fix handling of fill values; remove incorrect mock spacecraft packet test

Author: hafarooki

imap_processing/ialirt/l0/process_swapi.py

@@ -324,27 +324,29 @@ def process_swapi_ialirt(
                 pseudo_proton_temperature_list[-5:],
             )
 
-            if (
-                np.isfinite(avg_pseudo_proton_density)
-                and np.isfinite(avg_pseudo_proton_temperature)
-                and np.isfinite(avg_pseudo_proton_speed)
-            ):
-                swapi_data.append(
-                    _populate_instrument_header_items(met)
-                    | {
-                        "instrument": "swapi",
-                        "swapi_epoch": int(met_to_ttj2000ns(avg_swapi_met)),
-                        "swapi_pseudo_proton_speed": Decimal(
-                            f"{avg_pseudo_proton_speed:.3f}"
-                        ),
-                        "swapi_pseudo_proton_density": Decimal(
-                            f"{avg_pseudo_proton_density:.3f}"
-                        ),
-                        "swapi_pseudo_proton_temperature": Decimal(
-                            f"{avg_pseudo_proton_temperature:.3f}"
-                        ),
-                    }
-                )
+            # replace nans (resulting from geometric means that include fill values) with fill values
+            avg_pseudo_proton_speed, avg_pseudo_proton_density, avg_pseudo_proton_temperature = np.nan_to_num((
+                avg_pseudo_proton_speed,
+                avg_pseudo_proton_density,
+                avg_pseudo_proton_temperature
+            ), nan=FILLVAL_FLOAT32)
+
+            swapi_data.append(
+                _populate_instrument_header_items(met)
+                | {
+                    "instrument": "swapi",
+                    "swapi_epoch": int(met_to_ttj2000ns(avg_swapi_met)),
+                    "swapi_pseudo_proton_speed": Decimal(
+                        f"{avg_pseudo_proton_speed:.3f}"
+                    ),
+                    "swapi_pseudo_proton_density": Decimal(
+                        f"{avg_pseudo_proton_density:.3f}"
+                    ),
+                    "swapi_pseudo_proton_temperature": Decimal(
+                        f"{avg_pseudo_proton_temperature:.3f}"
+                    ),
+                }
+            )
     if incomplete_groups:
         logger.info(
             f"The following swapi groups were skipped due to "

imap_processing/tests/ialirt/unit/test_process_swapi.py

@@ -182,45 +182,6 @@ def test_process_swapi_ialirt(
         )
 
 
-@pytest.mark.external_test_data
-@mock.patch("imap_processing.ialirt.l0.process_swapi.process_sweep_data")
-def test_process_swapi_ialirt_zero_counts(
-    mock_process_sweep_data,
-    xarray_data,
-    ialirt_test_data,
-    sc_xarray_data,
-    esa_unit_conversion_table,
-):
-    """Test that the process_swapi_ialirt() function returns expected keys."""
-
-    mock_process_sweep_data.return_value = ialirt_test_data[0]
-
-    # Adding necessary time variables from spacecraft packet
-    xarray_data = xarray_data.assign(sc_sclk_sec=sc_xarray_data["sc_sclk_sec"])
-    xarray_data["sc_sclk_sec"].data = sc_xarray_data["sc_sclk_sec"][
-        0 : xarray_data["swapi_flag"].shape[0]
-    ].data
-    xarray_data = xarray_data.assign(sc_sclk_sub_sec=sc_xarray_data["sc_sclk_sub_sec"])
-    xarray_data["sc_sclk_sub_sec"].data = sc_xarray_data["sc_sclk_sub_sec"][
-        0 : xarray_data["swapi_flag"].shape[0]
-    ].data
-
-    vars_to_zero = [
-        "swapi_coin_cnt0",
-        "swapi_coin_cnt1",
-        "swapi_coin_cnt2",
-        "swapi_coin_cnt3",
-        "swapi_coin_cnt4",
-        "swapi_coin_cnt5",
-    ]
-
-    for v in vars_to_zero:
-        xarray_data[v] = xr.zeros_like(xarray_data[v])
-
-    swapi_result = process_swapi_ialirt(xarray_data, esa_unit_conversion_table)
-
-    assert swapi_result == []
-
 
 def test_count_rate():
     """Use random realistic values to test for expected output of count_rate()."""