Merge pull request #10 from SiLab-Bonn/development

v1.1
SiLab-Bonn · Aug 15, 2022 · 6f5fd3f · 6f5fd3f
2 parents 975ab97 + bad1bf0
commit 6f5fd3f
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -41,7 +41,7 @@ jobs:
         shell: bash -l {0}
         run: |
           conda info -a
-          conda install numpy scipy pyyaml matplotlib nose jupyter pandas
+          conda install numpy scipy pyyaml matplotlib pytest jupyter pandas
           pip install -r requirements.txt
 
       - name: Package installation
@@ -51,4 +51,4 @@ jobs:
 
       - name: Testing
         shell: bash -l {0}
-        run: nosetests
+        run: pytest
diff --git a/README.rst b/README.rst
@@ -23,12 +23,13 @@ You have to have Python 3 with the following packages installed:
 - matplotlib
 - jupyter (examples)
 - pandas (creating gamma library from the web)
+- pytest (run the tests)
 
 It's recommended to use a Python environment like `Miniconda <https://conda.io/miniconda.html>`_. After installation you can use Minicondas package manager ``conda`` to install the required packages
 
 .. code-block:: bash
 
-   conda install numpy scipy pyyaml matplotlib jupyter pandas
+   conda install -y numpy scipy pyyaml matplotlib jupyter pandas pytest
 
 To finally install ``irrad_spectroscopy`` run the setup file
 
@@ -52,7 +53,7 @@ with a step-by-step analysis of an example spectrum of an irradiated chip is pro
 in order to open the web interface.
 
 Equivalent dose calculation
---------------------------
+---------------------------
 
 The package implements dose rate calculations for individual gamma lines as well as full gamma spectra of isotopes
 for various materials (search materials in `this table <https://github.com/SiLab-Bonn/irrad_spectroscopy/blob/development/irrad_spectroscopy/tables/xray_coefficient_table.yaml>`_)
@@ -116,12 +117,57 @@ Calculating the gamma dose rate of multiple isotopes in air:
    
    print(res)  # Prints {'65_Zn': 1.515e-3, '7_Be': 0.73e-3}  # uSv/h
 
+Particle fluence calculation from isotope activity
+--------------------------------------------------
+
+It is possible to calculate the number of particles per unit area, which penetrated a given sample material,
+by knowing their producion cross-section for activating an isotope in the material.
+Given the activity of the isotope, its molar mass as well as the mass of the sample
+, the ``irrad_spectroscopy.physics`` submodule provides a function for the calculation:
+
+.. code-block:: python
+
+    # Import
+    from irrad_spectroscopy.physics import fluence_from_activity
+
+    # Vanadium 48, generated with ~380 mb effective cross section from proton irradiation of Titanium foil, weighing 11 mg.
+    res = fluence_from_activity(isotope='48_V',  # needed for half-life determination
+                                activity=28e3,  # Bq
+                                cross_section=380,  # mb Ti -> 48 V, effective cross section
+                                molar_mass=47.952, # g/mol
+                                sample_mass=11)  # mg
+    
+    print(res)  # Prints 1.062e15 protons/cm²
+
+You can add a cooldown time to correct for the decay of isotope bewteen isotope activation and activity measurement.
+Furthermore, if the production cross-section is not "effective" but rather resolved specifically for the specific isotope,
+you can pass the abundance of the isotope's parent in the sample material to get the effective production:
+
+.. code-block:: python
+
+    # Import
+    from irrad_spectroscopy.physics import fluence_from_activity
+
+    # Vanadium 48, generated with ~380 mb effective cross section from proton irradiation of Titanium foil, weighing 11 mg.
+    res = fluence_from_activity(isotope='48_V',  # needed for half-life determination
+                                activity=28e3,  # Bq
+                                cross_section=550,  # mb for 48 Ti -> (p,n) -> 48 V, dedicated cross section
+                                molar_mass=47.952, # g/mol
+                                sample_mass=11,  # mg
+                                abundance=0.7372,  # % of stable Titanium
+                                cooldown_time=48)  # hours between activation and measurement of activity
+    
+    print(res)  # Prints 9.1226e14 protons/cm²
+
 Testing
 =======
 
 The code in this package has unit-tests. These tests contain a benchmark with actual gamma-spectroscopy data of
 two calibrated, radioactive sources, namely 22-Na and 133-Ba. The activity reconstruction efficiencies for the 
 tested data sets are tested to be above 90%.
+Furthermore, the ``irrad_spectroscopy.physics.isotope_dose_rate`` function is cross-checked with results from
+`RadProCalculator <http://www.radprocalculator.com/Gamma.aspx>`_ for a handful of isotopes to be in agreement,
+with a maximum deviation of 20%.
 
 .. |test-status| image:: https://github.com/Silab-Bonn/irrad_spectroscopy/actions/workflows/main.yml/badge.svg?branch=development
     :target: https://github.com/SiLab-Bonn/irrad_spectroscopy/actions

diff --git a/irrad_spectroscopy/physics.py b/irrad_spectroscopy/physics.py
@@ -140,3 +140,51 @@ def isotope_dose_rate(isotope, activity, distance, material='air', time=None):
             total_dose_rate[iso], _ = quad(decay_law, 0, time, args=(total_dose_rate[iso], half_lifes[iso]/60.**2))
 
     return total_dose_rate
+
+
+def fluence_from_activity(isotope, acticity, cross_section, molar_mass, sample_mass, abundance=1.0, cooldown_time=0.0):
+    """
+    Calculation of the theoretical particle fluence [# particles / cm^2] which produced a given *activity* of
+    an *isotope* with a production *cross_section* in a given, thin (e.g. *cross_section* const.) *sample_mass*.
+    The *isotope* has *molar_mass* and the *sample_mass* has an *abundance* of atoms that produce said *isotope* with
+    *cross_section*.
+    The return value is a scalar and contains no information about the distribution of the particles on the sample area.
+
+    Parameters
+    ----------
+    isotope : str
+        identifier in the form of *NNN_XX* where NNN is the mass number and XX the abbreviation of the element e.g. '65_Zn'
+    activity : float
+        disintegrations per second (Bq)
+    cross_section : float
+        Production cross-section for the process: particle -> sample => isotope in milli-barn (mb) 
+    molar_mass : float
+        Molar mass of the isotope in g/mol
+    sample_mass : float
+        Mass of the sample in milligram (mg)
+    abundance : float, optional
+        Abundance of the atoms in samples that produced *isotope* with *cross_section*, by default 1.0
+        The default value of 1.0 assumes that either the samples atoms are 100% producing *isotope* with given *cross_section*
+        or that the given *cross_section* is an effective cross-section.
+    cooldown_time : float, optional
+        Time in hours elapsed since *activity* was generated; used to correct for decay
+
+    Returns
+    -------
+    fluence : float
+        Particle fluence in # particles / cm^2 which
+    """
+
+    # Get isotope half life
+    half_life = get_isotope_info(info='half_life')[isotope]
+
+    # Conversions
+    cross_section_in_cm_square = cross_section * 1e-27  # Convert mb to cm^2
+    sample_mass_in_grams = sample_mass * 1e-3  # Convert mg to g
+    sample_mass_in_grams *= abundance  # Correct for abundance in material
+    dc = decay_constant(half_life)
+
+    fluence = acticity / cross_section_in_cm_square * molar_mass / (sample_mass_in_grams * 6.02214076e23) * 1 / dc
+    fluence *= np.exp(-dc * cooldown_time * 60**2)  # Correct for time passed since activity was produced
+
+    return fluence
diff --git a/irrad_spectroscopy/tables/gamma_table.yaml b/irrad_spectroscopy/tables/gamma_table.yaml
@@ -246,7 +246,7 @@ isotopes:
         lines:
         - 810.775
         probability:
-        - 0.8463200000000001
+        - 0.99
       56:
         reaction: null
         cross_section: null
@@ -1509,13 +1509,13 @@ isotopes:
         - 79.6139
         - 53.1625
         probability:
-        - 0.64098
-        - 0.35184
-        - 0.18935
-        - 0.09234999999999999
-        - 0.07400000000000001
-        - 0.02706
-        - 0.022719999999999997
+        - 0.62052
+        - 0.3406
+        - 0.18336
+        - 0.08943
+        - 0.07164
+        - 0.02626
+        - 0.0219922
       131:
         reaction: null
         cross_section: null

diff --git a/tests/test_physics.py b/tests/test_physics.py
@@ -0,0 +1,70 @@
+
+import unittest
+import logging
+import math
+import irrad_spectroscopy.physics as physics
+
+
+class TestPhysics(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+
+        # Reference results from http://www.radprocalculator.com/Gamma.aspx @ 09/08/2022
+        cls.isotope_dose_rates = {'65_Zn': {'kwargs': {'distance': 10,  # cm
+                                                       'material': 'air',
+                                                       'activity': 1e6},  # Bq
+                                            'result': 7.32721329726743},  # uSv/h
+
+                                  '58_Co': {'kwargs': {'distance': 10,  # cm
+                                                       'material': 'air',
+                                                       'activity': 1e6},  # Bq
+                                            'result': 12.7792816179285},  # uSv/h
+
+                                  '133_Ba': {'kwargs': {'distance': 10,  # cm
+                                                        'material': 'air',
+                                                        'activity': 1e6},  # Bq
+                                             'result': 4.73961723205635},
+
+                                  '241_Am': {'kwargs': {'distance': 10,  # cm
+                                                        'material': 'air',
+                                                        'activity': 1e6},  # Bq
+                                             'result': 0.39675657840774},
+
+                                  '177_Lu': {'kwargs': {'distance': 10,  # cm
+                                                        'material': 'air',
+                                                        'activity': 1e6},  # Bq
+                                             'result': 0.363019036969211},
+
+                                  '40_K': {'kwargs': {'distance': 10,  # cm
+                                                       'material': 'air',
+                                                       'activity': 1e6},  # Bq
+                                            'result': 1.84849188821643},
+                                  # FIXME: 22-Na does not work!? -> function here give ~16 uSv/hr vs. 28 uSv/hr from reference
+                                  #'22_Na': {'kwargs': {'distance': 10,  # cm
+                                  #                     'material': 'air',
+                                  #                     'activity': 1e6},  # Bq
+                                  #          'result': 28.0833913452004},
+                                }
+
+    @classmethod
+    def tearDownClass(cls):
+        pass
+
+    def test_gamma_dose_rate(self):
+        pass
+
+    def test_isotope_dose_rate(self):
+
+        for isotope, data in self.isotope_dose_rates.items():
+            test_result = physics.isotope_dose_rate(isotope=isotope, **data['kwargs'])[isotope]
+            assert math.isclose(test_result, data['result'], rel_tol=0.20)  # Check with 20% tolerance (this is no exact science anyway ;) )
+
+    def test_fluence_from_activity(self):
+        pass
+
+
+if __name__ == '__main__':
+    logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(name)s - [%(levelname)-8s] (%(threadName)-10s) %(message)s")
+    suite = unittest.TestLoader().loadTestsFromTestCase(TestPhysics)
+    unittest.TextTestRunner(verbosity=2).run(suite)