Noise test fix (#124)

OceanStreamIO · Nov 8, 2023 · 73292e4 · 73292e4
1 parent 0622fdf
commit 73292e4
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Showing 2 changed files with 18 additions and 33 deletions.
diff --git a/oceanstream/L2_calibrated_data/noise_masks.py b/oceanstream/L2_calibrated_data/noise_masks.py
@@ -8,7 +8,6 @@
 import pathlib
 from typing import Union
 
-import xarray
 import xarray as xr
 from echopype.clean.api import (
     get_attenuation_mask_multichannel,
@@ -28,7 +27,8 @@
             # "n": 5,
             "thr": 20,
             "excludeabove": 250,
-            "operation": "percentile15",
+            "dask_chunking": {"ping_time": 100},
+            "operation": "mean",
         },
     },
     "attenuation": {
@@ -83,7 +83,8 @@
             # "n": 5,
             "thr": 20,
             "excludeabove": 250,
-            "operation": "percentile15",
+            "dask_chunking": {"ping_time": 100},
+            "operation": "mean",
         },
     },
     "attenuation": {
@@ -140,6 +141,7 @@
             "n": 5,
             "thr": 20,
             "excludeabove": 250,
+            "dask_chunking": {"ping_time": 100},
             "operation": "mean",
         },
     },
@@ -307,7 +309,7 @@ def create_seabed_mask(Sv, parameters, method):
     return mask
 
 
-def create_mask(source_Sv: xarray.Dataset, mask_type="impulse", params=MASK_PARAMETERS):
+def create_mask(source_Sv: xr.Dataset, mask_type="impulse", params=MASK_PARAMETERS):
     """
     A function that creates a single noise mask for a given dataset
 
@@ -341,7 +343,7 @@ def create_mask(source_Sv: xarray.Dataset, mask_type="impulse", params=MASK_PARA
     return mask
 
 
-def create_multiple_masks(source_Sv: xarray.Dataset, params=TEST_MASK_PARAMETERS):
+def create_multiple_masks(source_Sv: xr.Dataset, params=TEST_MASK_PARAMETERS):
     """
     A function that creates multiple noise masks for a given Sv dataset
 
@@ -366,7 +368,7 @@ def create_multiple_masks(source_Sv: xarray.Dataset, params=TEST_MASK_PARAMETERS
     return Sv_mask
 
 
-def create_noise_masks_rapidkrill(source_Sv: xarray.Dataset, params=RAPIDKRILL_MASK_PARAMETERS):
+def create_noise_masks_rapidkrill(source_Sv: xr.Dataset, params=RAPIDKRILL_MASK_PARAMETERS):
     """
     A function that creates noise masks for a given Sv dataset according to
     rapidkrill processing needs
@@ -391,7 +393,7 @@ def create_noise_masks_rapidkrill(source_Sv: xarray.Dataset, params=RAPIDKRILL_M
 
 
 def create_default_noise_masks_oceanstream(
-    source_Sv: xarray.Dataset, params=OCEANSTREAM_MASK_PARAMETERS
+    source_Sv: xr.Dataset, params=OCEANSTREAM_MASK_PARAMETERS
 ):
     """
     A function that creates noise masks for a given Sv dataset using default methods for oceanstream
@@ -416,7 +418,7 @@ def create_default_noise_masks_oceanstream(
 
 
 def create_seabed_masks_oceanstream(
-    source_Sv: xarray.Dataset, params=OCEANSTREAM_SEABED_MASK_PARAMETERS
+    source_Sv: xr.Dataset, params=OCEANSTREAM_SEABED_MASK_PARAMETERS
 ):
     """
     A function that creates seabed masks for a given Sv dataset using default methods for oceanstream
@@ -434,9 +436,7 @@ def create_seabed_masks_oceanstream(
     return Sv_mask
 
 
-def create_noise_masks_oceanstream(
-    source_Sv: xarray.Dataset, params=OCEANSTREAM_NOISE_MASK_PARAMETERS
-):
+def create_noise_masks_oceanstream(source_Sv: xr.Dataset, params=OCEANSTREAM_NOISE_MASK_PARAMETERS):
     """
     A function that creates noise masks for a given Sv dataset using default methods for oceanstream
 

diff --git a/tests/test_noise_mask.py b/tests/test_noise_mask.py
@@ -1,4 +1,5 @@
 import pytest
+from oceanstream.L2_calibrated_data.noise_masks import OCEANSTREAM_MASK_PARAMETERS
 
 from oceanstream.L2_calibrated_data.noise_masks import (
     create_attenuation_mask,
@@ -13,46 +14,29 @@
 
 def test_impulse(enriched_ek60_Sv):
     source_Sv = enriched_ek60_Sv
-    RYAN_DEFAULT_PARAMS = {"thr": 10, "m": 5, "n": 1}
+    RYAN_DEFAULT_PARAMS = OCEANSTREAM_MASK_PARAMETERS["impulse"]["params"]
     mask = create_impulse_mask(source_Sv, parameters=RYAN_DEFAULT_PARAMS)
     assert mask["channel"].shape == (3,)
 
 
 def test_transient(enriched_ek60_Sv):
     source_Sv = enriched_ek60_Sv
-    RYAN_DEFAULT_PARAMS = {
-        #    "m": 5,
-        #    "n": 20,
-        "m": 5,
-        "n": 5,
-        "thr": 20,
-        "excludeabove": 250,
-        "operation": "mean",
-    }
+    RYAN_DEFAULT_PARAMS = OCEANSTREAM_MASK_PARAMETERS["transient"]["params"]
     mask_ryan = create_transient_mask(
         source_Sv, parameters=RYAN_DEFAULT_PARAMS, method="ryan"
     )
     assert mask_ryan["channel"].shape == (3,)
 
 
 def test_attenuation(enriched_ek60_Sv):
-    DEFAULT_RYAN_PARAMS = {"r0": 180, "r1": 280, "n": 30, "thr": -6, "start": 0}
+    DEFAULT_RYAN_PARAMS = OCEANSTREAM_MASK_PARAMETERS["attenuation"]["params"]
     source_Sv = enriched_ek60_Sv
     mask = create_attenuation_mask(source_Sv, parameters=DEFAULT_RYAN_PARAMS)
     assert mask["channel"].shape == (3,)
 
 
 def test_seabed(enriched_ek60_Sv):
-    ARIZA_DEFAULT_PARAMS = {
-        "r0": 10,
-        "r1": 1000,
-        "roff": 0,
-        "thr": -40,
-        "ec": 1,
-        "ek": (1, 3),
-        "dc": 10,
-        "dk": (3, 7),
-    }
+    ARIZA_DEFAULT_PARAMS = OCEANSTREAM_MASK_PARAMETERS["seabed"]["params"]
     source_Sv = enriched_ek60_Sv
     mask = create_seabed_mask(
         source_Sv,
@@ -66,4 +50,5 @@ def test_create_masks(enriched_ek60_Sv):
     enriched_Sv = enriched_ek60_Sv
     Sv_mask = create_multiple_masks(enriched_Sv)
     assert Sv_mask["mask_seabed"].attrs["mask_type"] == "seabed"
-    assert Sv_mask["mask_impulse"].attrs["parameters"] == ["thr=10", "m=5", "n=1"]
+    assert Sv_mask["mask_impulse"].attrs["parameters"] == ["thr=3", "m=3", "n=1"]
+