TDCRPy 2.2.0__tar.gz → 2.5.0__tar.gz

{tdcrpy-2.2.0/TDCRPy.egg-info → tdcrpy-2.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TDCRPy
-Version: 2.2.0
+Version: 2.5.0
 Summary: TDCR model
 Home-page: https://pypi.org/project/TDCRPy/
 Author: RomainCoulon (Romain Coulon)

{tdcrpy-2.2.0 → tdcrpy-2.5.0/TDCRPy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: TDCRPy
-Version: 2.2.0
+Version: 2.5.0
 Summary: TDCR model
 Home-page: https://pypi.org/project/TDCRPy/
 Author: RomainCoulon (Romain Coulon)

{tdcrpy-2.2.0 → tdcrpy-2.5.0}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 import codecs
 import os
 
-VERSION = "2.2.0"
+VERSION = "2.5.0"
 
 DESCRIPTION = "TDCR model"
 

{tdcrpy-2.2.0 → tdcrpy-2.5.0}/tdcrpy/TDCRPy.py

@@ -84,7 +84,7 @@ def relaxAtom(daughter_relax,particle_vec,energy_vec,rad,Display=False,uncData=F
                 relaxation = False
     return particle_vec, energy_vec
 
-def TDCRPy(L, Rad, pmf_1, N, kB, V, mode="eff", Display=False, barp=False, Smodel=True, record = False, readRecHist = False, uncData=False):
+def TDCRPy(L, Rad, pmf_1, N, kB, V, mode="eff", Display=False, barp=False, Smodel=True, record = False, readRecHist = False, uncData = False, fullMC = False):
     """
     This is the main function of the TDCRPy package.
     The computation is made for a given solution containing a radionuclide (or a mixture of radionuclides), a given volume of scintillator V and a given Birks constant kB. 
@@ -254,7 +254,10 @@ def TDCRPy(L, Rad, pmf_1, N, kB, V, mode="eff", Display=False, barp=False, Smode
                     if decay != decaym:
                         if decay>0:
                             # print(decay-1,e_quenching,e_quenching2, evenement)
-                            efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2 = tl.detectProbabilities(L, e_quenching, e_quenching2, t1, evenement, extDT, measTime)
+                            if fullMC:
+                                efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2 = tl.detectProbabilitiesMC(L, e_quenching, e_quenching2, t1, evenement, extDT, measTime)
+                            else:
+                                efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2 = tl.detectProbabilities(L, e_quenching, e_quenching2, t1, evenement, extDT, measTime)
                             efficiency_S.append(efficiency0_S)
                             efficiency_T.append(efficiency0_T)
                             efficiency_D.append(efficiency0_D)
@@ -281,8 +284,11 @@ def TDCRPy(L, Rad, pmf_1, N, kB, V, mode="eff", Display=False, barp=False, Smode
                             e_quenching2.append(energy)
                         else:
                             e_quenching.append(energy)
-                            
-            efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2 = tl.detectProbabilities(L, e_quenching, e_quenching2, t1, evenement, extDT, measTime)
+            
+            if fullMC:
+                efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2 = tl.detectProbabilitiesMC(L, e_quenching, e_quenching2, t1, evenement, extDT, measTime)
+            else:
+                efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2 = tl.detectProbabilities(L, e_quenching, e_quenching2, t1, evenement, extDT, measTime)
             efficiency_S.append(efficiency0_S)
             efficiency_T.append(efficiency0_T)
             efficiency_D.append(efficiency0_D)
@@ -949,7 +955,10 @@ def TDCRPy(L, Rad, pmf_1, N, kB, V, mode="eff", Display=False, barp=False, Smode
             ====================
             '''
             if evenement == 1: e_quenching2 = 0; t1=0
-            efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2 = tl.detectProbabilities(L, e_quenching, e_quenching2, t1, evenement, extDT, measTime)
+            if fullMC:
+                efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2 = tl.detectProbabilitiesMC(L, e_quenching, e_quenching2, t1, evenement, extDT, measTime)
+            else:
+                efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2 = tl.detectProbabilities(L, e_quenching, e_quenching2, t1, evenement, extDT, measTime)
             efficiency_S.append(efficiency0_S)
             efficiency_T.append(efficiency0_T)
             efficiency_D.append(efficiency0_D)
@@ -1227,20 +1236,20 @@ def effA(TD, Rad, pmf_1, kB, V, L=1, maxiter=20, xatol=1e-7, disp=False):
 
 
 # mode = "eff"                # ask for efficiency calculation
-# Rad="Na-22"                 # radionuclides
+# Rad="Fe-55"                 # radionuclides
 # pmf_1="1"                   # relatives fractions of the radionulides
 # N = 1000                    # number of Monte Carlo trials
 # kB =1.0e-5                  # Birks constant in cm keV-1
 # V = 10                      # volume of scintillator in mL
-# L=np.logspace(-3,2,num=100) # free parameter in keV-1
+# L=np.logspace(-1,2,num=100) # free parameter in keV-1
 
-# # TDCRPy(1, Rad, pmf_1, 10, kB, V, mode, Display= True, barp=False, record=True)
 # # Record decay histories in temporary files
-# TDCRPy(L[0], Rad, pmf_1, N, kB, V, mode, barp=True, record=True)
+# TDCRPy(L[0], Rad, pmf_1, N, kB, V, mode, barp=False, record=True, fullMC=False)
+# # TDCRPy(100, Rad, pmf_1, N, kB, V, mode, barp=False, record=True, fullMC=True)
 
 # effS, u_effS, effD, u_effD, effT, u_effT, effD2, u_effD2 = [], [],[], [],[], [], [], []
 # for l in tqdm(L, desc="free parameters ", unit=" iterations"):
-#   out = TDCRPy(l, Rad, pmf_1, N, kB, V, mode, readRecHist=True)
+#   out = TDCRPy(l, Rad, pmf_1, N, kB, V, mode, readRecHist=True, fullMC=False)
 #   effS.append(out[2])
 #   u_effS.append(out[3])
 #   effD.append(out[2])

{tdcrpy-2.2.0 → tdcrpy-2.5.0}/tdcrpy/TDCR_model_lib.py

@@ -60,6 +60,7 @@ def readParameters(disp=False):
     diam_micelle = config["Inputs"].getfloat("diam_micelle")
     fAq = config["Inputs"].getfloat("fAq")
     micCorr = config["Inputs"].getboolean("micCorr")
+    alphaDir = config["Inputs"].getfloat("alphaDir")
     
     if disp:
         print(f"number of integration bins for electrons = {nE_electron}")
@@ -76,13 +77,14 @@ def readParameters(disp=False):
         print(f"activation of the micelle correction = {micCorr}")
         print(f"diameter of micelle = {diam_micelle} nm")
         print(f"acqueous fraction = {fAq}")
+        print(f"alpha parameter of the hidden Dirichlet process = {alphaDir}")
         print(f"coincidence resolving time = {tau} ns")
         print(f"extended dead time = {extDT} µs")
         print(f"measurement time = {measTime} min")
     
-    return nE_electron, nE_alpha, RHO, Z, A, depthSpline, Einterp_a, Einterp_e, diam_micelle, fAq, tau, extDT, measTime, micCorr, pH,pC,pN,pO,pP,pCl
+    return nE_electron, nE_alpha, RHO, Z, A, depthSpline, Einterp_a, Einterp_e, diam_micelle, fAq, tau, extDT, measTime, micCorr, alphaDir, pH,pC,pN,pO,pP,pCl
 
-nE_electron, nE_alpha, RHO, Z, A, depthSpline, Einterp_a, Einterp_e, diam_micelle, fAq, tau, extDT, measTime, micCorr, pH,pC,pN,pO,pP,pCl = readParameters()
+nE_electron, nE_alpha, RHO, Z, A, depthSpline, Einterp_a, Einterp_e, diam_micelle, fAq, tau, extDT, measTime, micCorr, alphaDir, pH,pC,pN,pO,pP,pCl = readParameters()
 
 p_atom = np.array([pH,pC,pN,pO,pP,pCl]) # atom abondance in the scintillator
 p_atom /= sum(p_atom) 
@@ -192,6 +194,12 @@ def modifyMicCorr(x):
     x0 = readParameters()[13]
     data1 = data0.replace(f"micCorr = {x0}",f"micCorr= {x}")
     writeConfifAsstr(data1)
+    
+def modifyAlphaDir(x):
+    data0 = readConfigAsstr()
+    x0 = readParameters()[14]
+    data1 = data0.replace(f"alphaDir = {x0}",f"alphaDir = {x}")
+    writeConfifAsstr(data1)
 
 def read_temp_files(copy=False, path="C:"):
     
@@ -2894,6 +2902,7 @@ def detectProbabilities(L, e_quenching, e_quenching2, t1, evenement, extDT, meas
         symm = False
     else:
         symm = True
+         
         
     if symm:
         # print(evenement !=1, t1 > extDT*1e-6, t1 < measTime*60)
@@ -2935,8 +2944,6 @@ def detectProbabilities(L, e_quenching, e_quenching2, t1, evenement, extDT, meas
             efficiency0_A2 = p_single
             efficiency0_B2 = efficiency0_A2
             efficiency0_D2 = p_single**2
-        
-                            
     else:
         if evenement !=1 and t1 > extDT*1e-6 and t1 < measTime*60:
             # TDCR            
@@ -3005,6 +3012,126 @@ def detectProbabilities(L, e_quenching, e_quenching2, t1, evenement, extDT, meas
     return efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2        
 
 
+def detectProbabilitiesMC(L, e_quenching, e_quenching2, t1, evenement, extDT, measTime, dir_param = alphaDir):
+    """
+    Calculate detection probabilities for LS counting systems - see Broda, R., Cassette, P., Kossert, K., 2007. Radionuclide metrology using liquid scintillation counting. Metrologia 44. https://doi.org/10.1088/0026-1394/44/4/S06 
+
+    Parameters
+    ----------
+    L : float or tuple
+        If L is float, then L is the global free parameter. If L is tuple, then L is a triplet of free parameters. unit keV-1
+    e_quenching : list
+        List of quenched deposited energies from prompt particles in keV.
+    e_quenching2 : list
+        List of quenched deposited energies from delayed particles in keV.
+    t1 : float
+        decay time of the delayed transitions in s.
+    evenement : interger
+        number of pulses per decay (prompt (1), prompt + delayed (2)).
+    extDT : float
+        extended dead time of the system in ns.
+    measTime : float
+        measurement time in minutes.
+
+    Returns
+    -------
+    efficiency0_S : float
+        detection probability of single event.
+    efficiency0_D : float
+        detection probability of double coincidences.
+    efficiency0_T : float
+        detection probability of triple coincidences.
+    efficiency0_AB : float
+        detection probability of coincidences between channels A and B.
+    efficiency0_BC : float
+        detection probability of coincidences between channels B and C.
+    efficiency0_AC : float
+        detection probability of coincidences between channels A and C.
+    efficiency0_D2 : float
+        detection probability of coincidences in a C/N system.
+
+    """
+    if isinstance(L, (tuple, list)):
+        symm = False
+    else:
+        symm = True
+    
+    alpha = 1
+    
+    if alpha < 1000:
+        dirichTD = np.random.dirichlet([alpha, alpha, alpha])
+        dirichCN = np.random.dirichlet([alpha, alpha])      
+    else:
+        dirichTD = [1/3, 1/3, 1/3]
+        dirichCN = [1/2, 1/2]
+    
+    efficiency0_S = 0;    efficiency0_T = 0;    efficiency0_D = 0
+    efficiency0_AB = 0;    efficiency0_BC = 0;    efficiency0_AC = 0
+    efficiency0_D2 = 0;
+    
+    if symm:
+        n_ph = np.random.poisson(sum(np.asarray(e_quenching))*L)
+        # TDCR
+        n_phPMT = np.random.multinomial(n_ph, dirichTD)
+        if sum(n_phPMT>1)>0: efficiency0_S =1
+        if sum(n_phPMT>1)>1: efficiency0_D =1
+        if sum(n_phPMT>1)>2: efficiency0_T =1
+        if n_phPMT[0]>1 and n_phPMT[1]>1: efficiency0_AB =1 
+        if n_phPMT[1]>1 and n_phPMT[2]>1: efficiency0_BC =1 
+        if n_phPMT[0]>1 and n_phPMT[2]>1: efficiency0_AC =1
+        # C/N
+        n_phPMT = np.random.multinomial(n_ph, dirichCN)
+        if sum(n_phPMT>1)>1: efficiency0_D2 =1
+        
+        if evenement !=1 and t1 > extDT*1e-6 and t1 < measTime*60:  
+            n_ph2 = np.random.poisson(sum(np.asarray(e_quenching2))*L)
+            # TDCR
+            n_phPMT2 = np.random.multinomial(n_ph2, dirichTD)
+            if sum(n_phPMT2>1)>0: efficiency0_S +=1
+            if sum(n_phPMT2>1)>1: efficiency0_D +=1
+            if sum(n_phPMT2>1)>2: efficiency0_T +=1
+            if n_phPMT2[0]>1 and n_phPMT2[1]>1: efficiency0_AB +=1 
+            if n_phPMT2[1]>1 and n_phPMT2[2]>1: efficiency0_BC +=1 
+            if n_phPMT2[0]>1 and n_phPMT2[2]>1: efficiency0_AC +=1
+            # C/N
+            n_phPMT2 = np.random.multinomial(n_ph2, dirichCN)
+            if sum(n_phPMT2>1)>1: efficiency0_D2 +=1           
+            
+    else: # asym
+        Lm = np.mean(L)
+        n_ph = np.random.poisson(sum(np.asarray((e_quenching))*Lm))
+        # TDCR
+        n_phPMT = np.random.multinomial(n_ph, [L[0]*dirichTD[0]/Lm, L[1]*dirichTD[1]/Lm, L[2]*dirichTD[2]/Lm])
+        if sum(n_phPMT>1)>0: efficiency0_S =1
+        if sum(n_phPMT>1)>1: efficiency0_D =1
+        if sum(n_phPMT>1)>2: efficiency0_T =1
+        if n_phPMT[0]>1 and n_phPMT[1]>1: efficiency0_AB =1 
+        if n_phPMT[1]>1 and n_phPMT[2]>1: efficiency0_BC =1 
+        if n_phPMT[0]>1 and n_phPMT[2]>1: efficiency0_AC =1
+        # C/N
+        n_phPMT = np.random.multinomial(n_ph, [L[0]/(2*Lm), L[1]/(2*Lm)])
+        if sum(n_phPMT>1)>1: efficiency0_D2 =1       
+        
+        if evenement !=1 and t1 > extDT*1e-6 and t1 < measTime*60:
+            n_ph2 = np.random.poisson(sum(np.asarray(e_quenching2))*Lm)
+            # TDCR
+            n_phPMT2 = np.random.multinomial(n_ph2, [L[0]*dirichCN[0]/Lm, L[1]*dirichCN[1]/Lm, L[2]*dirichCN[2]/Lm])
+            if sum(n_phPMT2>1)>0: efficiency0_S +=1
+            if sum(n_phPMT2>1)>1: efficiency0_D +=1
+            if sum(n_phPMT2>1)>2: efficiency0_T +=1
+            if n_phPMT2[0]>1 and n_phPMT2[1]>1: efficiency0_AB +=1 
+            if n_phPMT2[1]>1 and n_phPMT2[2]>1: efficiency0_BC +=1 
+            if n_phPMT2[0]>1 and n_phPMT2[2]>1: efficiency0_AC +=1
+            # C/N
+            n_phPMT2 = np.random.multinomial(n_ph2, [L[0]/(2*Lm), L[1]/(2*Lm)])
+            if sum(n_phPMT2>1)>1: efficiency0_D2 +=1   
+        
+    return efficiency0_S, efficiency0_D, efficiency0_T, efficiency0_AB, efficiency0_BC, efficiency0_AC, efficiency0_D2         
+
+
+
+
+
 def efficienciesEstimates(efficiency_S, efficiency_D, efficiency_T, efficiency_AB, efficiency_BC, efficiency_AC, efficiency_D2, N):
     """
     Calculate detection efficiencies from list of detection probabilities per decays.

{tdcrpy-2.2.0 → tdcrpy-2.5.0}/tdcrpy/config.toml

@@ -31,6 +31,10 @@ diam_micelle = 2
 # acqueous fraction of the scintillator
 fAq = 0.1
 
+## OPTICAL PROPERTIES
+# Dirichlet parameter
+alphaDir = 100000
+
 ## PROPERTIES OF THE COUNTER
 # Coincidence resolving time (ns)
 tau = 50