TDCRPy 0.0.1__py3-none-any.whl

Code/TDCR_model_lib.py

@@ -0,0 +1,1781 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Jan 23 16:04:46 2023
+
+Library of function of the TDCRpy code
+
+@author: Romain Coulon, Jialin Hu
+Bureau International des Poids et Mesures
+"""
+
+### IMPORT Python Module
+import urllib.request as rq
+import numpy as np
+from numpy.core.multiarray import where
+import zipfile as zf
+# import statsmodels.api as sm
+import matplotlib.pyplot as plt
+import time
+import re
+absolutePath = False
+
+
+def TicTocGenerator():
+    """
+    Generator that returns time differences
+    """
+    ti = 0           # initial time
+    tf = time.time() # final time
+    while True:
+        ti = tf
+        tf = time.time()
+        yield tf-ti # returns the time difference
+
+TicToc = TicTocGenerator() # create an instance of the TicTocGen generator
+
+# This will be the main function through which we define both tic() and toc()
+def toc(tempBool=True):
+    """
+    Prints the time difference yielded by generator instance TicToc
+    """
+    
+    tempTimeInterval = next(TicToc)
+    if tempBool:
+        print( "Elapsed time: %f seconds.\n" %tempTimeInterval )
+
+def tic():
+    """
+    Records a time in TicToc, marks the beginning of a time interval
+    """
+    toc(False)
+
+def normalise(p_x):
+    p_array = np.array(p_x)
+    if len(p_x)>1:
+        p_somme = sum(p_array)
+        if p_somme>0.0:
+            p_array = p_array/p_somme
+    else:
+        p_somme = p_x[0]
+        p_array = p_array/p_somme
+    p = list(p_array)
+    return p
+#print(normalise([1, 0.9974641, 0]))
+
+def sampling(p_x):
+    """
+    This function aims to sample in a pdf or a pmf
+
+    Parameters
+    ----------
+    p_x : float vector
+        Probability Density (or mass) Function (PDF or PMF) of the random variable x.
+
+
+    Returns
+    -------
+    i : integer
+        index in x pointing the sampled value of the random variable X.
+    """
+
+    cf = np.cumsum(p_x) # Cummulative Density (or mass) Function (CDF or CMF)
+    trial = float(np.random.rand(1)) # trial ~ U(0,1)
+    
+    for i, p in enumerate(cf):
+        if p> trial: break
+    return i
+
+
+def readPenNuc(rad):
+    """
+    This function reads the PenNuc files published in the DDEP web page
+    http://www.lnhb.fr/donnees-nucleaires/donnees-nucleaires-tableau/
+    
+    Parameters
+    ----------
+    rad : string
+        Indentifier of the radionuclide (e.g. Na-22).
+
+    Returns
+    -------
+    out : list
+        list of elements in list describing the decay of the radionuclide with,
+        *particle* is the list of particle of the decay branches 
+        *p_branch* is the list of probabilty of the decay branches
+        *e_branch* is the list of energy of the decay branches
+        *LevelDaughter* is the list of energy levels of the daughter nucleus following the decay branch
+        *levelNumber* is the list of number of the energy level of the daughter nucleus following the decay branch
+        *prob* is the list of probabilty of isomeric transitions
+        *levelEnergy* is the energy levels of the isomeric transitions
+        *transitionType* is the type of isomeric transitions
+        *e_trans* is the energy of the isomeric transitions
+        *next_level* is the possible next energy level following a given isomeric transtion 
+        *Q_value_vec[dd]* is the Q-value of the decay when decaying to the daughter of index dd
+        *Daughter_vec[dd]* is the vecteur of daugher nuclei
+        *Pdaughter_vec[dd]* is the probability of daughter nuclei
+    """
+    
+    url = "http://www.lnhb.fr/nuclides/"+rad+".PenNuc.txt"
+    file = rq.urlopen(url)
+    
+    # Format the data 
+    decayData = []
+    for line in file:
+      decayData.append(line.decode("utf-8"))
+      if "NDA " in decayData[-1]:    decayData[-1] = decayData[-1].replace("NDA ", "NDA; ") # number of daughter
+      if "DAU " in decayData[-1]:    decayData[-1] = decayData[-1].replace("DAU ", "DAU; ") # daughter
+      if "DDE " in decayData[-1]:    decayData[-1] = decayData[-1].replace("DDE ", "DDE; ") # daughter description : probability of disintegration to NDA, uncertainty, number of excited levels of NDA; number of branche to NDA
+      if "Q " in decayData[-1]:      decayData[-1] = decayData[-1].replace("Q ", "Q; ")     # total energy of the branch, uncertainty 
+      if "ALP " in decayData[-1]:    decayData[-1] = decayData[-1].replace("ALP ", "ALP; ") # type of the disintegration = alpha
+      if "CK " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CK ", "CK; ") # type of the disintegration = Electron Capture K shell
+      if "CL " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CL ", "CL; ") # type of the disintegration = Electron Capture L shell 1
+      if "CL1 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CL1 ", "CL1; ") # type of the disintegration = Electron Capture L shell 1
+      if "CL2 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CL2 ", "CL2; ") # type of the disintegration = Electron Capture L shell 2
+      if "CM " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CM ", "CM; ") # type of the disintegration = Electron Capture M shell
+      if "CN " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CN ", "CN; ") # type of the disintegration = Electron Capture N shell
+      if "BEM " in decayData[-1]:    decayData[-1] = decayData[-1].replace("BEM ", "BEM; ") # type disintegration-beta- :branching ratio, uncertainty, level fed in daughter, energy, uncertainty,prohibition factor for beta emission
+      if "BEP " in decayData[-1]:    decayData[-1] = decayData[-1].replace("BEP ", "BEP; ") # type disintegration-beta+ :branching ratio, uncertainty, level fed in daughter, energy, uncertainty,prohibition factor for beta emission
+      if "LED " in decayData[-1]:    decayData[-1] = decayData[-1].replace("LED ", "LED; ") # level description:energy of level,uncertainty, number of transitions that depopulate this level,level time,uncertainty,level number
+      if "GA " in decayData[-1]:     decayData[-1] = decayData[-1].replace("GA ", "GA; ")   # type transition: gamma
+      if "EK " in decayData[-1]:     decayData[-1] = decayData[-1].replace("EK ", "EK; ")   # type transition: internal conversion -- electron K
+      if "EL1 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("EL1 ", "EL1; ") # type transition: internal conversion -- electron L1
+      if "EL2 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("EL2 ", "EL2; ") # type transition: internal conversion -- electron L2
+      if "EL3 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("EL3 ", "EL3; ") # type transition: internal conversion -- electron L3
+      if "EM " in decayData[-1]:     decayData[-1] = decayData[-1].replace("EM ", "EM; ")   # type transition: internal conversion -- electron M
+      if "EN " in decayData[-1]:     decayData[-1] = decayData[-1].replace("EN ", "EN; ")   # type transition: internal conversion -- electron N
+      if "COM" in decayData[-1]:     decayData[-1] = decayData[-1].replace("COM ", "COM; ")   # commentaire
+      decayData[-1]=decayData[-1].split(";")
+      if "\r\n" in decayData[-1][-1]:  decayData[-1][-1] = decayData[-1][-1].replace("\r\n", " ")
+    
+   
+      
+    """
+    LOOP IN NDAUGH (Daughters)
+    """
+    Daughter_vec = []; Pdaughter_vec = []; Q_value_vec = []
+    for d in decayData:
+      if d[0] == "NDA": Ndaughter = int(d[1])   # Read the number of daughter
+      if d[0] == "DAU" :
+          d[1] = d[1].replace(" ","")
+          Daughter_vec.append(d[1])        # Read the daughter
+      if d[0] == "DDE": Pdaughter_vec.append(float(d[1])) # Read the probability of disintegration to daughter
+      if d[0] == "Q":   Q_value_vec.append(float(d[1]))   # Read the Q-value
+    
+    out = []
+    for dd in range(Ndaughter):
+        
+        # index_Daughter = sampling(np.asarray(Pdaughter_vec)/sum(np.asarray(Pdaughter_vec)))
+        # Daughter = Daughter_vec[index_Daughter]
+        # Pdaughter =  Pdaughter_vec[index_Daughter]
+        # Q_value = Q_value_vec[index_Daughter]    
+         
+        
+        """
+        LOOP IN NBRANCH (Branches of each daughter)
+        """
+        # Probablity vector of the decay branch
+        particle=[]; LevelDaughter = []; p_branch = []; u_p_branch = []; e_branch = []; u_e_branch = []
+        daughterFlag = True
+        countBranch = 0
+        for d in decayData:
+            if d[0] == "DAU" and d[1] == Daughter_vec[dd]:
+                daughterFlag = True
+            if d[0] == "DAU" and d[1] != Daughter_vec[dd]:
+                daughterFlag = False
+            
+            if daughterFlag:
+                # particle_i = []; p_branch_i=[]; u_p_branch_i=[];  e_branch_i=[];   u_e_branch_i=[];  LevelDaughter_i=[]
+                if d[0] =="COM":
+                    if "Branch" in d[1] or "Level" in d[1]:
+                        print(d[1])
+                        if countBranch % 2 == 1:
+                            p_branch.append(p_branch_i); u_p_branch.append(u_p_branch_i); # Branching ratio of the decay branch
+                            e_branch.append(e_branch_i); u_e_branch.append(u_e_branch_i); # Energy of the decay branch (kinetic energy of the particle)
+                            LevelDaughter.append(LevelDaughter_i); particle.append(particle_i)
+                            
+                            particle_i = []; p_branch_i=[]; u_p_branch_i=[];  e_branch_i=[];   u_e_branch_i=[];  LevelDaughter_i=[]
+                        else:
+                            particle_i = []; p_branch_i=[]; u_p_branch_i=[];  e_branch_i=[];   u_e_branch_i=[];  LevelDaughter_i=[]
+                    
+                    
+                        countBranch += 1    
+                    # p_branch=
+                
+                
+                if d[0] == "ALP" or d[0] == "BEM" or d[0] == "BEP" or d[0] == "CK" or d[0] == "CL" or d[0] == "CL1" or d[0] == "CL2" or d[0] == "CM" or d[0] == "CN":                         # Read information on the decay branch
+                    if d[0] == "ALP": particle_i.append("alpha")
+                    if d[0] == "BEP": particle_i.append("beta+")
+                    if d[0] == "BEM": particle_i.append("beta")
+                    if d[0] == "CK": particle_i.append("Atom_K")
+                    if d[0] == "CL": particle_i.append("Atom_L")
+                    if d[0] == "CL1": particle_i.append("Atom_L1")
+                    if d[0] == "CL2": particle_i.append("Atom_L2")
+                    if d[0] == "CM": particle_i.append("Atom_M")
+                    if d[0] == "CN": particle_i.append("Atom_N")
+                    if d[2] == "  ": d[2]=0
+            
+                    p_branch_i.append(float(d[1])); u_p_branch_i.append(float(d[2])); # Branching ratio of the decay branch
+                    e_branch_i.append(float(d[4])); u_e_branch_i.append(float(d[5])); # Energy of the decay branch (kinetic energy of the particle)
+                    LevelDaughter_i.append(int(d[3]))                               # Level fed in daughter
+                    
+                
+        
+        """
+        LOOP IN NLEVEL (Levels for each daughter, starting in NLEVEL, ending in 1)
+        """
+        levelEnergy = []; fromBranch = []; lineL=[]; listTran = []; levelNumber = []
+        transitionType = []; prob = []; u_prob = []; e_trans = []; u_e_trans = []; next_level = []
+        transitionType_i = []; prob_i = []; u_prob_i = []; e_trans_i = []; u_e_trans_i = []; next_level_i = []; levelEnergy_i = []
+        for d in decayData:
+          if d[0] == "DAU" and d[1] == Daughter_vec[dd]:
+                daughterFlag = True
+          if d[0] == "DAU" and d[1] != Daughter_vec[dd]:
+                daughterFlag = False
+          if daughterFlag:
+              if d[0] == "LED":
+                # record transition details of the previous level
+                 transitionType.append(transitionType_i); prob.append(prob_i); u_prob.append(u_prob_i); e_trans.append(e_trans_i); u_e_trans.append(u_e_trans_i); next_level.append(next_level_i);levelEnergy.append(levelEnergy_i)
+            #    if int(d[6]) in LevelDaughter :  # Read the information on the possible energy levels after the emission of the alpha particle 
+                 levelEnergy_i.append(float(d[1]))   #levelEnergy.append(float(d[1]));     # Energie (rounded) of the level
+                 listTran.append(int(d[3]))           # Number of transitions that depopulate this level
+                 levelNumber.append(int(d[6]))        # Level number
+                 transitionType_i = []; next_level_i = []; levelEnergy_i = [];prob_i = []; u_prob_i = []; e_trans_i = []; u_e_trans_i = [];
+                  
+              """
+              LOOP IN NTRANS (Transitions depopulating this level)
+              """
+              if d[0] == "GA" or d[0] == "EK" or d[0] == "EL1" or d[0] == "EL2" or d[0] == "EL3" or d[0] == "EM" or d[0] == "EN":
+                  if d[1] == '  ' or d[1] == '   ': d[1] = 0
+                  if d[2] == '  ': d[2] = 0
+                  if d[4] == '  ': d[4] = 0
+                  transitionType_i.append(d[0])                                          # Read the type of transtion
+                  prob_i.append(float(d[1])); u_prob_i.append(float(d[2]))                 # Read the emission probability of the transition
+                  e_trans_i.append(float(d[3])); u_e_trans_i.append(float(d[4]))           # Read the energy of the transition
+                  next_level_i.append(int(d[5]))                                         # Read the level fed by this transition
+            
+        transitionType.append(transitionType_i); prob.append(prob_i); u_prob.append(u_prob_i); e_trans.append(e_trans_i); u_e_trans.append(u_e_trans_i); next_level.append(next_level_i);levelEnergy.append(levelEnergy_i)
+    
+        out.append([particle, p_branch, e_branch, LevelDaughter, levelNumber, prob, levelEnergy, transitionType, e_trans, next_level, Q_value_vec[dd], Daughter_vec[dd], Pdaughter_vec[dd]])
+    return out
+#out = readPenNuc('Am-242')
+#print(len(out),out)
+# tic()
+# readPenNuc("Co-60")
+# toc() # 0.016 s
+
+if absolutePath: file_pennuc = 'G:\Python_modules\Jialin\Code\decayData\\All-nuclides_PenNuc.zip'
+else: file_pennuc = "decayData//All-nuclides_PenNuc.zip"
+
+z_PenNuc = zf.ZipFile(file_pennuc)
+
+def readPenNuc2(rad,z1=z_PenNuc):
+    '''
+     =========
+     PARAMETRE
+     =========
+     rad -- type: str (par exemple: "Am-241") -- radionucléide 
+
+     ======
+     RETURN
+     ======
+     daughter -- indice 0 -- des noyaux fils -- len = nb de noyaux fils
+     prob_daug -- indice 1 -- des probabilités de noyaux fils -- len = nb de noyaux fils
+     energy_Q -- indice 2 -- des énergies de désintégrations -- len = nb de noyaux fils
+
+     desin_type_tot -- indice 3 -- des types de désintégrations/particules émis
+         len = nb de noyaux fils 
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des désintégrations possibles de chaque branch -- len de sous-list de sous-list = nb de type de désintégrations de chaque branch
+
+     desin_energy_tot -- indice 4 -- des énergies de désintégrations/énergies de patricules émis
+         len = nb de noyaux fils 
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des énergies de désintégrations possibles de chaque branch -- len de sous-list de sous-list = nb de type de désintégrations de chaque branch
+
+     desin_prob_tot -- indice 5 -- des probabilités de désintégrations
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des probabilités de désintégrations possibles de chaque branch -- len de sous-list de sous-list = nb de type de désintégrations de chaque branch
+     
+     desin_level_tot -- indice 6 -- des niveaux atteints après des désintégrations
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des niveaux après des désintégrations de chaque branch -- len de sous-list de sous-list = nb de type de désintégrations de chaque branch
+     
+     prob_branch_tot -- indice 7 -- probabilités de chaque branch
+         len = nb de noyaux fils
+         sous-list -- des probabilités de branchs de noyau fil -- len de sous-list = nb de branch de chaque fil
+         
+     tran_type_tot -- indice 8 -- transitions possibles 
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des transitions possibles de chaque branch -- len de sous-list de sous-list = nb de type de transitions de chaque branch
+     
+     tran_energy_tot -- indice 9 -- énergies de transitions
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des énergies de transitions possibles de chaque branch -- len de sous-list de sous-list = nb de type de transitions de chaque branch
+     
+     tran_prob_tot -- indice 10 -- probabilités de transitions
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des probabilités de transitions possibles de chaque branch -- len de sous-list de sous-list = nb de type de transitions de chaque branch
+     
+     tran_level_tot -- indice 11 -- niveaux de branch correspondants
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des niveaux de chaque branch avant des transitions -- len de sous-list de sous-list = 1
+     
+     tran_level_end_tot -- indice 12 -- niveaux après des transitions
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des niveaux après des transitions de chaque branch -- len de sous-list de sous-list = nb de type de transitions de chaque branch
+     
+     level_energy_tot -- indice 13 -- énergies de niveaux
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des énergies de niveaux de chaque branch -- len de sous-list de sous-list = 1
+
+     prob_tran_tot -- indice 14 -- la somme de transition de chaque branch
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des énergies de niveaux de chaque branch -- len de sous-list de sous-list = 1
+     '''
+    doc = rad + ".PenNuc.txt"
+    with z1.open(doc) as file_P:
+        decayData = file_P.readlines()
+
+    for i in range(np.size(decayData)):
+        decayData[i] = str(decayData[i])
+        decayData[i] = decayData[i].replace("b'","")
+        decayData[i] = decayData[i].replace("\\r\\n","")
+        decayData[i] = decayData[i].replace("'","") 
+
+    for il in range(len(decayData)):
+        if "NDA " in decayData[il]: decayData[il] = decayData[il].replace("NDA ","NDA; ") 
+        if "DAU " in decayData[il]: decayData[il] = decayData[il].replace("DAU ","DAU; ") 
+        if "DDE " in decayData[il]: decayData[il] = decayData[il].replace("DDE ","DDE; ")
+        if "Q " in decayData[il]: decayData[il] = decayData[il].replace("Q ","Q; ")
+        if "ALP " in decayData[il]: decayData[il] = decayData[il].replace("ALP ","ALP; ")
+        if "CK " in decayData[il]: decayData[il] = decayData[il].replace("CK ","CK; ")
+        if "CL " in decayData[il]: decayData[il] = decayData[il].replace("CL ","CL; ")
+        if "CO " in decayData[il]: decayData[il] = decayData[il].replace("CO ","CO; ")
+        if "CL1 " in decayData[il]: decayData[il] = decayData[il].replace("CL1 ","CL1; ")
+        if "CL2 " in decayData[il]: decayData[il] = decayData[il].replace("CL2 ","CL2; ")
+        if "CL3 " in decayData[il]: decayData[il] = decayData[il].replace("CL3 ","CL3; ")
+        if "CN " in decayData[il]: decayData[il] = decayData[il].replace("CN ","CN; ")
+        if "CM " in decayData[il]: decayData[il] = decayData[il].replace("CM ","CM; ")
+        if "BEM " in decayData[il]: decayData[il] = decayData[il].replace("BEM ","BEM; ")
+        if "BEP " in decayData[il]: decayData[il] = decayData[il].replace("BEP ","BEP; ")
+        if "LED " in decayData[il]: decayData[il] = decayData[il].replace("LED ","LED; ")
+        if "GA " in decayData[il]: decayData[il] = decayData[il].replace("GA ","GA; ")
+        if "EK " in decayData[il]: decayData[il] = decayData[il].replace("EK ","EK; ")
+        if "EL " in decayData[il]: decayData[il] = decayData[il].replace("EL ","EL; ")
+        if "EL1 " in decayData[il]: decayData[il] = decayData[il].replace("EL1 ","EL1; ")
+        if "EL2 " in decayData[il]: decayData[il] = decayData[il].replace("EL2 ","EL2; ")
+        if "EL3 " in decayData[il]: decayData[il] = decayData[il].replace("EL3 ","EL3; ")
+        if "EM " in decayData[il]: decayData[il] = decayData[il].replace("EM ","EM; ")
+        if "EN " in decayData[il]: decayData[il] = decayData[il].replace("EN ","EN; ")
+        if "COM " in decayData[il]: decayData[il] = decayData[il].replace("COM ","COM; ")
+        decayData[il] = decayData[il].split(';')
+
+    for a1 in decayData:
+        for a2 in range(len(a1)):
+            a1[a2] = a1[a2].strip()
+
+    '''
+     ========================
+     Repérer chaque noyau fil
+     ========================
+
+     daughter -- noyau(x) fil(s)
+     posi_daug -- l'indice de démarcation de noyau fil
+     posi_branch -- l'indice de démarcation de chaque branch
+     posi_tran -- l'indice de démarcation de transition
+     prob_daug -- probabilité de produire des noyaux fils
+     nb_branch -- nombre de branch possible au dessus de l'état fonda (n>0)
+     energy_Q -- l'énergie de désintégration
+
+    '''    
+    daughter = [];posi_daug = [];prob_daug=[];nb_branch=[];energy_Q=[];
+    end = len(decayData)
+    for indice,line in enumerate(decayData):
+        if "NDA" == line[0]:
+            nb_daug = int(line[1])
+        if "DAU" == line[0]:
+            daughter.append(line[1].replace(" ",""))
+        if "COM" == line[0] and "Daughter" in line[1]:
+            posi_daug.append(indice)
+        if "Q" == line[0]:
+            energy_Q.append(float(line[1]))
+        if "DDE" == line[0]:
+            prob_daug.append(float(line[1]))
+            nb_branch.append(int(line[-2]))
+    '''
+     ==========
+     LOOP START
+     ==========
+
+    ''' 
+    posi_end=[]
+    desin_type_tot=[];desin_energy_tot=[];desin_prob_tot=[];desin_level_tot=[]
+    tran_type_tot=[];tran_energy_tot=[];tran_prob_tot=[];tran_level_end_tot=[]; 
+    tran_level_tot=[];level_energy_tot=[]
+    prob_branch_tot=[];prob_tran_tot=[] 
+
+    '''
+     =============
+     LOOP DAUGHTER 
+     =============
+
+    '''
+    for i1 in range(nb_daug):
+        start_p = posi_daug[i1]
+        if i1+1 == nb_daug:
+            end_p = end
+        else:
+            end_p = posi_daug[i1+1]
+
+        posi_end_i = []
+        for i2 in range(start_p,end_p):
+            if "COM" == decayData[i2][0] and "Branch" in decayData[i2][1]:
+                posi_end_i.append(i2)
+            if "COM" == decayData[i2][0] and "Level" in decayData[i2][1]:
+                posi_end_i.append(i2)
+        if end_p == end:
+            posi_end_i.append(end)
+        else:
+            posi_end_i.append(posi_daug[i1+1])
+        posi_end.append(posi_end_i)
+
+        '''
+         ==========================
+         LOOP Branch and Transition
+         ==========================
+        '''
+        desin_type_daug=[];desin_energy_daug=[];desin_prob_daug=[];desin_level_daug=[];
+        tran_type_daug=[];tran_energy_daug=[];tran_prob_daug=[];tran_level_end_daug=[];
+        tran_level_daug=[];level_energy_daug=[]
+        prob_branch_daug=[];prob_tran_daug=[]
+
+        for i3 in range(len(posi_end_i)-1):
+            start_p1 = posi_end_i[i3]
+            end_p1 = posi_end_i[i3+1]
+            branch = False
+            transition = False
+            if "COM" == decayData[start_p1][0] and "Branch" in decayData[start_p1][1]:
+                branch=True
+            if "COM" == decayData[start_p1][0] and "Level" in decayData[start_p1][1]:
+                transition = True
+
+            '''
+             ====================================
+             LOOP EACH BLOCK OF BRANCH/TRANSITION
+             ====================================
+            ''' 
+            tran_type_b=[];tran_prob_b=[];tran_energy_b=[]; tran_level_end_b=[];
+            tran_level_b=[];level_energy_b=[]
+            desin_type_b=[];desin_energy_b=[];desin_prob_b=[];desin_level_b=[];
+             
+            for i4 in decayData[start_p1+1:end_p1]:
+                if start_p1+1 == end_p1:
+                    break
+                if branch:
+                    if "ALP" == i4[0]:
+                        desin_type_b.append("alpha")
+                    if "BEP" == i4[0]:
+                        desin_type_b.append("beta+")
+                    if "BEM" == i4[0]:
+                        desin_type_b.append("beta")
+                    if "CK" == i4[0]:
+                        desin_type_b.append("Atom_K")
+                    if "CL" == i4[0]:
+                        desin_type_b.append("Atom_L")
+                    if "CL1" == i4[0]:
+                        desin_type_b.append("Atom_L1")
+                    if "CL2" == i4[0]:
+                        desin_type_b.append("Atom_L2")
+                    if "CL3" == i4[0]:
+                        desin_type_b.append("Atom_L3")
+                    if "CM" == i4[0]:
+                        desin_type_b.append("Atom_M")
+                    if "CN" == i4[0]:
+                        desin_type_b.append("Atom_N")
+                    if "CO" == i4[0]:
+                        desin_type_b.append("Atom_O")
+                    desin_prob_b.append(float(i4[1]))
+                    desin_level_b.append(int(i4[3]))
+                    desin_energy_b.append(float(i4[4]))
+                if transition:
+                    if i4[1] == '' or i4[1] == ' ': i4[1] = 0
+                    if len(i4)>2 and i4[2] == '': i4[2] = 0
+                    if len(i4)>4 and i4[4] == '': i4[4] = 0
+                    if len(i4)>5 and i4[5] == '': i4[5] = 0
+                    if "LED" == i4[0]:
+                        tran_level_b.append(int(i4[-1]))
+                        level_energy_b.append(float(i4[1]))
+                    if i4[0] == "GA" or i4[0] == "EK" or i4[0] == "EL" or i4[0] == "EL1" or i4[0] == "EL2" or i4[0] == "EL3" or i4[0] == "EM" or i4[0] == "EN":
+                        #print(i4)
+                        tran_type_b.append(i4[0])
+                        tran_prob_b.append(float(i4[1]))
+                        tran_energy_b.append(float(i4[3]))
+                        tran_level_end_b.append(int(i4[5]))
+            if branch:
+                desin_type_daug.append(desin_type_b)
+                desin_energy_daug.append(desin_energy_b)
+                desin_prob_daug.append(desin_prob_b)
+                desin_level_daug.append(desin_level_b)
+             
+            if transition:
+                tran_type_daug.append(tran_type_b)
+                tran_energy_daug.append(tran_energy_b)
+                tran_prob_daug.append(tran_prob_b)
+                tran_level_end_daug.append(tran_level_end_b)
+                tran_level_daug.append(tran_level_b)
+                level_energy_daug.append(level_energy_b)
+
+            if len(desin_prob_b)>0:
+                desin_prob_array = np.array(desin_prob_b)
+                prob_branch_i = np.sum(desin_prob_array)
+                if prob_branch_i >= 1:
+                    prob_branch_i = 1
+                prob_branch_daug.append(prob_branch_i)
+            elif branch and len(desin_prob_b)==0:
+                prob_branch_daug.append(0)
+
+            if len(tran_prob_b)>0:
+                tran_prob_array = np.array(tran_prob_b)
+                prob_tran_i = np.sum(tran_prob_array)
+                if prob_tran_i >= 1:
+                    prob_tran_i = 1
+                prob_tran_daug.append(prob_tran_i)
+            elif transition and len(tran_prob_b)==0:
+                prob_tran_daug.append(0)
+
+        tran_type_daug.append([])
+        tran_prob_daug.append([])
+        tran_energy_daug.append([])
+        tran_level_end_daug.append([])
+        tran_level_daug.append([])
+        level_energy_daug.append([])
+        prob_tran_daug.append(0)
+
+        desin_type_tot.append(desin_type_daug)
+        desin_energy_tot.append(desin_energy_daug)
+        desin_prob_tot.append(desin_prob_daug)
+        desin_level_tot.append(desin_level_daug)
+
+        tran_type_tot.append(tran_type_daug)
+        tran_energy_tot.append(tran_energy_daug)
+        tran_prob_tot.append(tran_prob_daug)
+        tran_level_end_tot.append(tran_level_end_daug)
+        tran_level_tot.append(tran_level_daug)
+        level_energy_tot.append(level_energy_daug)
+        prob_branch_tot.append(prob_branch_daug)
+        prob_tran_tot.append(prob_tran_daug)
+    out = [daughter,prob_daug,energy_Q,desin_type_tot,desin_energy_tot,desin_prob_tot,desin_level_tot,prob_branch_tot,tran_type_tot,tran_energy_tot,tran_prob_tot,tran_level_tot,tran_level_end_tot,level_energy_tot,prob_tran_tot]
+    return out
+#tic()
+#o = readPenNuc2("Sb-127")
+#toc()
+#print(o[-4])
+
+
+def readPenNuc1(rad):
+     '''
+     =========
+     PARAMETRE
+     =========
+     rad -- type: str (par exemple: "Am-241") -- radionucléide 
+
+     ======
+     RETURN
+     ======
+     daughter -- indice 0 -- des noyaux fils -- len = nb de noyaux fils
+     prob_daug -- indice 1 -- des probabilités de noyaux fils -- len = nb de noyaux fils
+     energy_Q -- indice 2 -- des énergies de désintégrations -- len = nb de noyaux fils
+
+     desin_type_tot -- indice 3 -- des types de désintégrations/particules émis
+         len = nb de noyaux fils 
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des désintégrations possibles de chaque branch -- len de sous-list de sous-list = nb de type de désintégrations de chaque branch
+
+     desin_energy_tot -- indice 4 -- des énergies de désintégrations/énergies de patricules émis
+         len = nb de noyaux fils 
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des énergies de désintégrations possibles de chaque branch -- len de sous-list de sous-list = nb de type de désintégrations de chaque branch
+
+     desin_prob_tot -- indice 5 -- des probabilités de désintégrations
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des probabilités de désintégrations possibles de chaque branch -- len de sous-list de sous-list = nb de type de désintégrations de chaque branch
+     
+     desin_level_tot -- indice 6 -- des niveaux atteints après des désintégrations
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des niveaux après des désintégrations de chaque branch -- len de sous-list de sous-list = nb de type de désintégrations de chaque branch
+     
+     prob_branch_tot -- indice 7 -- probabilités de chaque branch
+         len = nb de noyaux fils
+         sous-list -- des probabilités de branchs de noyau fil -- len de sous-list = nb de branch de chaque fil
+         
+     tran_type_tot -- indice 8 -- transitions possibles 
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des transitions possibles de chaque branch -- len de sous-list de sous-list = nb de type de transitions de chaque branch
+     
+     tran_energy_tot -- indice 9 -- énergies de transitions
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des énergies de transitions possibles de chaque branch -- len de sous-list de sous-list = nb de type de transitions de chaque branch
+     
+     tran_prob_tot -- indice 10 -- probabilités de transitions
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des probabilités de transitions possibles de chaque branch -- len de sous-list de sous-list = nb de type de transitions de chaque branch
+     
+     tran_level_tot -- indice 11 -- niveaux de branch correspondants
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des niveaux de chaque branch avant des transitions -- len de sous-list de sous-list = 1
+     
+     tran_level_end_tot -- indice 12 -- niveaux après des transitions
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des niveaux après des transitions de chaque branch -- len de sous-list de sous-list = nb de type de transitions de chaque branch
+     
+     level_energy_tot -- indice 13 -- énergies de niveaux
+         len = nb de noyaux fils
+         sous-list -- des branchs possibles de noyau fil -- len de sous-list = nb de branch de chaque fil
+         sous-list de sous-list -- des énergies de niveaux de chaque branch -- len de sous-list de sous-list = 1
+     '''
+
+     url = "http://www.lnhb.fr/nuclides/"+rad+".PenNuc.txt"
+     file = rq.urlopen(url)
+     
+     # Format the data 
+     decayData = []
+     for line in file:
+        decayData.append(line.decode("utf-8"))
+        if "NDA " in decayData[-1]:    decayData[-1] = decayData[-1].replace("NDA ", "NDA; ") # number of daughter
+        if "DAU " in decayData[-1]:    decayData[-1] = decayData[-1].replace("DAU ", "DAU; ") # daughter
+        if "DDE " in decayData[-1]:    decayData[-1] = decayData[-1].replace("DDE ", "DDE; ") # daughter description : probability of disintegration to NDA, uncertainty, number of excited levels of NDA; number of branche to NDA
+        if "Q " in decayData[-1]:      decayData[-1] = decayData[-1].replace("Q ", "Q; ")     # total energy of the branch, uncertainty 
+        if "ALP " in decayData[-1]:    decayData[-1] = decayData[-1].replace("ALP ", "ALP; ") # type of the disintegration = alpha
+        if "CK " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CK ", "CK; ") # type of the disintegration = Electron Capture K shell
+        if "CL " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CL ", "CL; ") # type of the disintegration = Electron Capture L shell
+        if "CL1 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CL1 ", "CL1; ") # type of the disintegration = Electron Capture L shell 1
+        if "CL2 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CL2 ", "CL2; ") # type of the disintegration = Electron Capture L shell 2
+        if "CL3 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CL3 ", "CL3; ") # type of the disintegration = Electron Capture L shell 3
+        if "CM " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CM ", "CM; ") # type of the disintegration = Electron Capture M shell
+        if "CN " in decayData[-1]:    decayData[-1] = decayData[-1].replace("CN ", "CN; ") # type of the disintegration = Electron Capture N shell
+        if "BEM " in decayData[-1]:    decayData[-1] = decayData[-1].replace("BEM ", "BEM; ") # type disintegration-beta- :branching ratio, uncertainty, level fed in daughter, energy, uncertainty,prohibition factor for beta emission
+        if "BEP " in decayData[-1]:    decayData[-1] = decayData[-1].replace("BEP ", "BEP; ") # type disintegration-beta+ :branching ratio, uncertainty, level fed in daughter, energy, uncertainty,prohibition factor for beta emission
+        if "LED " in decayData[-1]:    decayData[-1] = decayData[-1].replace("LED ", "LED; ") # level description:energy of level,uncertainty, number of transitions that depopulate this level,level time,uncertainty,level number
+        if "GA " in decayData[-1]:     decayData[-1] = decayData[-1].replace("GA ", "GA; ")   # type transition: gamma
+        if "EK " in decayData[-1]:     decayData[-1] = decayData[-1].replace("EK ", "EK; ")   # type transition: internal conversion -- electron K
+        if "EL " in decayData[-1]:    decayData[-1] = decayData[-1].replace("EL ", "EL; ") # type transition: internal conversion -- electron L
+        if "EL1 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("EL1 ", "EL1; ") # type transition: internal conversion -- electron L1
+        if "EL2 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("EL2 ", "EL2; ") # type transition: internal conversion -- electron L2
+        if "EL3 " in decayData[-1]:    decayData[-1] = decayData[-1].replace("EL3 ", "EL3; ") # type transition: internal conversion -- electron L3
+        if "EM " in decayData[-1]:     decayData[-1] = decayData[-1].replace("EM ", "EM; ")   # type transition: internal conversion -- electron M
+        if "EN " in decayData[-1]:     decayData[-1] = decayData[-1].replace("EN ", "EN; ")   # type transition: internal conversion -- electron N
+        if "COM " in decayData[-1]:    decayData[-1] = decayData[-1].replace("COM ", "COM; ") 
+        decayData[-1]=decayData[-1].split(";")
+        if "\r\n" in decayData[-1][-1]:  decayData[-1][-1] = decayData[-1][-1].replace("\r\n", " ")
+
+     '''
+     ========================
+     Repérer chaque noyau fil
+     ========================
+
+     daughter -- noyau(x) fil(s)
+     posi_daug -- l'indice de démarcation de noyau fil
+     posi_branch -- l'indice de démarcation de chaque branch
+     posi_tran -- l'indice de démarcation de transition
+     prob_daug -- probabilité de produire des noyaux fils
+     nb_branch -- nombre de branch possible au dessus de l'état fonda (n>0)
+     energy_Q -- l'énergie de désintégration
+
+     '''    
+     daughter = [];posi_daug = [];prob_daug=[];nb_branch=[];energy_Q=[];
+     end = len(decayData)
+     for indice,line in enumerate(decayData):
+         if "NDA" == line[0]:
+             nb_daug = int(line[1])
+         if "DAU" == line[0]:
+             daughter.append(line[1].replace(" ",""))
+         if "COM" == line[0] and "Daughter" in line[1]:
+             posi_daug.append(indice)
+         if "Q" == line[0]:
+             energy_Q.append(float(line[1]))
+         if "DDE" == line[0]:
+             prob_daug.append(float(line[1]))
+             nb_branch.append(int(line[-2]))
+
+     '''
+     ==========
+     LOOP START
+     ==========
+
+     '''  
+     posi_end=[]
+     desin_type_tot=[];desin_energy_tot=[];desin_prob_tot=[];desin_level_tot=[]
+     tran_type_tot=[];tran_energy_tot=[];tran_prob_tot=[];tran_level_end_tot=[]; 
+     tran_level_tot=[];level_energy_tot=[]
+     prob_branch_tot=[]
+
+     '''
+     =============
+     LOOP DAUGHTER 
+     =============
+     '''
+     for i1 in range(nb_daug):
+        start_p = posi_daug[i1]
+        if i1+1 == nb_daug:
+            end_p = end
+        else:
+            end_p = posi_daug[i1+1]
+
+        posi_end_i = []
+        for i2 in range(start_p,end_p):
+            if "COM" == decayData[i2][0] and "Branch" in decayData[i2][1]:
+                posi_end_i.append(i2)
+            if "COM" == decayData[i2][0] and "Level" in decayData[i2][1]:
+                posi_end_i.append(i2)
+        if end_p == end:
+            posi_end_i.append(end)
+        else:
+            posi_end_i.append(posi_daug[i1+1])
+        posi_end.append(posi_end_i)
+     
+        '''
+        ==========================
+        LOOP Branch and Transition
+        ==========================
+        '''
+
+        desin_type_daug=[];desin_energy_daug=[];desin_prob_daug=[];desin_level_daug=[];
+        tran_type_daug=[];tran_energy_daug=[];tran_prob_daug=[];tran_level_end_daug=[];
+        tran_level_daug=[];level_energy_daug=[]
+        prob_branch_daug=[]
+
+        for i3 in range(len(posi_end_i)-1):
+            start_p1 = posi_end_i[i3]
+            end_p1 = posi_end_i[i3+1]
+            branch = False
+            transition = False
+            if "COM" == decayData[start_p1][0] and "Branch" in decayData[start_p1][1]:
+                branch=True
+            if "COM" == decayData[start_p1][0] and "Level" in decayData[start_p1][1]:
+                transition = True
+
+            '''
+            ====================================
+            LOOP EACH BLOCK OF BRANCH/TRANSITION
+            ====================================
+            ''' 
+            tran_type_b=[];tran_prob_b=[];tran_energy_b=[]; tran_level_end_b=[];
+            tran_level_b=[];level_energy_b=[]
+            desin_type_b=[];desin_energy_b=[];desin_prob_b=[];desin_level_b=[];
+             
+            for i4 in decayData[start_p1+1:end_p1]:
+                
+                if start_p1+1 == end_p1:
+                    break
+                if branch:
+                    if "ALP" == i4[0]:
+                        desin_type_b.append("alpha")
+                    if "BEP" == i4[0]:
+                        desin_type_b.append("beta+")
+                    if "BEM" == i4[0]:
+                        desin_type_b.append("beta")
+                    if "CK" == i4[0]:
+                        desin_type_b.append("Atom_K")
+                    if "CL" == i4[0]:
+                        desin_type_b.append("Atom_L")
+                    if "CL1" == i4[0]:
+                        desin_type_b.append("Atom_L1")
+                    if "CL2" == i4[0]:
+                        desin_type_b.append("Atom_L2")
+                    if "CL3" == i4[0]:
+                        desin_type_b.append("Atom_L3")
+                    if "CM" == i4[0]:
+                        desin_type_b.append("Atom_M")
+                    if "CN" == i4[0]:
+                        desin_type_b.append("Atom_N")
+                    desin_prob_b.append(float(i4[1]))
+                    desin_level_b.append(int(i4[3]))
+                    desin_energy_b.append(float(i4[4]))
+
+                if transition:
+                    if i4[1] == '  ' or i4[1] == '   ': i4[1] = 0
+                    if len(i4)>2 and i4[2] == '  ': i4[2] = 0
+                    if len(i4)>4 and i4[4] == '  ': i4[4] = 0
+                    if len(i4)>5 and i4[5] == '  ': i4[5] = 0
+                    if "LED" == i4[0]:
+                        tran_level_b.append(int(i4[-1]))
+                        level_energy_b.append(float(i4[1]))
+                    if i4[0] == "GA" or i4[0] == "EK" or i4[0] == "EL" or i4[0] == "EL1" or i4[0] == "EL2" or i4[0] == "EL3" or i4[0] == "EM" or i4[0] == "EN":
+                        tran_type_b.append(i4[0])
+                        tran_prob_b.append(float(i4[1]))
+                        tran_energy_b.append(float(i4[3]))
+                        tran_level_end_b.append(float(i4[5]))
+
+            if branch:
+                desin_type_daug.append(desin_type_b)
+                desin_energy_daug.append(desin_energy_b)
+                desin_prob_daug.append(desin_prob_b)
+                desin_level_daug.append(desin_level_b)
+             
+            if transition:
+                tran_type_daug.append(tran_type_b)
+                tran_energy_daug.append(tran_energy_b)
+                tran_prob_daug.append(tran_prob_b)
+                tran_level_end_daug.append(tran_level_end_b)
+                tran_level_daug.append(tran_level_b)
+                level_energy_daug.append(level_energy_b)
+
+            if len(desin_prob_b)>0:
+                desin_prob_array = np.array(desin_prob_b)
+                prob_branch_i = np.sum(desin_prob_array)
+                if prob_branch_i >= 1:
+                    prob_branch_i = 1
+                prob_branch_daug.append(prob_branch_i)
+            elif branch and len(desin_prob_b)==0:
+                prob_branch_daug.append(0)
+
+        tran_type_daug.append([])
+        tran_prob_daug.append([])
+        tran_energy_daug.append([])
+        tran_level_end_daug.append([])
+        tran_level_daug.append([])
+        level_energy_daug.append([])
+
+        desin_type_tot.append(desin_type_daug)
+        desin_energy_tot.append(desin_energy_daug)
+        desin_prob_tot.append(desin_prob_daug)
+        desin_level_tot.append(desin_level_daug)
+
+        tran_type_tot.append(tran_type_daug)
+        tran_energy_tot.append(tran_energy_daug)
+        tran_prob_tot.append(tran_prob_daug)
+        tran_level_end_tot.append(tran_level_end_daug)
+        tran_level_tot.append(tran_level_daug)
+        level_energy_tot.append(level_energy_daug)
+        prob_branch_tot.append(prob_branch_daug)
+
+     out = [daughter,prob_daug,energy_Q,desin_type_tot,desin_energy_tot,desin_prob_tot,desin_level_tot,prob_branch_tot,tran_type_tot,tran_energy_tot,tran_prob_tot,tran_level_tot,tran_level_end_tot,level_energy_tot]
+     return out
+
+#tic()
+#o = readPenNuc1("Ag-110m")
+#print(o[-4])
+#toc()
+#===============================================================================================================
+'''
+rad = "Am-244m"
+out1 = readPenNuc1(rad)
+print(rad)
+print("    ")
+print("DAU",out1[0])
+print("    ")
+print("prob_daug",out1[1])
+print("    ")
+print("Q",out1[2])
+print("    ")
+print("desin_type",out1[3],len(out1[3]))
+print("    ")
+print("desin-prob",out1[5],len(out1[5]))
+print("    ")
+print("desin-level",out1[6],len(out1[6]))
+print("    ")
+print("prob-branch",out1[7])
+print("    ")
+print("len-tran-type",len(out1[8]))
+for i in range(len(out1[8])):
+    print("fil",i)
+    for i1,p1 in enumerate(out1[8][i]):
+        print(p1,len(p1))
+    print("energy")
+    for i2,p2 in enumerate(out1[9][i]):
+        print(p2,len(p2))
+    print("tran-prob")
+    for i4,p4 in enumerate(out1[10][i]):
+        print(p4)
+    print("end_level")
+    for i3,p3 in enumerate(out1[12][i]):
+        print(p3,len(p3))
+'''
+#print(readPenNuc1('Tc-99m'))
+#out = readPenNuc1('Tc-99m')
+#print(sampling(out[1]))
+#================================== StoppingPower for alpha particle ===========================================
+
+if absolutePath: f_alpha = open('G:\Python_modules\Jialin\Code\Quenching\\alpha_toulene.txt')
+else: f_alpha = open('Quenching/alpha_toulene.txt')
+data_ASTAR = f_alpha.readlines()
+f_alpha.close()
+energy_alph = []
+dEdx_alph = []
+for i in range(np.size(data_ASTAR)):
+    data_ASTAR[i] = data_ASTAR[i].split()
+    for j in range(2):
+        data_ASTAR[i][j] = float(data_ASTAR[i][j])*1e3  # dEdx from MeV.cm2/g to keV.cm2/g; energy from MeV to keV
+    energy_alph.append(data_ASTAR[i][0])
+    dEdx_alph.append(data_ASTAR[i][1])
+
+def stoppingpowerA(e,rho=0.96,energy_alpha=energy_alph,dEdx_alpha=dEdx_alph):
+    """
+    Estimation of the stopping power of alpha particles using tabulated values form the ASTAR code
+    ref: https://dx.doi.org/10.18434/T4NC7P
+    
+    Parameters
+    ----------
+    e : float
+        energy of the alpha particle in keV.
+    rho : float, optional
+        density of the source in g.cm-3. The default is 0.96.
+    energy_alpha : list, optional
+        the list of energy (in keV) for which the stopping power was calculated with ASTAR. The default is energy_alph.
+    dEdx_alpha : list, optional
+        the list of stopping powers (in keV.cm2/g) associated with the energy vector. The default is dEdx_alph.
+
+    Returns
+    -------
+    float
+        Interpolated ASTAR estimation of the stopping power.
+
+    """
+
+    energy_alpha = np.array(energy_alpha)
+    dEdx_alpha = np.array(dEdx_alpha)
+    dEdx = np.interp(e,energy_alpha ,dEdx_alpha)   
+    return dEdx*rho                        #unit keV.cm-1
+
+# tic()
+# stoppingpowerA(5000,rho=0.96,energy_alpha=energy_alph,dEdx_alpha=dEdx_alph)
+# toc() # 0 s
+
+#===============================================================================================
+
+#========================   Nouveau modèle pour calculer le pouvoir d'arrête d'électron ========
+
+
+if absolutePath: file_TanXia=open('G:\Python_modules\Jialin\Code\Quenching\\TandataUG.txt', "r")
+else: file_TanXia=open('Quenching/TandataUG.txt', "r")
+data_TanXia=file_TanXia.read(); file_TanXia.close()
+data_TanXia=data_TanXia.split("\n"); data_TanXia_f = np.empty(len(data_TanXia))
+for i, x in enumerate(data_TanXia):
+  if i<len(data_TanXia)-1: data_TanXia_f[i]=float(x)
+
+def stoppingpower(e,rho=0.96,Z=5.2,A=11.04,emin=0,file=data_TanXia_f):
+    """
+    The stopping power of electrons between 20 keV and 1000 keV is a mixture of a radiative loss model [1], and a collision model [2] that has been validated agaisnt the NIST model ESTAR [3] recommanded by the ICRU Report 37 [4].
+    At low energy - between 10 eV and 20 keV - the model from Tan and Xia [5] is implemented.
+    Refs:
+        [1] https://doi.org/10.1016/0020-708x(82)90244-7
+        [2] https://www.ijstr.org/final-print/jan2017/Calculations-Of-Stopping-Power-And-Range-Of-Electrons-Interaction-With-Different-Material-And-Human-Body-Parts.pdf
+        [3] https://dx.doi.org/10.18434/T4NC7P
+        [4] ICRU Report 37, Stopping Powers for Electrons and Positrons
+        [5] https://doi.org/10.1016/j.apradiso.2011.08.012
+        
+    Parameters
+    ----------
+    e : float
+        Energy of the electron in eV.
+    rho : float, optional
+        density of the source in g.cm-3. The default is 0.96.
+    Z : float, optional
+        mean charge number of the source. The default is 5.2.
+    A : float, optional
+        mean mass number of the source. The default is 11.04.
+    emin : float, optional
+        the minimal energy to consider. The default is 0.
+    file : list, optional
+        tabulated data form the Tan and Xia model. The default is data_TanXia_f.
+
+    Returns
+    -------
+    dEdx : float
+        Calculated stopping power in MeV.cm-1.
+
+    """
+    # e:eV ;rho: g.cm-3
+    mc_2 = 0.511 #MeV
+    I = 65e-6 #MeV
+    NA = 6.02e23
+    ahc = 1.437e-13   #MeV.cm
+    if e>=20000:
+        e1 = e*1e-6 #MeV
+        gamma = (e1+mc_2)/mc_2
+        gamma_2 = gamma*gamma
+        beta = np.sqrt(1-(1/gamma_2))
+        beta_2 = beta**2
+        tau = e1/mc_2
+        terma = np.log(tau**2*(tau+2)/2)
+        termb = 1+tau*tau/8-(2*tau+1)*np.log(2)
+        termc = (tau+1)**2
+        B0 = terma + termb/termc
+        sc = 0.1535/beta_2*Z/A*(B0-2*np.log(I/mc_2))  
+        term3 = NA*(Z**2)*rho*(e1+mc_2)/(137*(mc_2**2)*A)
+        term4 = 4* np.log(2*gamma) -4/3
+        sr = (ahc**2)*term3*term4
+        #if T<1:sr=0
+        dEdx = (sc + sr)*rho  #MeV.cm-1
+    else:
+            if e>emin:
+                dEdx=float(file[int(e)]) #MeV.cm-1
+            else:
+                dEdx=0
+    if dEdx<0:
+        dEdx=0
+    return dEdx    
+
+# tic()
+# stoppingpower(100,rho=0.96,Z=5.2,A=11.04,emin=0,file=data_TanXia_f)
+# toc() # 0 s
+#===================================================================================================
+
+#===================================================================================================
+#============================tracer stopping power of electron and alpha ===========================
+
+'''
+e1 = np.linspace(10,1.99e4,10000)
+e2 = np.linspace(1.99e4,1e8,20000)
+sp1 = []
+for i in e1:
+    sp1.append(stoppingpower(i))
+sp2=[]
+for i in e2:
+    sp2.append(stoppingpower(i))
+
+ea = np.linspace(1,8e3,4000)
+spa = []
+for i in ea:
+    spa.append(stoppingpowerA(i)*1e-3)
+x = ea*1e3
+plt.plot(e1,sp1,color='blue',label="pouvoir d'arrête électron")
+plt.plot(e2,sp2,color='blue')
+plt.plot(x,spa,label="pouvoir d'arrête alpha")
+plt.xscale('log')
+plt.yscale('log')
+plt.title("pouvoir d'arrête d'electron et alpha")
+plt.ylabel("pouvoir d'arrête/MeV.cm-1")
+plt.xlabel('énergie cinétique/eV')
+plt.legend(fontsize=10,loc='best')
+plt.savefig('Quenching/stoppingpowerE_A.png')
+
+'''
+
+#=============================================================================================
+
+#====================  Fonction pour lire BetaShape   ========================================
+file_betashape = "decayData//All-nuclides_BetaShape.zip"
+z_betashape = zf.ZipFile(file_betashape)
+
+def readBetaShape(rad,mode,level,z=z_betashape):
+    """
+    This funcion reads the beta spectra calculated by the code BetaShape and published in the DDEP web page.
+    refs:
+        https://doi.org/10.1103/PhysRevC.92.059902
+        http://www.lnhb.fr/ddep_wg/
+
+    Parameters
+    ----------
+    rad : string
+        identifier of the radionuclide. e.g. 'Na-22'
+    mode : string
+        identifier of the decay mode. 'beta-' or 'beta+'
+    level : int
+        level of the daughter after decay.  0,1,2,3 ....
+    Returns
+    -------
+    e : list
+        the energy vector in keV.
+    dNdx : list
+        the probability density in keV-1.
+
+    """
+
+    Rad = rad.replace('-','')
+    name_doc = Rad+'/'+mode+'_'+Rad+'_'+ "trans" + str(level) +'.bs'
+    with z.open(name_doc) as file_trans:
+        data = file_trans.readlines()
+
+    for i in range(np.size(data)):
+        data[i] = str(data[i])
+        data[i] = data[i].replace("b'",'')
+        data[i] = data[i].replace("\\r\\n",'')
+        data[i] = data[i].replace("'",'')
+    for i in range(np.size(data)):
+        data[i] = data[i].split()
+    e = []
+    dNdx = []
+    
+    while [] in data:
+        data.remove([])
+    
+    for i in range(len(data)):
+        ind = i
+        if data[i][0] == 'E(keV)':break
+    
+    for j in range(i+1,len(data)):
+        e.append(float(data[j][0])) # convert to float
+        dNdx.append(float(data[j][1])) # convert to float
+    dNdx /= sum(np.asarray(dNdx)) # normalization
+    dNdx = list(dNdx)
+    return e, dNdx
+
+#tic()
+#e,p = readBetaShape('C-11','beta+',0)
+#toc()
+#print(p,type(p))
+
+# tic()
+# e,p = readBetaShape('C-11','beta+',0)
+# toc() # 0.016 s > 0s
+
+def readTDCR17spectra(rad):
+    file = open("decayData/spectra/spectrumTDCR17_"+rad+".dat")
+    data = file.read()
+    file.close()
+    data = data.split("\n")
+    e = []; r = []
+    for i in data:
+        if "keV" not in i:
+            a = i.split("  ")
+            if len(a)>1:
+                e.append(float(a[1])*1e-3)
+                r.append(float(a[2]))
+    return e, r
+
+
+# tic()
+# e,r =  readBetaShape("Nb-95m", "beta-", 1)
+# # print(e[-1])
+# toc() # 0.016 s > 0 s
+
+#=====================================================================================
+
+## Display beta spectra
+# rplot = "S-35"
+# out = readBetaShape(rplot, "beta-", "tot"); print(sum(out[1]))
+# out_t = readTDCR17spectra(rplot); print(sum(out_t[1])) # TDCR17 spectra
+# plt.figure("beta spectrum")
+# plt.clf()
+# plt.plot(out[0],out[1]/(out[0][1]-out[0][0]),label='Beta spectrum - BetaShape',ls='-',color='red',lw=3)
+# plt.plot(out_t[0],np.asarray(out_t[1])/(out_t[0][1]-out_t[0][0]),label='Beta spectrum - TDCR17',ls='-',color='blue',lw=3)
+# plt.xscale('linear')
+# plt.legend(fontsize=12,loc='best')
+# plt.xlabel(r'$E$ /keV', fontsize=12)
+# plt.ylabel(r'd$N$/d$E$ /keV$^{-1}$',fontsize=12)
+# plt.savefig("decayData/spectra/BetaSpectrum_"+rplot+".png")
+
+#=======================================================================================
+
+#============================  Fonction quenching  =====================================
+
+def E_quench_e(e,kB,nE):
+    """
+    This function calculate the quenched energy of electrons according to the Birks model of scintillation quenching
+
+    Parameters
+    ----------
+    e : float
+        energy of the electron in eV.
+    kB : float
+        Birks constant in cm/MeV.
+
+    Returns
+    -------
+    float
+        Quenched energy in eV.
+
+    """
+    
+    e_dis = np.linspace(0,e,nE)
+    delta = e_dis[2] - e_dis[1]
+    q = 0
+    for i in e_dis:
+        q += delta/(1+kB*stoppingpower(i))
+    return q
+
+def E_quench_a(e,kB,nE): 
+    """
+    This function calculate the quenched energy alpha particles according to  the Birks model of scintillation quenching
+
+    Parameters
+    ----------
+    e : float
+        energy of the alpha particle in keV.
+    kB : float
+        Birks constant in cm/keV.
+
+    Returns
+    -------
+    float
+        Quenched energy in keV.
+
+    """
+
+    e_dis = np.linspace(1,e,nE)
+    delta = e_dis[2] - e_dis[1]
+    q = 0
+    for i in e_dis:
+        q += delta/(1+kB*stoppingpowerA(i))
+    return q
+
+#=========================================================================================
+
+
+
+#print(E_quench_e(3.996e5,1e-2,1000)*1e-3)
+
+#======================================================================================
+
+#========================= Tracer les courbes avec kB différents ======================
+
+'''
+
+# s1 = []
+# s2 = []
+# s3 = []
+# x = np.linspace(5,8000,4000) 
+
+# for i in x:
+#     s1.append(E_quench_a(i,kB=7e-6)/i)
+#     s2.append(E_quench_a(i,kB=1e-5)/i)
+#     s3.append(E_quench_a(i,kB=1.4e-5)/i)
+
+# plt.plot(x,s1,label='kB=0.007cm/MeV',color='green',lw=2)
+# plt.plot(x,s2,label='kB=0.01cm/MeV',ls=':',color='red',lw=3)
+# plt.plot(x,s3,label='kB=0.014cm/MeV')
+# plt.xscale('log')
+# #plt.yscale('log')
+# plt.legend(fontsize=12,loc='best')
+# plt.xlabel('E de particule/keV')
+# plt.ylabel("énergie d'extinction/E")
+# plt.savefig("Quenching/beta 100-10K E_Q sur E.png")
+
+#'''
+#============================================================================================
+
+#============================================================================================
+
+#========================= énergie gamma ===================================================
+#'''
+if absolutePath: 
+    fp1 = 'G:\Python_modules\Jialin\Code\\MCNP-MATRIX/matrice/fichier/matrice_p_1_200k.txt'       #gamma-10ml-1-200keV-niveau 0
+    fp2 = 'G:\Python_modules\Jialin\Code\\MCNP-MATRIX/matrice/fichier/matrice_p_200_2000k.txt'    #gamma-10ml-200-2000keV-niveau 0
+    fp3 = 'G:\Python_modules\Jialin\Code\\MCNP-MATRIX/matrice/fichier/matrice_p_2000_10000k.txt'  #gamma-10ml-2000-10000keV-niveau 0
+    fe = "G:\Python_modules\Jialin\Code\\MCNP-MATRIX/matrice/fichier/E_depose.txt"  
+else:
+    fp1 = 'MCNP-MATRIX/matrice/fichier/matrice_p_1_200k.txt'      #gamma-10ml-1-200keV-niveau 0
+    fp2 = 'MCNP-MATRIX/matrice/fichier/matrice_p_200_2000k.txt'   #gamma-10ml-200-2000keV-niveau 0
+    fp3 = 'MCNP-MATRIX/matrice/fichier/matrice_p_2000_10000k.txt' #gamma-10ml-2000-10000keV-niveau 0
+    fe = "MCNP-MATRIX/matrice/fichier/E_depose.txt"
+'''
+data1 = f1.readlines()
+data2 = f2.readlines()
+data3 = f3.readlines()
+data_e = fe.readlines()
+
+Matrice1 = np.zeros((1003,200))
+Matrice2 = np.zeros((1003,901))
+Matrice3 = np.zeros((1003,801))
+Matrice_e = np.zeros((1002,3))
+
+for i in range(1002):
+    data_e[i] = data_e[i].split()
+    for j in range(3):
+        Matrice_e[i][j] = float(data_e[i][j])
+for i in range(1003):
+    data1[i] = data1[i].split()
+    data2[i] = data2[i].split()
+    data3[i] = data3[i].split()
+    for j in range(200):
+        Matrice1[i][j] = float(data1[i][j])
+    for k in range(901):
+        Matrice2[i][k] = float(data2[i][k])
+    for l in range(801):
+        Matrice3[i][l] = float(data3[i][l])
+'''
+
+def read_matrice(path,niveau):
+    f = open(path)
+    data = f.readlines()
+    if niveau == 0:
+        taille_x = 200
+        taille_y = 1003
+    elif niveau == 1:
+        taille_x = 901
+        taille_y = 1003
+    elif niveau == 2:
+        taille_x = 801
+        taille_y = 1003
+    elif niveau=='e':
+        taille_x = 3
+        taille_y = 1002
+
+    matrice = np.zeros((taille_y,taille_x))
+    for i in range(taille_y):
+        data[i] = data[i].split()
+        for j in range(taille_x):
+            matrice[i][j] = float(data[i][j])
+    return matrice
+
+
+Matrice10_p_1 = read_matrice(fp1,0)
+Matrice10_p_2 = read_matrice(fp2,1)
+Matrice10_p_3 = read_matrice(fp3,2)
+Matrice_e = read_matrice(fe,'e')
+
+def energie_dep_gamma(e_inci,*,matrice10_1=Matrice10_p_1,matrice10_2=Matrice10_p_2,matrice10_3=Matrice10_p_3,ed=Matrice_e):
+    """ 
+    ----------
+    Parameters
+    ----------
+    e_inci : float
+        l'énergie incidente de particule.
+    * : TYPE
+        DESCRIPTION.
+    matrice10_1 : matrix
+        matrice de photon de 1-200keV de solution 10ml.
+    matrice2 : TYPE, optional
+        matrice de photon de 200-2000keV de solution 10ml.
+    matrice3 : TYPE, optional
+        matrice de photon de 2000-10000keV de solution 10ml.
+    ed : TYPE, optional
+        matrice de bins d'énergie. colonne 0: 1-200keV; colonne 1: 200-2000keV
+
+    Returns
+    -------
+    result : float
+        l'énergie déposée.
+
+    """
+    ## sort keV / entrée : keV
+    if e_inci <= 200:
+        index = int(e_inci)            # index de colonne de la matrice de l'énergie incidente la plus proche 
+        #doc = 'MCNP-MATRIX/matrice/matrice_p_1_200k.txt'
+        matrice = matrice1
+        #taille_x = 200
+        e = ed[:,0]
+    
+    elif e_inci <= 2000:
+        index = int((e_inci-200)/2)
+        #doc = 'MCNP-MATRIX/matrice/matrice_p_200_2000k.txt'
+        matrice = matrice2
+        #taille_x = 901
+        e = ed[:,1]
+
+    else:
+        index = (int(e_inci)-2000)//10
+        #doc = 'MCNP-MATRIX/matrice/matrice_p_2000_10000k.txt'
+        matrice = matrice3
+        #taille_x = 801
+        e = ed[:,2]
+    
+    '''
+    with open(doc) as f:
+        data = f.readlines()
+    
+        matrice = np.zeros((1002,taille_x))
+
+        for i in range(1002):
+            data[i] = data[i].split()
+            for j in range(taille_x):
+                matrice[i][j] = float(data[i][j])
+    '''
+    inde = sampling(matrice[1:,index])
+    if inde == 1 : result = 0
+        #elif e_inci<25: result = e[inde-1]*1e3*e_inci/matrice[0][index]
+    else: result = e[inde]*1e3*e_inci/matrice[0][index]
+    if result  > e_inci: result = e_inci
+    return result
+
+#for i in range(50):
+    #print(energie_dep_gamma(511))
+
+
+if absolutePath: 
+    fe1 = 'G:\Python_modules\Jialin\Code\\MCNP-MATRIX/matrice/fichier/matrice_beta-_1_200k.txt' # electron-10ml-1-200keV-niveau 0
+    fe2 = 'G:\Python_modules\Jialin\Code\\MCNP-MATRIX/matrice/fichier/matrice_beta-_200_2000k.txt' # electron-10ml-200-2000keV-niveau 1
+    fe3 = 'G:\Python_modules\Jialin\Code\\MCNP-MATRIX/matrice/fichier/matrice_beta-_2000_10000k.txt' # electron-10ml-2000-10000keV-niveau 2
+    fe = "G:\Python_modules\Jialin\Code\\MCNP-MATRIX/matrice/fichier/E_depose.txt"   # electron-10ml-énergie-niveau 'e'
+else:
+    fe1 = 'MCNP-MATRIX/matrice/fichier/matrice_beta-_1_200k.txt' # electron-10ml-1-200keV-niveau 0
+    fe2 = 'MCNP-MATRIX/matrice/fichier/matrice_beta-_200_2000k.txt' # electron-10ml-200-2000keV-niveau 1
+    fe3 = 'MCNP-MATRIX/matrice/fichier/matrice_beta-_2000_10000k.txt' # electron-10ml-2000-10000keV-niveau 2
+    fe = "MCNP-MATRIX/matrice/fichier/E_depose.txt" # electron-10ml-énergie-niveau 'e'
+
+
+
+Matrice10_e_1 = read_matrice(fe1,0)
+Matrice10_e_2 = read_matrice(fe2,1)
+Matrice10_e_3 = read_matrice(fe3,2)
+#Matrice_e = read_matrice(fe,'e')
+
+
+def energie_dep_beta(e_inci,*,matrice10_1=Matrice10_e_1,matrice10_2=Matrice10_e_2,matrice10_3=Matrice10_e_3,ed=Matrice_e):
+    """ 
+    ----------
+    Parameters
+    ----------
+    e_inci : float
+        l'énergie incidente de particule.
+    * : TYPE
+        DESCRIPTION.
+    matrice10_1 : matrix
+        matrice d'électrons de 1-200keV de solution 10ml.
+    matrice2 : TYPE, optional
+        matrice d'électrons de 200-2000keV de solution 10ml.
+    matrice3 : TYPE, optional
+        matrice d'électrons de 2000-10000keV de solution 10ml.
+    ed : TYPE, optional
+        matrice de bins d'énergie. colonne 0: 1-200keV; colonne 1: 200-2000keV
+
+    Returns
+    -------
+    result : float
+        l'énergie déposée.
+
+    """
+    ## sort keV / entrée : keV
+    if e_inci <= 200:
+        index = int(e_inci)            # index de colonne de la matrice de l'énergie incidente la plus proche 
+        #doc = 'MCNP-MATRIX/matrice/matrice_p_1_200k.txt'
+        matrice = matrice10_1
+        #taille_x = 200
+        e = ed[:,0]
+    
+    elif e_inci <= 2000:
+        index = int((e_inci-200)/2)
+        #doc = 'MCNP-MATRIX/matrice/matrice_p_200_2000k.txt'
+        matrice = matrice10_2
+        #taille_x = 901
+        e = ed[:,1]
+
+    else:
+        index = (int(e_inci)-2000)//10
+        #doc = 'MCNP-MATRIX/matrice/matrice_p_2000_10000k.txt'
+        matrice = matrice10_3
+        #taille_x = 801
+        e = ed[:,2]
+    
+    inde = sampling(matrice[1:,index])
+    if inde == 1 : result = 0
+        #elif e_inci<25: result = e[inde-1]*1e3*e_inci/matrice[0][index]
+    else: result = e[inde]*1e3*e_inci/matrice[0][index]
+    if result  > e_inci: result = e_inci
+    return result
+
+'''
+r = []   
+for i in range(10):
+    r.append(energie_dep_beta(17.055))
+print(r)
+'''
+#print(Matrice_e[0:5,:])
+
+# tic()
+# energie_dep_gamma(800)
+# toc()   # 0 s
+
+
+
+## Non parametric regression
+
+# def regress(x,y):
+#     z = sm.nonparametric.lowess(y, x, return_sorted = True)
+#     return z
+
+    
+
+def writeEffcurves(x,y,uy,rad,p,kB,SDT):
+    if SDT == "S":
+        file = open("EfficiencyCurves/"+''.join(rad)+"/EffS_"+''.join(rad)+'_'+''.join(str(p))+'_'+str(kB)+".txt","w")
+    elif SDT == "D":
+        file = open("EfficiencyCurves/"+''.join(rad)+"/EffD_"+''.join(rad)+'_'+''.join(str(p))+'_'+str(kB)+".txt","w")
+    elif SDT == "T":
+        file = open("EfficiencyCurves/"+''.join(rad)+"/EffT_"+''.join(rad)+'_'+''.join(str(p))+'_'+str(kB)+".txt","w")
+    else:
+        print("Warning: unknown profil type")
+    for i, xi in enumerate(x):
+        file.write(str(xi)+" "+str(y[i])+" "+str(uy[i])+"\n")
+    file.close()
+
+#======================== read ENSDF ============================================
+def transf_name(rad):     #  transformer le nom de rad par exemple '11C' à 'C11'
+    """
+    ---------
+    PARAMETRE
+    ---------
+    rad -- type: str par exemple '108AG'
+    
+    ------
+    RETURN
+    ------
+    RAD -- type: str par exemple 'AG108' qui correspond à la structure de fille de PenNuc
+
+    """
+    # rad -- type : str par exemple '108AG'
+
+    name_lis = re.split('(\d+)',rad)
+    RAD = name_lis[2]+name_lis[1]
+    return RAD
+
+#print(transf_name('108PD'))
+
+file_ensdf = 'decayData//All-nuclides_Ensdf.zip'
+z_ensdf = zf.ZipFile(file_ensdf)
+#print(z.namelist())
+def readEShape(rad, *, z=z_ensdf):
+    """
+    --------------------------------------------------
+    pour lire les fichiers dans All-nuclides_Ensdf.zip
+    --------------------------------------------------
+    ---------
+    PARAMETRE
+    ---------
+    rad -- type: str par exemple 'Ag-108'
+    z -- ENSDF files
+    
+    ------
+    RETURN
+    ------
+    daug_name -- type: list -- les filles de désintégration
+    Energy ----- type: list -- chaque élément comprend toutes les énergies de transition de la fille de même indice
+    Prob ------- type: list -- chaque élément comprend toutes les proba de transition de la fille de même indice
+    Type ------- type: list -- chaque élément comprend touts les types de transition de la fille de même indice
+
+    """
+       
+    name = rad + '.txt'
+    with z.open(name) as f:
+        data = f.readlines()
+        nl = np.size(data)
+        #print(data)
+        for i in range(nl):
+            data[i] = str(data[i])
+            data[i] = data[i].replace("b",'')
+            data[i] = data[i].replace("\\r\\n",'')
+            data[i] = data[i].replace("'",'')
+            if "\\n" in data[i]:data[i] = data[i].replace("\\n","")     # pour traiter "\\n" dans Mn-52 et Mn-52m (cas particuliers)
+        #print(data)
+        for i in range(nl):
+            data[i] = data[i].split()
+        
+        for i in range(nl):
+            if i>0 and ('L' in data[i]) and ("AUGER" in data[i]) and ("|]" in data[i-1]):
+                data.insert(i,[data[i][0],'T'])
+    #print(data)
+    index_auger = []
+    index_end = []
+    daug_name = []
+    posi = []
+    for i,p in enumerate(data):
+        if 'DECAY' in p:
+            daug_name.append(transf_name(p[0]))
+        if 'Auger' in p:
+            index_auger.append(i)
+        if len(p)==2 and 'T' in p:
+            posi.append(i)
+        if 'P' in p:
+            index_end.append(i)
+            posi.append(i)
+
+    Energy = []           # enregistrer les résultats (énergie) complètes
+    energy = []           # enregistrer les résultats (énergie) d'une fille
+    Type = []             # enregistrer les résultats (type de transition) complètes
+    type_ = []            # enregistrer les résultats (type de transition) d'une fille
+    Prob = []             # enregistrer les résultats (proba de transition) complètes
+    prob = []             # enregistrer les résultats (proba de transition) d'une fille
+
+    for i in range(len(posi)-1):
+        start = posi[i]+1
+        end = posi[i+1]
+        d = data[start:end]   # bloc
+        e = []                # enregistrer les résultats (énergie) d'un bloc
+        prob_b = []           # enregistrer les résultats (proba) d'un bloc
+        type_b = []           # enregistrer les résultats (type) d'un bloc
+        if start==end:        # sauter les lignes blaches et continues
+            continue
+        if start-1 in index_end:   # sauter le bloc entre deux filles
+            continue
+
+        for n,p1 in enumerate(d):   
+            if '-' in p1[2]:                # calculer et remplacer les intervalles
+                x = p1[2].split('-') 
+                p1[2] = round((float(x[0])+float(x[1]))/2,3)
+
+            if '(total)' in d[0]:           # traiter le bloc qui comprend (total) dans la première ligne 
+                if '(total)' in p1:
+                    prob_b.append(float(p1[3]))
+                    e.append(p1[2])
+                    type_b.append(p1[-2])
+                continue 
+            elif '|]' in p1:                # traiter un bloc qui comprend |]
+                if len(p1)>6:               # repérer la ligne qui comprend la proba
+                    prob_b.append(float(p1[4]))
+                e.append(float(p1[2]))      # enregistrer les valeurs d'énergie
+                if 'AUGER' in p1:           # traiter le cas d'auger et |] 
+                    if 'K' in p1[-2]:       # Auger K
+                        type_b.append('Auger K')
+                    else:
+                        print('erreur')
+                elif 'X' in p1[-1]:         # Rayon X
+                    type_b.append(p1[-1][0:3])
+            else:                           # traiter le cas sans |] ni (total)
+                if len(p1)==4 and 'X' in p1[-1]:   # le cas de rayon X sans |] ni (total) ni proba
+                    continue                       # sauter cette ligne
+                elif len(p1)==5 and 'L' in p1:     # le cas de Auger L sans |] ni (total) ni proba
+                    continue                       # sauter cette ligne
+                else:                       # traiter le cas sans |] ni (total) mais complet
+                    e.append(float(p1[2]))         # enregistrer énergie
+                    prob_b.append(float(p1[3]))    # enregistrer proba
+                    if 'L' in p1:
+                        type_b.append('Auger L')   # enregistrer type Auger L
+                    else:
+                        type_b.append(p1[-1][0:3]) # enregistrer type Rayon X
+
+        if len(prob_b)==1 and len(e)>1:            # calculer la valeur moyenne et l'enregistrer au cas où |] compris et valeurs complètes
+            energy.append(np.mean(e))
+            prob.append(prob_b[0])
+            type_.append(type_b[0])
+        elif len(e)==len(prob_b) and len(e)>=1:    # enregistrer les valeurs au cas où sans |] et valeurs complètes
+            for i in range(len(e)):
+                energy.append(e[i])
+                prob.append(prob_b[i])
+                type_.append(type_b[i])
+        if end in index_end or end+1 in index_end: # enregistrer les résultats à la fin d'une fille
+            Energy.append(energy)
+            Prob.append(prob)
+            Type.append(type_)
+            energy = []
+            prob = []
+            type_ = []
+    #Energy =  np.array(Energy)
+    #Prob =  np.array(Prob)         
+    return  daug_name,Energy,Prob,Type        
+
+# tic()
+# d,e,p,t = readEShape('Cf-252')
+# toc() # 0 s
+#========  tester readEShape ==============
+# tic()
+# d,e,p,t = readEShape('Cf-252')
+#print(d,e,p,t)
+#d1,e1,p1,t1 = readEShape('At-218')
+#print(d1,e1,p1,t1)
+# toc()
+# print(d,e[0][1],p[1][2],t)
+# print('  ')
+# for i in range(len(d)):
+#     print(d[i],e[i],p[i],t[i])
+#     print(' ')
+#     print(len(e[i]),len(p[i]),len(t[i]))
+
+#============  traiter la relaxation ===============
+def relaxation_atom(daugther,rad,lacune='defaut'):
+    """
+    ---------
+    PARAMETRE
+    ---------
+    daugther -- type: str -- la fille tirée dans cette itération (par exemple NB95,PD110 etc.)
+    rad ------- type: str -- le radionucléide étudié (par exemple Am-241, C-11 etc.) 
+    lacuen ---- type: str -- la lacune atomique (par exemple 'Atom_K','Atom_L' etc.)
+
+    ------
+    RETURN
+    ------
+    Type ---- type de transition: Auger L ou K ou Rayon X
+    Energy -- énergie correspondante
+
+    """
+    daug_name,Energy,Prob,Type = readEShape(rad)  # tirer les vecteurs de rad d'Ensdf 
+
+    index_daug = daug_name.index(daugther)        # repérer l'indice de fille correspondante
+    
+    Energie = np.array(Energy[index_daug])                  # tirer le vecteur d'énergie
+    probability = np.array(Prob[index_daug])                # tirer le vecteur de proba
+    type_transi = Type[index_daug]                # tirer le vecteur de type
+
+
+    if len(probability) > 0:                      # le cas où le vecteur de proba/energie/type n'est pas vide
+        '''
+        posi_L = []
+        posi_K = []
+        
+        for i, p in enumerate(type_transi):       # repérer les indices de transition L ou K
+            if 'L' in p:
+                posi_L.append(i)                  # enregistrer la posotion de transition L
+
+            elif 'K' in p:
+                posi_K.append(i)                  # enregistrer la posotion de transition L
+        '''
+        if 'L' in lacune:                         # traiter le transition de couche L
+            prob_2 = []
+            energy_2 = []
+            type_2 = []
+            for il, pl in enumerate(type_transi):
+                if 'L' in pl:
+                    prob_2.append(probability[il])    # enregistrer les proba de transition L
+                    energy_2.append(Energie[il])      # enregistrer les energies de transition L
+                    type_2.append(type_transi[il])    # enregistrer les types de transition L
+
+        elif 'K' in lacune:                           # traiter le transition de couche K
+            prob_2 = []
+            energy_2 = []
+            type_2 = []
+            for ik, pk in enumerate(type_transi):     
+                if 'K' in pk:
+                    prob_2.append(probability[ik])    # enregistrer les proba de transition K
+                    energy_2.append(Energie[ik])      # enregistrer les energie de transition K
+                    type_2.append(type_transi[ik])    # enregistrer les type de transition K
+
+        #elif lacune=='defaut':                        # traiter le cas particulier qui ne précise pas la lacune
+            #prob_2 = probability
+            #energy_2 = Energie
+            #type_2 = type_transi
+            
+        else: # try to debugg
+            # print("issue: ", lacune)
+            prob_2 = 0   #probability
+            energy_2 = 0  # Energie
+            #if "M" in lacune:
+                #type_2 = "Atom_M"  #type_transi
+            #if "N" in lacune:
+                #type_2 = "Atom_N"            
+        
+     # sampling
+        #if len(probability)>1:               # le cas où la taille du vecteur de proba supérieur à 1
+
+            #prob_somme = np.sum(prob_2)      # calculer la somme de proba
+            #prob_2 /= prob_somme             # normaliser la proba
+        if lacune != "Atom_M" and lacune != "Atom_N":
+            if len(prob_2) != 0:
+                prob_2 = np.array(prob_2)           # convert to array
+                if len(probability)>1:
+                    prob_somme = np.sum(prob_2)      # calculer la somme de proba
+                    prob_2 /= prob_somme 
+                index_fin = sampling(prob_2)        # sample in probability of transition
+                type_fin = type_2[index_fin]        # type of transition     
+                energie_fin = energy_2[index_fin]   # energy of the transition
+            else:
+                # print("pas de transition de rayon X ni d'électron Auger pour cette lacune: ",lacune)
+                type_fin = 'NON'
+                energie_fin = 0            
+        else:
+            type_fin = 'NON'
+            energie_fin = 0 
+    else:                                            # le cas où le vecteur de proba est vide 
+        #print("pas de transition de rayon X ni d'électron Auger")
+        type_fin = 'NON'
+        energie_fin = 0
+    return type_fin,energie_fin
+# tic()
+# tf,ef = relaxation_atom('CR52', 'Mn-52', 'Atom_K')
+# toc() # 0 s
+#print(tf,ef)