Fix test values (#143)

oceanstream/L3_regridded_data/shoal_detection_handler.py

@@ -40,8 +40,8 @@
     "thr": -70,
     "maxvgap": 5,
     "maxhgap": 5,
-    "minvlen": 0,
-    "minhlen": 0,
+    "minvlen": 5,
+    "minhlen": 5,
     "dask_chunking": {"ping_time": 1000, "range_sample": 1000},
 }
 

tests/test_applying_masks_handler.py

@@ -61,6 +61,6 @@ def test_apply_mask_organisms_in_order(enriched_ek60_Sv):
     }
 
     ds_processed = apply_mask_organisms_in_order(ds_Sv_with_shoal_combined_mask, process_parameters)
-    assert np.nanmean(ds_processed["Sv"].values) == pytest.approx(-56.85248587691882, 0.0001)
+    assert np.nanmean(ds_processed["Sv"].values) == pytest.approx(-63.41369478688135, 0.0001)
     with pytest.raises(ValueError, match="Unexpected mask"):
         apply_selected_noise_masks_and_or_noise_removal(ds_processed, "invalid_parameters")

tests/test_nasc_process.py

@@ -2,7 +2,7 @@
 
 from oceanstream.L3_regridded_data.csv_export_nasc import *
 
-@pytest.mark.ignore
+# @pytest.mark.ignore
 def test_compute_per_dataset_nasc(ek_60_Sv_full_denoised):
     dataset = ek_60_Sv_full_denoised
     nasc = base_nasc_data(dataset)
@@ -12,15 +12,15 @@ def test_compute_per_dataset_nasc(ek_60_Sv_full_denoised):
     assert len(short_nasc) == 3
     assert "fish_NASC_38000.0" in short_nasc
 
-@pytest.mark.ignore
+# @pytest.mark.ignore
 def test_compute_masked_nasc(ek_60_Sv_shoal):
     dataset = ek_60_Sv_shoal
     fish_nasc = mask_nasc_data(dataset, {"mask_shoal": False}, True, "fish_NASC")
-    assert fish_nasc['fish_NASC_38000.0'] == pytest.approx(130821359, 0.0001)
+    assert fish_nasc['fish_NASC_38000.0'] == pytest.approx(103252307.9526562, 0.0001)
 
-@pytest.mark.ignore
+# @pytest.mark.ignore
 def test_compute_full_nasc(ek_60_Sv_shoal):
     dataset = ek_60_Sv_shoal
     nasc = full_nasc_data(dataset, BASE_NASC_PARAMETERS)
     assert len(nasc) == 24
-    assert nasc['fish_NASC_38000.0'] == pytest.approx(130821359, 0.0001)
+    assert nasc['fish_NASC_38000.0'] == pytest.approx(103252307.9526562, 0.0001)

tests/test_shoal_detection_handler.py

@@ -23,7 +23,7 @@ def shoal_masks(ek_60_Sv_denoised):
 @pytest.mark.ignore
 def test_create_shoal_mask_multichannel(ek_60_Sv_denoised):
     mask = create_shoal_mask_multichannel(ek_60_Sv_denoised)
-    assert _count_false_values(mask) == 4873071
+    assert _count_false_values(mask) == 4471604
 
 
 @pytest.mark.ignore
@@ -33,5 +33,5 @@ def test_attach_shoal_mask_to_ds(ek_60_Sv_denoised):
         ds_Sv_shoal_combined, ds_Sv_shoal_combined["mask_shoal"]
     )
     assert np.nanmean(ds_Sv_shoal_combined["Sv"].values) == pytest.approx(
-        -56.46381852479049, 0.0001
+        -61.21094022368077, 0.0001
     )

tests/test_shoal_process.py

@@ -1,6 +1,4 @@
-from oceanstream.L3_regridded_data.shoal_detection_handler import attach_shoal_mask_to_ds, WEILL_DEFAULT_PARAMETERS
-import pytest
-
+from oceanstream.L3_regridded_data.shoal_detection_handler import attach_shoal_mask_to_ds
 
 from oceanstream.L3_regridded_data.shoal_process import (
     process_shoals,
@@ -9,9 +7,17 @@
 )
 from oceanstream.utils import tfc
 
-@pytest.mark.ignore
+WEILL_DEFAULT_PARAMETERS = {
+    "thr": -55,
+    "maxvgap": 5,
+    "maxhgap": 5,
+    "minvlen": 5,
+    "minhlen": 5,
+    "dask_chunking": {"ping_time": 1000, "range_sample": 1000},
+}
+
+# @pytest.mark.ignore
 def prep_dataset(Sv):
-    # parameters = {"thr": -55, "maxvgap": -5, "maxhgap": 0, "minvlen": 5, "minhlen": 5}
     parameters = WEILL_DEFAULT_PARAMETERS
     shoal_dataset = attach_shoal_mask_to_ds(Sv, parameters=parameters, method="will")
     shoal_dataset["mask_shoal"][:, :, 0:25] = False
@@ -20,34 +26,27 @@ def prep_dataset(Sv):
     shoal_dataset["mask_shoal"][:, 800:, :] = False
     return shoal_dataset
 
-@pytest.mark.ignore
+# @pytest.mark.ignore
 def test_split_shoal(ek_60_Sv_denoised):
-    expected_results = [
-        (10362, 6104418),
-        (11155, 6103625),
-        (44, 6114736),
-        (21, 6114759),
-        (21, 6114759),
-        (20, 6114760),
-    ]
+    expected_results = [(13671, 6101109), (13465, 6101315), (30, 6114750)]
     shoal_dataset = prep_dataset(ek_60_Sv_denoised)
     res = split_shoal_mask(shoal_dataset)
     res_tfc = [tfc(r) for r in res]
     assert res_tfc == expected_results
 
-@pytest.mark.ignore
+# @pytest.mark.ignore
 def test_single_shoal(ek_60_Sv_denoised):
     shoal_dataset = prep_dataset(ek_60_Sv_denoised)
     mask = split_shoal_mask(shoal_dataset)[0]
     res = process_single_shoal(shoal_dataset, mask)
     assert len(res) == 3
     assert len(res[0]) == 24
-    assert res[0]["area"] == 4252
+    assert res[0]["area"] == 6017
 
-@pytest.mark.ignore
+# @pytest.mark.ignore
 def test_shoals(ek_60_Sv_denoised):
     shoal_dataset = prep_dataset(ek_60_Sv_denoised)
     res = process_shoals(shoal_dataset)
     none_res = [r for r in res if r is None]
-    assert len(res) == 10
+    assert len(res) == 7
     assert len(none_res) == 0