Merge branch 'main' into v0.1

nerea/calculated.py

@@ -5,6 +5,7 @@
 import pandas as pd
 
 from .utils import _make_df, ratio_v_u
+from .constants import ATOMIC_MASS
 
 __all__ = ['_Calculated',
            'CalculatedSpectralIndex',
@@ -22,7 +23,7 @@ def calculate(self) -> None:
 class CalculatedSpectralIndex(_Calculated):
     data: pd.DataFrame
     model_id: str
-    deposit_ids: list[str]
+    deposit_ids: list[str]  # 0: num, 1: den
 
     @classmethod
     def from_sts(cls, file: str, detector_name: str, **kwargs):
@@ -48,12 +49,12 @@ def from_sts(cls, file: str, detector_name: str, **kwargs):
         >>> c_instance = CalculatedSpectralIndex.from_sts('file_det0.m',
                                                     'SI_detector', model_id='Model1')
         """
-        ## works with relative uncertainties for the moment.
-        ## Shall be homogenized with the rest of the API
         v, u = sts.read(file).detectors[detector_name].bins[0][-2:]
+        mass_norm = ATOMIC_MASS[kwargs['deposit_ids'][1]]['value'] / ATOMIC_MASS[kwargs['deposit_ids'][0]]['value']
         # Serpent detector uncertainty is relative
-        kwargs['data'] = _make_df(v, u * v).assign(VAR_FRAC_C_n=None,
-                                                   VAR_FRAC_C_d=None)
+        kwargs['data'] = _make_df(v * mass_norm, u * v * mass_norm
+                                  ).assign(VAR_FRAC_C_n=None,
+                                           VAR_FRAC_C_d=None)
         return cls(**kwargs)
 
     @classmethod
@@ -85,7 +86,10 @@ def from_sts_detectors(cls, file: str, detector_names: dict[str, str], **kwargs)
         v2, u2_ = sts.read(file).detectors[detector_names['denominator']].bins[0][-2:]
         # Serpent detector uncertainty is relative
         u1, u2 = u1_ * v1, u2_ * v2
-        v, u = ratio_v_u(_make_df(v=v1, u=u1), _make_df(v=v2, u=u2))
+        v, u = ratio_v_u(_make_df(v=v1 / ATOMIC_MASS[kwargs['deposit_ids'][0]]['value'],
+                                  u=u1 / ATOMIC_MASS[kwargs['deposit_ids'][0]]['value']),
+                         _make_df(v=v2 / ATOMIC_MASS[kwargs['deposit_ids'][1]]['value'],
+                                  u=u2 / ATOMIC_MASS[kwargs['deposit_ids'][1]]['value']))
         S1, S2= 1 / v2, v1 / v2 **2
         kwargs['data'] = _make_df(v, u).assign(VAR_FRAC_C_n=(S1 * u1) **2,
                                                VAR_FRAC_C_d=(S2 * u2) **2)

nerea/constants.py

@@ -0,0 +1,25 @@
+import pandas as pd
+import numpy as np
+
+from .utils import _make_df
+
+AVOGADRO = 6.02214076e23
+
+# The isotopic mass data is from G. Audi, A. H. Wapstra Nucl. Phys A. 1993, 565, 1-65 and G. Audi, A. H. Wapstra Nucl. Phys A. 1995,
+# 595, 409-480. The percent natural abundance data is from the 1997 report of the IUPAC Subcommittee for Isotopic
+# Abundance Measurements by K.J.R. Rosman, P.D.P. Taylor Pure Appl. Chem. 1999, 71, 1593-1607.
+# WHEN AVAILABLE, nucleon number otherwise.
+ATOMIC_MASS = pd.DataFrame(
+    {"U233": [233.0, 0.0],
+     "U234": [234.040916, 0.0],
+     "U235": [235.043923, 0.0],
+     "U236": [236.0, 0.0],
+     "U238": [238.050783, 0.0],
+     "Np237": [237.048167, 0.0],
+     "Pu238": [238.0, 0.0],
+     "Pu239": [239.0521634, 0.0],
+     "Pu240": [240.053807, 0.0],
+     "Pu241": [241.0, 0.0],
+     "Pu242": [242.0, 0.0],
+     "Am241": [241.0, 0.0]
+     }, index=['value', 'uncertainty'])

nerea/experimental.py

@@ -5,6 +5,7 @@
 from .effective_mass import EffectiveMass
 from .reaction_rate import ReactionRate, ReactionRates
 from .utils import ratio_v_u, product_v_u, _make_df
+from .constants import ATOMIC_MASS
 
 import pandas as pd
 import numpy as np
@@ -166,10 +167,10 @@ def _time_normalization(self) -> pd.DataFrame:
         pd.DataFrame
             with normalization value and uncertainty
         """
-        r, l = self.fission_fragment_spectrum.real_time, self.fission_fragment_spectrum.life_time
-        v = r / l**2
-        u = np.sqrt((1 / l **2 * self.fission_fragment_spectrum.real_time_uncertainty) **2 +
-                    (2 * r / l **3 * self.fission_fragment_spectrum.life_time_uncertainty)**2)
+        l = self.fission_fragment_spectrum.life_time
+        v = 1 / l
+        u = np.sqrt((1 / self.fission_fragment_spectrum.life_time **2 \
+                     * self.fission_fragment_spectrum.life_time_uncertainty)**2)
         return _make_df(v, u)
 
     @property
@@ -429,17 +430,26 @@ def _compute_correction(self, one_g_xs: pd.DataFrame) -> pd.DataFrame:
         """
         imp = self.numerator.effective_mass.composition_.set_index('nuclide')
         imp.columns = ['value', 'uncertainty']
-        # normalize impurities and one group xs
+
+        # normalize Serpent output per unit mass
+        v = one_g_xs['value'] / ATOMIC_MASS.T['value']
+        u = one_g_xs['uncertainty'] / ATOMIC_MASS.T['value']
+        xs = pd.concat([v.dropna(), u.dropna()], axis=1)
+        xs.columns = ["value", "uncertainty"]
+
+        # normalize impurities and one group xs to the numerator deposit
         imp_v, imp_u = ratio_v_u(imp,
                                  imp.loc[self.numerator.deposit_id])
-        xs_v, xs_u = ratio_v_u(one_g_xs,
-                               one_g_xs.loc[self.denominator.deposit_id])
+        xs_v, xs_u = ratio_v_u(xs,
+                               xs.loc[self.denominator.deposit_id])
+
         # remove information on the main isotope
         # will sum over all impurities != self.numerator.deposit_id
         imp_v = imp_v.drop(self.numerator.deposit_id)
         imp_u = imp_u.drop(self.numerator.deposit_id)
         xs_v = xs_v.drop(self.numerator.deposit_id)
         xs_u = xs_u.drop(self.numerator.deposit_id)
+
         # compute correction and its uncertainty
         if not all([i in xs_v.index] for i in imp_v.index):
             warnings.warn("Not all impurities were provided with a cross section.")

pyproject.toml

@@ -21,19 +21,19 @@ classifiers = [
 ]
 
 dependencies = [
-  "numpy == 1.23.4",
-  "pandas == 1.5.1",
-  "serpentTools == 0.10.1",
-  "xlwt == 1.3.0"
+  "numpy >= 1.23.4, < 2.0",
+  "pandas >= 1.5.1",
+  "serpentTools >= 0.10.1",
+  "xlwt >= 1.3.0"
 ]
 
 [tool.setuptools.dynamic]
 version = {attr = "nerea.__version__"}
 
 [project.optional-dependencies]
 test = [
-  "pytest == 8.2.0",
-  "pytest-cov == 4.0.0"
+  "pytest >= 8.2.0",
+  "pytest-cov >= 4.0.0"
 ]
 
 [project.urls]

requirements.txt

@@ -1,6 +1,6 @@
-numpy==1.23.4
-pandas==1.5.1
-pytest==8.2.0
-serpentTools==0.10.1
-pytest-cov==4.0.0
-xlwt==1.3.0
+numpy<=1.26.4
+pandas>=1.5.1
+pytest>=8.2.0
+serpentTools>=0.10.1
+pytest-cov>=4.0.0
+xlwt>=1.3.0

tests/test_NormalizedFissionFragmentSpectrum.py

@@ -75,7 +75,7 @@ def test_time_normalization(nffs):
     tmp = nffs
     tmp.fission_fragment_spectrum.life_time_uncertainty = .1
     tmp.fission_fragment_spectrum.real_time_uncertainty = .1
-    pd.testing.assert_frame_equal(tmp._time_normalization, _make_df(.1, np.sqrt(5) * 1e-3))
+    pd.testing.assert_frame_equal(tmp._time_normalization, _make_df(.1, 1/10 **2 * .1))
 
 def test_power_normalization(nffs):
     pd.testing.assert_frame_equal(nffs._power_normalization,

tests/test_SpectralIndex.py

@@ -38,26 +38,26 @@ def sample_spectrum_1(sample_spectrum_data):
     return FissionFragmentSpectrum(start_time=datetime(2024, 5, 18, 20, 30, 15),
                                    life_time=10, real_time=10,
                                    data=sample_spectrum_data, campaign_id="A", experiment_id="B",
-                                   detector_id="C1", deposit_id="D1", location_id="E", measurement_id="F1")
+                                   detector_id="C1", deposit_id="U238", location_id="E", measurement_id="F1")
 
 @pytest.fixture
 def sample_spectrum_2(sample_spectrum_data):
     return FissionFragmentSpectrum(start_time=datetime(2024, 5, 18, 20, 30, 15),
                                    life_time=10, real_time=10,
                                    data=sample_spectrum_data, campaign_id="A", experiment_id="B",
-                                   detector_id="C2", deposit_id="D2", location_id="E", measurement_id="F2")
+                                   detector_id="C2", deposit_id="U235", location_id="E", measurement_id="F2")
 
 @pytest.fixture
 def effective_mass_1(sample_integral_data):
-    data = pd.DataFrame({'a1': [0.1, 0.01], 'a2': [0.2, 0.02], 'D1': [0.7, 0.07]}).T.reset_index()
+    data = pd.DataFrame({'U236': [0.1, 0.01], 'U234': [0.2, 0.02], 'U238': [0.7, 0.07]}).T.reset_index()
     data.columns = ['nuclide', 'share', 'uncertainty']
-    return EffectiveMass(deposit_id="D1", detector_id="C1", data=sample_integral_data, bins=42, composition=data)
+    return EffectiveMass(deposit_id="U238", detector_id="C1", data=sample_integral_data, bins=42, composition=data)
 
 @pytest.fixture
 def effective_mass_2(sample_integral_data):
-    data = pd.DataFrame({'b1': [0.15, 0.015], '12': [0.25, 0.025], 'D1': [0.6, 0.06]}).T.reset_index()
+    data = pd.DataFrame({'U234': [0.15, 0.015], 'U238': [0.25, 0.025], 'U235': [0.6, 0.06]}).T.reset_index()
     data.columns = ['nuclide', 'share', 'uncertainty']
-    return EffectiveMass(deposit_id="D2", detector_id="C2", data=sample_integral_data, bins=42, composition=data)
+    return EffectiveMass(deposit_id="U235", detector_id="C2", data=sample_integral_data, bins=42, composition=data)
 
 @pytest.fixture
 def power_monitor(sample_power_monitor_data):
@@ -77,13 +77,13 @@ def si(rr_1, rr_2):
 
 @pytest.fixture
 def synthetic_one_g_xs_data():
-    data = pd.DataFrame({'a1': [0.07, 0.001], 'a2': [0.08, 0.002],
-                         'D1': [0.9, 0.003], 'D2': [0.6, 0.004]}).T.reset_index()
+    data = pd.DataFrame({'U236': [0.07, 0.001], 'U234': [0.08, 0.002],
+                         'U238': [0.9, 0.003], 'U235': [0.6, 0.004]}).T.reset_index()
     data.columns = ['nuclide', 'value', 'uncertainty']
     return data.set_index('nuclide')
 
 def test_deposit_ids(si):
-    assert si.deposit_ids == ['D1', 'D2']
+    assert si.deposit_ids == ['U238', 'U235']
 
 def test_get_long_output(si):
     expected_df = pd.DataFrame({'FFS_n': 8.79100000e+02,
@@ -138,7 +138,7 @@ def test_process(si):
 
 def test_compute_correction(si, synthetic_one_g_xs_data):
     w1, uw1, w2, uw2, wd, uwd = .1, .01, .2, .02, .7, .07
-    x1, ux1, x2, ux2, xd, uxd = .07, .001, .08, .002, .6, .004
+    x1, ux1, x2, ux2, xd, uxd = .07 / 236., .001 / 236., .08 / 234., .002 / 234., .6 / 235.043923, .004 / 235.043923
     v = (w1/wd * x1/xd) + (w2/wd * x2/xd)
 
     W1, X1 = w1 / wd, x1 / xd
@@ -149,7 +149,12 @@ def test_compute_correction(si, synthetic_one_g_xs_data):
 
     data = pd.DataFrame({'value': [v], 'uncertainty': [u], 'uncertainty [%]': u / v * 100}, index=['value'])
 
-    pd.testing.assert_frame_equal(data, si._compute_correction(synthetic_one_g_xs_data))
+    nerea_ = si._compute_correction(synthetic_one_g_xs_data)
+
+    np.testing.assert_equal(data.index.values, nerea_.index.values)
+    np.testing.assert_equal(data.columns.values, nerea_.columns.values)
+    np.testing.assert_almost_equal(data['value'].values, nerea_['value'].values, decimal=5)
+    np.testing.assert_almost_equal(data['uncertainty'].values, nerea_['uncertainty'].values, decimal=6)
 
 def test_compute_with_correction(si, synthetic_one_g_xs_data):
     w1, uw1, w2, uw2, wd, uwd = .1, .01, .2, .02, .7, .07
@@ -167,4 +172,8 @@ def test_compute_with_correction(si, synthetic_one_g_xs_data):
 
     data = pd.DataFrame({'value': [v_], 'uncertainty': [u_], 'uncertainty [%]': u_ / v_ * 100}, index=['value'])
 
-    pd.testing.assert_frame_equal(data, si.process(synthetic_one_g_xs_data)[['value', 'uncertainty', 'uncertainty [%]']])
+    nerea_ = si.process(synthetic_one_g_xs_data)
+    np.testing.assert_equal(data.index.values, nerea_.index.values)
+    np.testing.assert_equal(data.columns.values, nerea_[['value', 'uncertainty', 'uncertainty [%]']].columns.values)
+    np.testing.assert_almost_equal(data['value'].values, nerea_['value'].values, decimal=4)
+    np.testing.assert_almost_equal(data['uncertainty'].values, nerea_['uncertainty'].values, decimal=5)