_fit):
 
     V = float(items[2].replace('V', '').replace('p', '.'))
 
+    f_tau_hmt = f_tau(V, V_bd_hmt, V_0_hmt)  
+
+
     print("\n\n")
     print("===============================================================")
     print("FIT {:d} - {:s}".format(i, file))
@@ -51,18 +71,23 @@ for i, (file, path) in enumerate(files_to_fit):
     data = np.loadtxt(path, skiprows=8)
 
     ## Create a PeakOTron Fit Object. 
-    f_data = PeakOTron(verbose=True)
+    f_data = PeakOTron(verbose=False)
 
     ## Perform fit. 
     f_data.Fit(data, 
-          tau=21.953,  #SLOW PULSE COMPONENT TIME CONSTANT (ns)
-          t_gate=104, #GATE LENGTH (ns)
-          t_0 = 64, #INTEGRATION TIME BEFORE GATE (ns)               
-          tau_R=21.953
+          tau=tau,  #SLOW PULSE COMPONENT TIME CONSTANT (ns)
+          t_gate=t_gate, #GATE LENGTH (ns)
+          t_0 = t_0, #INTEGRATION TIME BEFORE GATE (ns)               
+          tau_R=f_tau_hmt*tau,
+          bin_0 = bin_0,
+          truncate_nsigma0_up = truncate_nsigma0_up,
+          truncate_nsigma0_do = truncate_nsigma0_do
+
 
     ) #BINNING RULE "knuth", "freedman", "scott" - use bw= #### to override. it is still required for DCR calculation. 
 
-    f_data.PlotFit(xlabel="ADC", display=False, save_directory="./Results/{0}_fit.png".format(os.path.splitext(file)[0]))
+    f_data.PlotFit(plot_in_bins=True, display=False, save_directory="./Results/{0}_fit.png".format(os.path.splitext(file)[0]))
+