Merge branch 'LIBRA-project:main' into compass_collin

Author: cdunn314

libra_toolbox/neutron_detection/diamond/process_data.py

@@ -74,7 +74,7 @@ def get_count_rate(self, bin_time: float, energy_window: tuple = None):
         time_values = self.time_values.copy()
         energy_values = self.energy_values.copy()
 
-        time_bins = np.arange(0, time_values[-2], bin_time)
+        time_bins = np.arange(time_values.min(), time_values[-2], bin_time)
 
         if energy_window is not None:
             peak_mask = (energy_values > energy_window[0]) & (
@@ -113,10 +113,10 @@ def get_avg_rate(self, t_min: float, t_max: float, energy_window: tuple = None):
             time_values = time_values[peak_mask]
 
         # Create mask to only count pulses of any energy in section time window
-        idx = np.logical_and(self.time_values > t_min, self.time_values < t_max)
+        idx = np.logical_and(time_values > t_min, time_values < t_max)
 
-        counts = len(self.time_values[idx])
-        error = np.sqrt(len(self.time_values[idx]))
+        counts = len(time_values[idx])
+        error = np.sqrt(len(time_values[idx]))
         delta_t = t_max - t_min
         count_rate = counts / delta_t
         count_rate_err = error / delta_t

libra_toolbox/neutronics/vault.py

@@ -4,6 +4,7 @@ def build_vault_model(
     added_cells=[],
     added_materials=[],
     overall_exclusion_region=None,
+    cross_sections_destination="cross_sections",
 ) -> "openmc.model.Model":
     """
     Builds a complete OpenMC model for a simulation setup representing a
@@ -95,6 +96,7 @@ def build_vault_model(
         libraries=["ENDFB-8.0-NNDC"],
         set_OPENMC_CROSS_SECTIONS=True,
         particles=["neutron"],
+        destination=cross_sections_destination,
     )
     #
     # Definition of the spherical void/blackhole boundary

test/neutron_detection/test_diamond.py

@@ -143,3 +143,18 @@ def test_get_count_rate(tmpdir):
     assert np.allclose(count_rates_peak2, expected_count_rate_peak2, rtol=0.1)
 
     assert len(count_rate_bins_total) == total_time_s / bin_time
+
+
+def test_count_rate_doesnt_ignore_data():
+    """Test to catch the bug in #48"""
+
+    # create a processor with time from -100 to 100 and energy values from -100 to 100
+    processor = DataProcessor()
+    processor.time_values = np.linspace(-100, 100, 1000)
+    processor.energy_values = np.linspace(-100, 100, 1000)
+
+    # calculate the count rates
+    count_rates, time_bins = processor.get_count_rate(bin_time=1)
+
+    # the first time bin should be -100
+    assert np.isclose(time_bins[0], -100)