TDCRPy 2.0.5__tar.gz → 2.0.7__tar.gz

{tdcrpy-2.0.5/TDCRPy.egg-info → tdcrpy-2.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: TDCRPy
-Version: 2.0.5
+Version: 2.0.7
 Summary: TDCR model
 Home-page: https://pypi.org/project/TDCRPy/
 Author: RomainCoulon (Romain Coulon)
@@ -28,14 +28,18 @@ Requires-Dist: configparser
 Requires-Dist: importlib.resources
 Requires-Dist: matplotlib
 
-# TDCRPy
+# 1. About TDCRPy
 
-`TDCRPy` is a Python code to calculate detection efficiency of a liquid scintillation counter using 3-photomultiplier tubes.
-The calculation is based on the photo-physical model called of the Triple-to-Double-Coincidence-Ratio method (TDCR) and a Monte-Carlo sampling allowing to adress complexe decay schemes and radionuclide mixtures.
+`TDCRPy` is a Python code to estimate detection efficiencies of liquid scintillation counters (TDCR or CIEMAT/NIST).
+The calculation is based on a photo-physical stochastic model allowing to adress complexe decay schemes and radionuclide mixtures.
 
 The code is developped and maintained by the BIPM (MIT license).
 
-## Installation
+Technical details can be found in
+
+http://dx.doi.org/10.13140/RG.2.2.15682.80321
+
+## 1.1 Installation
 
 `TDCRPy` requires that the following packages are installed in your `Python` environement.
 
@@ -66,7 +70,7 @@ The module can be imported in your Python code such as.
 import tdcrpy
 ```
 
-## Test
+## 1.2 Test
 
 To run the unit tests of the package:
 
@@ -81,20 +85,239 @@ coverage run -m unittest tdcrpy.test.test_tdcrpy
 coverage report -m
 ```
 
+# 2. Quick start with the TDCRPy code
+
+```python
+import tdcrpy
+```
+
+## 2.1 Symmetric PMTs
+
+### 2.1.1 Estimation of detection efficiencies given the free parameter
+
+
+```python
+mode = "eff"               # ask for efficiency calculation
+L = 1.2                    # free parameter in keV-1
+Rad="Co-60"                # radionuclide
+pmf_1="1"                  # relative fraction of the radionulide
+N = 1000                   # number of Monte Carlo trials
+kB =1.0e-5                 # Birks constant in cm keV-1
+V = 10                     # volume of scintillator in mL
+```
+
+
+```python
+result = tdcrpy.TDCRPy.TDCRPy(L, Rad, pmf_1, N, kB, V, mode)
+```
+
+
+```python
+print(f"efficiency S = {round(result[0],4)} +/- {round(result[1],4)}")
+print(f"efficiency D = {round(result[2],4)} +/- {round(result[3],4)}")
+print(f"efficiency T = {round(result[4],4)} +/- {round(result[5],4)}")
+print(f"efficiency D (C/N system) = {round(result[12],4)} +/- {round(result[13],4)}")
+```
+
+    efficiency S = 0.9859 +/- 0.0031
+    efficiency D = 0.9738 +/- 0.0043
+    efficiency T = 0.9527 +/- 0.0057
+    efficiency D (C/N system) = 0.9702 +/- 0.0045
+    
+
+### 2.1.2 Estimation of detection efficiencies given the measured TDCR parameter
+
+
+```python
+TD = 0.977667386529166     # TDCR parameter
+```
+
+
+```python
+result = tdcrpy.TDCRPy.eff(TD, Rad, pmf_1, kB, V)
+```
+
+    global free parameter = 1.1991314352332345 keV-1
+    
+
+
+```python
+print(f"free parameter = {round(result[0],4)} keV-1")
+print(f"efficiency S = {round(result[2],4)} +/- {round(result[3],4)}")
+print(f"efficiency D = {round(result[4],4)} +/- {round(result[5],4)}")
+print(f"efficiency T = {round(result[6],4)} +/- {round(result[7],4)}")
+print(f"efficiency D (C/N system) = {round(result[14],4)} +/- {round(result[15],4)}")
+```
+
+    free parameter = 1.1991 keV-1
+    efficiency S = 0.9858 +/- 0.001
+    efficiency D = 0.973 +/- 0.0014
+    efficiency T = 0.9512 +/- 0.0018
+    efficiency D (C/N system) = 0.9692 +/- 0.0014
+    
+
+## 2.2 Asymmetric PMTs
+
+### 2.2.1 Estimation of detection efficiencies given the free parameters
+
+
+```python
+mode = "eff"               # ask for efficiency calculation
+L = (1.1, 1.3, 1.2)        # free parameter in keV-1
+Rad="Co-60"                # radionuclide
+pmf_1="1"                  # relative fraction of the radionulide
+N = 1000                   # number of Monte Carlo trials
+kB =1.0e-5                 # Birks constant in cm keV-1
+V = 10                     # volume of scintillator in mL
+```
+
+
+```python
+result = tdcrpy.TDCRPy.TDCRPy(L, Rad, pmf_1, N, kB, V)
+```
+
+
+```python
+print(f"efficiency S = {round(result[0],4)} +/- {round(result[1],4)}")
+print(f"efficiency D = {round(result[2],4)} +/- {round(result[3],4)}")
+print(f"efficiency T = {round(result[4],4)} +/- {round(result[5],4)}")
+print(f"efficiency AB = {round(result[6],4)} +/- {round(result[7],4)}")
+print(f"efficiency BC = {round(result[8],4)} +/- {round(result[9],4)}")
+print(f"efficiency AC = {round(result[10],4)} +/- {round(result[11],4)}")
+print(f"efficiency D (C/N system) = {round(result[12],4)} +/- {round(result[13],4)}")
+```
+
+    efficiency S = 0.9904 +/- 0.0024
+    efficiency D = 0.9803 +/- 0.0037
+    efficiency T = 0.9625 +/- 0.005
+    efficiency AB = 0.9684 +/- 0.0045
+    efficiency BC = 0.9696 +/- 0.0044
+    efficiency AC = 0.9674 +/- 0.0046
+    efficiency D (C/N system) = 0.9772 +/- 0.0039
+    
+
+### 2.2.2 Estimation of detection efficiencies given the measured TDCR parameters
+
+
+```python
+TD = [0.977667386529166, 0.992232838598821, 0.992343419459002, 0.99275350064608]
+```
+
 
-# Modify the parameters of the model (advanced settings)
+```python
+result = tdcrpy.TDCRPy.eff(TD, Rad, pmf_1, kB, V)
+```
+
+    global free parameter = 1.2369501044018718 keV-1
+    free parameters = [1.2369501 1.2369501 1.2369501] keV-1
+    
 
 
 ```python
-#pip install TDCRPy --upgrade
+print(f"Global free parameter = {round(result[0],4)} keV-1")
+print(f"free parameter of PMT A = {round(result[1][0],4)} keV-1")
+print(f"free parameter of PMT B = {round(result[1][1],4)} keV-1")
+print(f"free parameter of PMT C = {round(result[1][2],4)} keV-1")
+print(f"efficiency S = {round(result[2],4)} +/- {round(result[3],4)}")
+print(f"efficiency D = {round(result[4],4)} +/- {round(result[5],4)}")
+print(f"efficiency T = {round(result[6],4)} +/- {round(result[7],4)}")
+print(f"efficiency AB = {round(result[8],4)} +/- {round(result[9],4)}")
+print(f"efficiency BC = {round(result[10],4)} +/- {round(result[11],4)}")
+print(f"efficiency AC = {round(result[12],4)} +/- {round(result[13],4)}")
+print(f"efficiency D (C/N system) = {round(result[14],4)} +/- {round(result[15],4)}")
 ```
 
+    Global free parameter = 1.237 keV-1
+    free parameter of PMT A = 1.237 keV-1
+    free parameter of PMT B = 1.237 keV-1
+    free parameter of PMT C = 1.237 keV-1
+    efficiency S = 0.9872 +/- 0.0009
+    efficiency D = 0.9751 +/- 0.0013
+    efficiency T = 0.9533 +/- 0.0018
+    efficiency AB = 0.9606 +/- 0.0016
+    efficiency BC = 0.9606 +/- 0.0016
+    efficiency AC = 0.9606 +/- 0.0016
+    efficiency D (C/N system) = 0.9714 +/- 0.0014
+    
+
+## 2.3 Radionuclide mixture
+
+### 2.3.1 Estimation of detection efficiencies given the free parameter
+
+
+```python
+mode = "eff"               # ask for efficiency calculation
+mode2 = "sym"              # specify that symmetric PMTs is considered
+L = 1.2                    # free parameter in keV-1
+Rad="Co-60, H-3"           # radionuclides
+pmf_1="0.8, 0.2"                  # 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
+```
+
+
+```python
+result = tdcrpy.TDCRPy.TDCRPy(L, Rad, pmf_1, N, kB, V)
+```
+
+
+```python
+print(f"efficiency S = {round(result[0],4)} +/- {round(result[1],4)}")
+print(f"efficiency D = {round(result[2],4)} +/- {round(result[3],4)}")
+print(f"efficiency T = {round(result[4],4)} +/- {round(result[5],4)}")
+print(f"efficiency D (C/N system) = {round(result[12],4)} +/- {round(result[13],4)}")
+```
+
+    efficiency S = 0.9622 +/- 0.0045
+    efficiency D = 0.9163 +/- 0.007
+    efficiency T = 0.8482 +/- 0.0096
+    efficiency D (C/N system) = 0.9037 +/- 0.0074
+    
+
+### 2.3.2 Estimation of detection efficiencies given the measured TDCR parameter
+
+
+```python
+TD = 0.977667386529166     # TDCR parameter
+```
+
+
+```python
+result = tdcrpy.TDCRPy.eff(TD, Rad, pmf_1, kB, V)
+```
+
+    global free parameter = 4.999573818598962 keV-1
+    
+
+
+```python
+print(f"free parameter = {round(result[0],4)} keV-1")
+print(f"efficiency S = {round(result[2],4)} +/- {round(result[3],4)}")
+print(f"efficiency D = {round(result[4],4)} +/- {round(result[5],4)}")
+print(f"efficiency T = {round(result[6],4)} +/- {round(result[7],4)}")
+print(f"efficiency D (C/N system) = {round(result[14],4)} +/- {round(result[15],4)}")
+```
+
+    free parameter = 4.9996 keV-1
+    efficiency S = 0.9835 +/- 0.001
+    efficiency D = 0.9677 +/- 0.0015
+    efficiency T = 0.9397 +/- 0.002
+    efficiency D (C/N system) = 0.9629 +/- 0.0016
+    
+
+
+```python
+
+```
+
+# 3. Advanced settings
 
 ```python
 import tdcrpy as td
 ```
 
-## Read the parameters
+## 3.1 Read the parameters
 
 
 ```python
@@ -119,7 +342,7 @@ print("\nparameters in a list: ", td.TDCR_model_lib.readParameters(disp=True))
     parameters in a list:  (1000, 1000, 0.96, 5.2, 11.04, 5, 100.0, 1.5, 2.0, 0.1, 50, 10, 20, False)
     
 
-### Change energy binning the quenching function of electrons 
+## 3.2 Change energy binning the quenching function of electrons 
 
 
 ```python
@@ -147,7 +370,7 @@ td.TDCR_model_lib.modifynE_electron(1000)
     measurement time = 20 min
     
 
-### Change energy binning the quenching function of alpha particles
+## 3.3 Change energy binning the quenching function of alpha particles
 
 
 ```python
@@ -175,7 +398,7 @@ td.TDCR_model_lib.modifynE_alpha(1000)
     measurement time = 20 min
     
 
-### Change the density (in g/cm3) of the LS source
+## 3.4 Change the density (in g/cm3) of the LS source
 
 
 ```python
@@ -203,7 +426,7 @@ td.TDCR_model_lib.modifyDensity(0.96)
     measurement time = 20 min
     
 
-### Change the mean charge number of the LS source
+## 3.5 Change the mean charge number of the LS source
 
 
 ```python
@@ -231,7 +454,7 @@ td.TDCR_model_lib.modifyZ(5.2)
     measurement time = 20 min
     
 
-### Change the mean atomic mass number of the LS source
+## 3.6 Change the mean atomic mass number of the LS source
 
 
 ```python
@@ -259,7 +482,7 @@ td.TDCR_model_lib.modifyA(11.04)
     measurement time = 20 min
     
 
-### Change the depht paramerter of the spline interpolation of the quenching function
+## 3.7 Change the depht paramerter of the spline interpolation of the quenching function
 
 
 ```python
@@ -287,7 +510,7 @@ td.TDCR_model_lib.modifyDepthSpline(5)
     measurement time = 20 min
     
 
-### Change the energy threshold (in keV) above which the interpolation is applied (for alpha particles)
+## 3.8 Change the energy threshold (in keV) above which the interpolation is applied (for alpha particles)
 
 
 ```python
@@ -315,7 +538,7 @@ td.TDCR_model_lib.modifyEinterp_a(100)
     measurement time = 20 min
     
 
-### Change the energy threshold (in keV) above which the interpolation is applied (for electrons)
+## 3.9 Change the energy threshold (in keV) above which the interpolation is applied (for electrons)
 
 
 ```python
@@ -343,7 +566,7 @@ td.TDCR_model_lib.modifyEinterp_e(1.5)
     measurement time = 20 min
     
 
-### Activate/desactivate the micelles correction
+## 3.10 Activate/desactivate the micelles correction
 
 
 ```python
@@ -371,7 +594,7 @@ td.TDCR_model_lib.modifyMicCorr(True)
     measurement time = 20 min
     
 
-### Change the diameter of reverse micelles (in nm)
+## 3.11 Change the diameter of reverse micelles (in nm)
 
 
 ```python
@@ -399,7 +622,7 @@ td.TDCR_model_lib.modifyDiam_micelle(2.0)
     measurement time = 20 min
     
 
-### Change the acqueous fraction of the LS source
+## 3.12 Change the acqueous fraction of the LS source
 
 
 ```python
@@ -427,7 +650,7 @@ td.TDCR_model_lib.modifyfAq(0.1)
     measurement time = 20 min
     
 
-### Change the coincidence resolving time of the TDCR counter (in ns)
+## 3.13 Change the coincidence resolving time of the TDCR counter (in ns)
 
 
 ```python
@@ -455,7 +678,7 @@ td.TDCR_model_lib.modifyTau(50)
     measurement time = 20 min
     
 
-### Change the extended dead time of the TDCR counter (in µs)¶
+## 3.14 Change the extended dead time of the TDCR counter (in µs)¶
 
 
 ```python
@@ -483,7 +706,7 @@ td.TDCR_model_lib.modifyDeadTime(10)
     measurement time = 20 min
     
 
-### Change the measurement time (in min)¶
+## 3.15 Change the measurement time (in min)¶
 
 
 ```python
@@ -510,132 +733,7 @@ td.TDCR_model_lib.modifyMeasTime(20)
     extended dead time = 10 µs
     measurement time = 60 min
     
-
-
-# Efficiency curves using TDCRPy
-
-
-```python
-# pip install TDCRPy --upgrade
-```
-
-
-```python
-import tdcrpy as td
-import numpy as np
-from tqdm import tqdm
-import matplotlib.pyplot as plt
-```
-
-
-```python
-mode = "eff"                # ask for efficiency calculation
-Rad="Co-60"                 # 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
-
-# Record decay histories in temporary files
-td.TDCRPy.TDCRPy(L[0], Rad, pmf_1, N, kB, V, mode, barp=True, record=True)
-
-effS, u_effS, effD, u_effD, effT, u_effT, effD2, u_effD2 = [], [],[], [],[], [], [], []
-for l in tqdm(L, desc="free parameters ", unit=" iterations"):
-  out = td.TDCRPy.TDCRPy(l, Rad, pmf_1, N, kB, V, mode, readRecHist=True)
-  effS.append(out[2])
-  u_effS.append(out[3])
-  effD.append(out[2])
-  u_effD.append(out[3])
-  effT.append(out[4])
-  u_effT.append(out[5])
-  effD2.append(out[12])
-  u_effD2.append(out[13])
-```
-
-    
-     ______  ______  ______ _______  ________
-    |__  __||  ___ \|  ___||  ___ | |  ____ |
-      | |   | |  | || |    | |  | | | |___| |___     ___
-      | |   | |  | || |    | |__| | |  _____|\  \   |  |
-      | |   | |__| || |____|  __  \ | |       \  \  |  |
-      |_|   |_____/ |_____||_|  \__\|_|        \  \_|  |
-      +++++++++++++++++++++++++++++++++++++++++/      /
-      ________________________________________/      /
-     |______________________________________________/     
-    
-    
-    version 2.0.2
-    BIPM 2023 - license MIT 
-    distribution: https://pypi.org/project/TDCRPy 
-    developement: https://github.com/RomainCoulon/TDCRPy 
-    
-    start calculation...
-    
-
-    Processing: 100%|█████████████████████████████████████████████████████████████| 1000/1000 [00:24<00:00, 40.79 decays/s]
-    free parameters : 100%|█████████████████████████████████████████████████████| 100/100 [00:02<00:00, 35.96 iterations/s]
-    
-
-
-```python
-effS=np.asarray(effS)
-effT=np.asarray(effT)
-effD=np.asarray(effD)
-effD2=np.asarray(effD2)
-u_effS=np.asarray(u_effS)
-u_effT=np.asarray(u_effT)
-u_effD=np.asarray(u_effD)
-u_effD2=np.asarray(u_effD2)
-
-tdcr=effT/effD
-u_tdcr=np.sqrt(u_effD**2*effT**2/effD**4+u_effT**2/effD**2)
-
-plt.figure("efficiency vs free parameter")
-plt.clf()
-plt.errorbar(L,effD,yerr=u_effD,fmt="-k",label="double coincidences")
-plt.errorbar(L,effT,yerr=u_effT,fmt="-r",label="triple coincidences")
-plt.errorbar(L,effD2,yerr=u_effD2,fmt="-g",label="double coincidences (CIEMAT/NIST)")
-plt.xscale('log')
-plt.xlabel(r'$L$ /keV$^{-1}$', fontsize=14)
-plt.ylabel(r'$\epsilon$', fontsize=14)
-plt.legend()
-
-plt.figure("efficiency vs TDCR")
-plt.clf()
-plt.errorbar(tdcr,effD,xerr=u_tdcr,yerr=u_effD,fmt="-k")
-#plt.xscale('log')
-plt.xlabel(r'$R_T/R_D$', fontsize=14)
-plt.ylabel(r'$\epsilon_{D}$', fontsize=14)
-```
-
-
-
-
-    Text(0, 0.5, '$\\epsilon_{D}$')
-
-
-
-
-    
-![png](output_4_1.png)
-    
-
-
-
-    
-![png](output_4_2.png)
-    
-
-
-
-# Read Beta spectrum
-
-
-```python
-# pip install TDCRPy --upgrade
-```
-
+# 4. Read Beta spectrum
 
 ```python
 import tdcrpy as td
@@ -647,10 +745,10 @@ import numpy as np
 ```python
 radionuclide = "Sr-89"
 mode = "beta-" # 'beta-' or 'beta+'
-level = 'tot' # 0,1,2,3 .... or 'tot'
+level = 'tot'  # 0,1,2,3 .... or 'tot'
 ```
 
-## Get information about the BetaShape version
+## 4.1 Get information about the BetaShape version
 
 
 ```python
@@ -661,7 +759,7 @@ print(td.TDCR_model_lib.readBetaShapeInfo(radionuclide,mode,level))
      (05/2024), DDEP 2004 evaluation and Q-value from AME2020-
     
 
-## Read the energy spectrum tabulated from BetaShape
+## 4.2 Read the energy spectrum tabulated from BetaShape
 
 
 ```python
@@ -683,11 +781,11 @@ plt.ylabel(r'$p(E)$ /(keV$^{-1}$)', fontsize=14)
 
 
     
-![png](output_7_1.png)
+![png](docs/readBetaSpectrum/output_7_1.png)
     
 
 
-## Read the deposited energy spectrum
+## 4.3 Read the deposited energy spectrum
 
 This spectrum is built by TDCRPy (function `buildBetaSpectra`) to be used for the analytical TDCR model
 
@@ -713,7 +811,7 @@ plt.ylabel(r'$p(E)$ /(keV$^{-1}$)', fontsize=14)
 
 
     
-![png](output_9_1.png)
+![png](docs/readBetaSpectrum/output_9_1.png)
     
 
 
@@ -722,14 +820,7 @@ plt.ylabel(r'$p(E)$ /(keV$^{-1}$)', fontsize=14)
 
 ```
 
-
-# Estimation of stopping powers in liquid scintillator
-
-
-```python
-# pip install TDCRPy --upgrade
-```
-
+# 5. Stopping power
 
 ```python
 import tdcrpy as td
@@ -737,7 +828,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 ```
 
-## Stopping power at a given energy
+## 5.1 Stopping power at a given energy
 
 
 ```python
@@ -753,7 +844,7 @@ print(f"dE/dx = {result_electron*1e3:.4g} keV/cm for electrons" )
     dE/dx = 3419 keV/cm for electrons
     
 
-## Plot stopping power curves
+## 5.2 Plot stopping power curves
 
 
 ```python
@@ -781,18 +872,9 @@ plt.legend()
 
 
     
-![png](output_6_1.png)
+![png](docs/stoppingPower/output_6_1.png)
     
-
-
-
-# Simulation of the scintillation quenching
-
-
-```python
-# pip install TDCRPy --upgrade
-```
-
+# 6. Scintillation quenching model
 
 ```python
 import tdcrpy as td
@@ -800,7 +882,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 ```
 
-## Calculate the quenched energy from the Birks model
+## 6.1 Calculate the quenched energy from the Birks model
 
 
 ```python
@@ -818,7 +900,7 @@ print(f"For alpha particles => Initial energy = {ei} keV, quenched energy = {eq_
     For alpha particles => Initial energy = 1000 keV, quenched energy = 48.934 keV
     
 
-## Correction of the micelle effect
+## 6.2 Correction of the micelle effect
 
 The deposited energy ratios were evaluation by GEANT4-DNA [1].
 
@@ -868,11 +950,11 @@ plt.legend()
 
 
     
-![png](output_6_1.png)
+![png](docs/quenchingModel/output_6_1.png)
     
 
 
-## Scintillation quenching function from the Birks model (with micelle effect)
+## 6.3 Scintillation quenching function from the Birks model (with micelle effect)
 
 
 ```python
@@ -906,7 +988,7 @@ plt.legend()
 
 
     
-![png](output_8_1.png)
+![png](docs/quenchingModel/output_8_1.png)
     
 
 
@@ -915,17 +997,10 @@ plt.legend()
 
 ```
 
-
 ```python
-# Simulation of the interaction of ionizing particles in the scintillant
+# 7. Interaction of ionizing particles
 ```
 
-
-```python
-#pip install TDCRPy --upgrade
-```
-
-
 ```python
 # pip install opencv-python
 ```
@@ -938,11 +1013,7 @@ import numpy as np
 import cv2
 ```
 
-## Response for a given initial energy
-
-## Read bivariate distributions
-
-### Electrons from 0 keV to 200 keV
+## 7.1 Distributions for electrons from 0 keV to 200 keV
 
 
 ```python
@@ -967,11 +1038,11 @@ plt.show()
 
 
     
-![png](output_7_0.png)
+![png](docs/interaction/output_7_0.png)
     
 
 
-### Electrons from 200 keV to 2 MeV
+## 7.2 Distributions for electrons from 200 keV to 2 MeV
 
 
 ```python
@@ -997,11 +1068,11 @@ plt.show()
 
 
     
-![png](output_9_0.png)
+![png](docs/interaction/output_9_0.png)
     
 
 
-### Electrons from 2 MeV to 8 MeV
+## 7.3 Distributions for electrons from 2 MeV to 8 MeV
 
 
 ```python
@@ -1027,11 +1098,11 @@ plt.show()
 
 
     
-![png](output_11_0.png)
+![png](docs/interaction/output_11_0.png)
     
 
 
-### Photons from 0 keV to 200 keV
+## 7.4 Distributions for photons from 0 keV to 200 keV
 
 
 ```python
@@ -1076,20 +1147,15 @@ plt.show()
 
 
     
-![png](output_13_0.png)
+![png](docs/interaction/output_13_0.png)
     
-
-
     escape probability =  0.5623307322837948
     
-
-
-    
-![png](output_13_2.png)
+![png](docs/interaction/output_13_2.png)
     
 
 
-### Photons from 200 keV to 2 MeV
+## 7.5 Distributions for photons from 200 keV to 2 MeV
 
 
 ```python
@@ -1135,24 +1201,15 @@ plt.show()
 
 
     
-![png](output_15_0.png)
+![png](docs/interaction/output_15_0.png)
     
-
-
     escape probability =  1999.9999999999998
     
-
-    C:\Users\romain.coulon\AppData\Local\Temp\ipykernel_16916\4017156075.py:26: RuntimeWarning: divide by zero encountered in log
-      y_1 = np.log(A[:, col_idx])
-    
-
-
-    
-![png](output_15_3.png)
+![png](docs/interaction/output_15_3.png)
     
 
 
-### Photons from 2 MeV to 10 MeV
+## 7.6 Distributions for photons from 2 MeV to 10 MeV
 
 
 ```python
@@ -1198,20 +1255,15 @@ plt.show()
 
 
     
-![png](output_17_0.png)
+![png](docs/interaction/output_17_0.png)
     
-
-
     escape probability =  0.03360101175407434
     
-
-
-    
 ![png](output_17_2.png)
     
 
 
-## Sample a deposited energy given an initial energy
+## 7.7 Sample a deposited energy given an initial energy
 
 
 ```python
@@ -1227,7 +1279,7 @@ print(f"The electron of initial energy = {ei} keV, has deposited = {ed_e} keV in
     The electron of initial energy = 100 keV, has deposited = 100 keV in the scintillant.
     
 
-## Deposited energy of photons as a function of the sintillant volume
+## 7.8 Deposited energy of photons as a function of the sintillant volume
 
 
 ```python
@@ -1255,32 +1307,15 @@ plt.xlabel(r"$V$ /mL", fontsize=14)
 plt.ylabel(r"$\bar{y}$ /(keV)", fontsize=14)
 ```
 
-
-
-
-    Text(0, 0.5, '$\\bar{y}$ /(keV)')
-
-
-
-
     
-![png](output_22_1.png)
+![png](docs/interaction/output_22_1.png)
     
 
-
-
 ```python
 
 ```
 
-
-# Efficiency calculation using the analytical TDCR model
-
-
-```python
-# pip install TDCRPy --upgrade
-```
-
+# 8. Efficiency curves
 
 ```python
 import tdcrpy as td
@@ -1292,25 +1327,51 @@ import matplotlib.pyplot as plt
 
 ```python
 mode = "eff"                # ask for efficiency calculation
-Rad="H-3"                   # radionuclides
+Rad="Co-60"                 # radionuclides
 pmf_1="1"                   # relatives fractions of the radionulides
-N = 1000                    # number of Monte Carlo trials (not used)
+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
 
-effS, u_effS, effD, u_effD, effT, u_effT = [], [],[], [],[], []
+# 8.1 Record decay histories in temporary files
+td.TDCRPy.TDCRPy(L[0], Rad, pmf_1, N, kB, V, mode, barp=True, record=True)
+
+effS, u_effS, effD, u_effD, effT, u_effT, effD2, u_effD2 = [], [],[], [],[], [], [], []
 for l in tqdm(L, desc="free parameters ", unit=" iterations"):
-  out = td.TDCRPy.TDCRPy(l, Rad, pmf_1, N, kB, V, mode, Smodel=False)
+  out = td.TDCRPy.TDCRPy(l, Rad, pmf_1, N, kB, V, mode, readRecHist=True)
   effS.append(out[2])
   u_effS.append(out[3])
   effD.append(out[2])
   u_effD.append(out[3])
   effT.append(out[4])
   u_effT.append(out[5])
+  effD2.append(out[12])
+  u_effD2.append(out[13])
 ```
 
-    free parameters : 100%|█████████████████████████████████████████████████████| 100/100 [00:15<00:00,  6.50 iterations/s]
+    
+     ______  ______  ______ _______  ________
+    |__  __||  ___ \|  ___||  ___ | |  ____ |
+      | |   | |  | || |    | |  | | | |___| |___     ___
+      | |   | |  | || |    | |__| | |  _____|\  \   |  |
+      | |   | |__| || |____|  __  \ | |       \  \  |  |
+      |_|   |_____/ |_____||_|  \__\|_|        \  \_|  |
+      +++++++++++++++++++++++++++++++++++++++++/      /
+      ________________________________________/      /
+     |______________________________________________/     
+    
+    
+    version 2.0.2
+    BIPM 2023 - license MIT 
+    distribution: https://pypi.org/project/TDCRPy 
+    developement: https://github.com/RomainCoulon/TDCRPy 
+    
+    start calculation...
+    
+
+    Processing: 100%|█████████████████████████████████████████████████████████████| 1000/1000 [00:24<00:00, 40.79 decays/s]
+    free parameters : 100%|█████████████████████████████████████████████████████| 100/100 [00:02<00:00, 35.96 iterations/s]
     
 
 
@@ -1318,9 +1379,11 @@ for l in tqdm(L, desc="free parameters ", unit=" iterations"):
 effS=np.asarray(effS)
 effT=np.asarray(effT)
 effD=np.asarray(effD)
+effD2=np.asarray(effD2)
 u_effS=np.asarray(u_effS)
 u_effT=np.asarray(u_effT)
 u_effD=np.asarray(u_effD)
+u_effD2=np.asarray(u_effD2)
 
 tdcr=effT/effD
 u_tdcr=np.sqrt(u_effD**2*effT**2/effD**4+u_effT**2/effD**2)
@@ -1329,6 +1392,7 @@ plt.figure("efficiency vs free parameter")
 plt.clf()
 plt.errorbar(L,effD,yerr=u_effD,fmt="-k",label="double coincidences")
 plt.errorbar(L,effT,yerr=u_effT,fmt="-r",label="triple coincidences")
+plt.errorbar(L,effD2,yerr=u_effD2,fmt="-g",label="double coincidences (CIEMAT/NIST)")
 plt.xscale('log')
 plt.xlabel(r'$L$ /keV$^{-1}$', fontsize=14)
 plt.ylabel(r'$\epsilon$', fontsize=14)
@@ -1342,33 +1406,14 @@ plt.xlabel(r'$R_T/R_D$', fontsize=14)
 plt.ylabel(r'$\epsilon_{D}$', fontsize=14)
 ```
 
-
-
-
-    Text(0, 0.5, '$\\epsilon_{D}$')
-
-
-
-
     
-![png](output_4_1.png)
+![png](docs/efficiencyCurve/output_4_1.png)
     
-
-
-
     
-![png](output_4_2.png)
+![png](docs/efficiencyCurve/output_4_2.png)
     
 
-
-
-# Efficiency with radionuclide mixtures
-
-
-```python
-# pip install TDCRPy --upgrade
-```
-
+# 9. Efficiency with radionuclide mixtures
 
 ```python
 import tdcrpy as td
@@ -1377,8 +1422,7 @@ import numpy as np
 from tqdm import tqdm
 ```
 
-## Fixed parameters
-
+## 9.1 Fixed parameters
 
 ```python
 mode = "eff"                # ask for efficiency calculation
@@ -1390,15 +1434,13 @@ V = 10                      # volume of scintillator in mL
 L=1                         # free parameter in keV-1
 ```
 
-## Mixture parameters
-
+## 9.2 Mixture parameters
 
 ```python
 C = np.arange(0,1,0.05)     # relative fraction of the second nuclide
 ```
 
-## Efficiency calculation
-
+## 9.3 Efficiency calculation
 
 ```python
 effS, ueffS, effD, ueffD, effT, ueffT, effD2, ueffD2 = [], [], [], [], [], [], [], []
@@ -1418,7 +1460,7 @@ TDCR = effT/effD
     Processing items: 100%|████████████████████████████████████████████████████████████████| 20/20 [03:52<00:00, 11.63s/it]
     
 
-## Plot the efficiency curves
+## 9.4 Plot the efficiency curves
 
 
 ```python
@@ -1434,25 +1476,15 @@ plt.legend()
 plt.savefig("stopping_power_plot.png")
 ```
 
-
-    
-![png](output_10_0.png)
+![png](docs/mixture/output_10_0.png)
     
-
-
-
-# Dynamic efficiency estimation
+# 10. Dynamic efficiency estimation
 
 This notebook presents how to link the `TDCRPy` package with the `radioactivedecay` package [1] to simulate dynamic TDCR measurements.
 
 [1] Alex Malins & Thom Lemoine, radioactivedecay: A Python package for radioactive decay calculations. Journal of Open Source Software, 7 (71), 3318 (2022). https://doi.org/10.21105/joss.03318.
 
 
-```python
-# pip install tdcrpy --upgrade
-```
-
-
 ```python
 # pip install radioactivedecay
 ```
@@ -1465,7 +1497,7 @@ import numpy as np
 import matplotlib.pyplot as plt
 ```
 
-## Input parameters
+## 10.1 Input parameters
 
 
 ```python
@@ -1482,7 +1514,7 @@ V = 10                 # volume of scintillator (mL)
 N = 1000                # number of simulated decays
 ```
 
-## Run radioactivedecay
+## 10.2 Run radioactivedecay
 
 
 ```python
@@ -1510,49 +1542,28 @@ for key, val in A_t1.items(): print(f"\t {key}: {val/As_t1}")
     	 Tc-99m: 0.4801545238018309
     
 
-## Display the decay graph
+## 10.3 Display the decay graph
 
 
 ```python
 nuc = rd.Nuclide(radionuclide)
 nuc.plot()
 ```
-
-
-
-
-    (<Figure size 450x750 with 1 Axes>, <Axes: >)
-
-
-
-
     
-![png](output_9_1.png)
+![png](docs/dynamicDecay/output_9_1.png)
     
-
-
-## Display the decay curve
+## 10.4 Display the decay curve
 
 
 ```python
 rad_t0 .plot(coolingTime, time_unit, yunits=activity_unit)
 ```
-
-
-
-
-    (<Figure size 640x480 with 1 Axes>,
-     <Axes: xlabel='Time (h)', ylabel='Activity (Bq)'>)
-
-
-
-
     
 ![png](output_11_1.png)
     
 
 
-## Efficiency calculation as a function of the time
+## 10.5 Efficiency calculation as a function of the time
 
 
 ```python
@@ -1579,14 +1590,9 @@ effD = np.asarray(effD); effT = np.asarray(effT); ueffD = np.asarray(ueffD); uef
 effD2 = np.asarray(effD2); effS = np.asarray(effS); ueffD2 = np.asarray(ueffD2); ueffS = np.asarray(ueffS);
 tdcr = effT/effD
 ```
+  
 
-    warning p not equal to 1
-    warning p not equal to 1
-    warning p not equal to 1
-    warning p not equal to 1
-    
-
-## Plot efficiency curves
+## 10.6 Plot efficiency curves
 
 
 ```python
@@ -1611,164 +1617,14 @@ plt.show()
 
 
     
-![png](output_15_0.png)
-    
-
-
-
-```python
-
-```
-
-
-# Distribution of TDCR measurements
-
-
-```python
-# pip install TDCRPy --upgrade
-```
-
-
-```python
-import tdcrpy as td
-import numpy as np
-from tqdm import tqdm
-import matplotlib.pyplot as plt
-```
-
-## Record the decay histories in temporary files
-
-
-```python
-mode = "eff"                # ask for efficiency calculation
-Rad="Cd-109"                # radionuclides
-pmf_1="1"                   # relatives fractions of the radionulides
-N = 1500                    # number of Monte Carlo trials
-kB =1.0e-5                  # Birks constant in cm keV-1
-V = 10                      # volume of scintillator in mL
-L=1                         # free parameter in keV-1
-
-out = td.TDCRPy.TDCRPy(1, Rad, pmf_1, N, kB, V, mode, record=True, barp=True)
-```
-
-    
-     ______  ______  ______ _______  ________
-    |__  __||  ___ \|  ___||  ___ | |  ____ |
-      | |   | |  | || |    | |  | | | |___| |___     ___
-      | |   | |  | || |    | |__| | |  _____|\  \   |  |
-      | |   | |__| || |____|  __  \ | |       \  \  |  |
-      |_|   |_____/ |_____||_|  \__\|_|        \  \_|  |
-      +++++++++++++++++++++++++++++++++++++++++/      /
-      ________________________________________/      /
-     |______________________________________________/     
-    
-    
-    version 2.0.2
-    BIPM 2023 - license MIT 
-    distribution: https://pypi.org/project/TDCRPy 
-    developement: https://github.com/RomainCoulon/TDCRPy 
-    
-    start calculation...
-    
-
-    Processing: 100%|█████████████████████████████████████████████████████████████| 1500/1500 [00:46<00:00, 32.36 decays/s]
-    
-
-## Read initial energy from the decay process
-
-
-```python
-temp1, temp2, temp3, temp4 = td.TDCR_model_lib.read_temp_files()
-
-ee_vec, eg_vec, ep_vec, ea_vec = td.TDCR_model_lib.energyVectors1(temp1)
-nbins=50
-plt.figure("1")
-plt.hist(eg_vec, bins=nbins, edgecolor='none',density=True,label='photons')
-plt.hist(ee_vec, bins=nbins, edgecolor='none',density=True,label='electrons')
-plt.hist(ep_vec, bins=nbins, edgecolor='none',density=True,label='positrons')
-plt.hist(ea_vec, bins=nbins, edgecolor='none',density=True,label='alphas')
-plt.title('Distribution of Initial Energies')
-plt.xlabel('Energy /keV')
-plt.ylabel('Frequency')
-plt.legend()
-plt.show()
-```
-
-    C:\Users\romain.coulon\AppData\Local\anaconda3\Lib\site-packages\numpy\lib\histograms.py:885: RuntimeWarning: invalid value encountered in divide
-      return n/db/n.sum(), bin_edges
-    
-
-
-    
-![png](output_6_1.png)
+![png](docs/dynamicDecay/output_15_0.png)
     
 
 
-## Read deposited energy in the scintillator
-
 
 ```python
-ee_vec, ep_vec, ea_vec = td.TDCR_model_lib.energyVectors2(temp2)
-nbins=50
-plt.figure("2")
-plt.hist(ee_vec, bins=nbins, edgecolor='none',density=True,label='electrons')
-plt.hist(ep_vec, bins=nbins, edgecolor='none',density=True,label='positrons')
-plt.hist(ea_vec, bins=nbins, edgecolor='none',density=True,label='alphas')
-plt.title('Distribution of Deposited Energies')
-plt.xlabel('Energy /keV')
-plt.ylabel('Frequency')
-plt.legend()
-plt.show()
-```
-
-
-    
-![png](output_8_0.png)
-    
-
-
-## Read quenched deposited energy in the scintillator
-
-
-```python
-ee_vec = td.TDCR_model_lib.energyVectors3(temp3)
-nbins=50
-plt.figure("3")
-plt.hist(ee_vec, bins=nbins, edgecolor='none',density=True,label='electrons')
-plt.title('Distribution of Quenched Deposited Energies')
-plt.xlabel('Energy /keV')
-plt.ylabel('Frequency')
-plt.legend()
-plt.show()
-```
 
-
-    
-![png](output_10_0.png)
-    
-
-
-## Read detection probabilities per decay event
-
-
-```python
-s_vec, d_vec, t_vec = td.TDCR_model_lib.effVector(temp4)
-nbins=50
-plt.figure("4")
-plt.hist(s_vec, bins=nbins, edgecolor='none',density=True,label='single events')
-plt.hist(d_vec, bins=nbins, edgecolor='none',density=True,label='double coincidences')
-plt.hist(t_vec, bins=nbins, edgecolor='none',density=True,label='triple coincidences')
-plt.title('Distribution of detection probabilities per decay event')
-plt.xlabel('Detection probability')
-plt.ylabel('Frequency')
-plt.legend()
-plt.show()
 ```
 
 
-    
-![png](output_12_0.png)
-    
-
-