Merge/add transient noise mask (#82)

.ci_helpers/run-test.py

@@ -118,15 +118,24 @@
     for k, v in test_to_run.items():
         print(f"=== RUNNING {k.upper()} TESTS===")
         print(f"Touched files: {','.join([os.path.basename(p) for p in v])}")
-        if k == "root":
-            file_glob_str = "echopype/tests/test_*.py"
-            cov_mod_arg = ["--cov=echopype"]
+        # Run specific test files
+        # The input files must all starts with "test" in their name
+        # otherwise module globbing for specific test files will
+        # be used
+        if all(f.name.startswith("test") for f in v):
+            # For specific test files
+            test_files = [str(p) for p in v]
         else:
-            file_glob_str = f"echopype/tests/{k}/*.py"
-            cov_mod_arg = [f"--cov=echopype/{k}"]
-        if args.include_cov:
-            pytest_args = original_pytest_args + cov_mod_arg
-        test_files = glob.glob(file_glob_str)
+            # Run all tests in a module
+            if k == "root":
+                file_glob_str = "echopype/tests/test_*.py"
+                cov_mod_arg = ["--cov=echopype"]
+            else:
+                file_glob_str = f"echopype/tests/{k}/*.py"
+                cov_mod_arg = [f"--cov=echopype/{k}"]
+            if args.include_cov:
+                pytest_args = original_pytest_args + cov_mod_arg
+            test_files = glob.glob(file_glob_str)
         final_args = pytest_args + test_files
         print(f"Pytest args: {final_args}")
         exit_code = pytest.main(final_args)

docs/source/contributing.rst

@@ -145,13 +145,20 @@ the latter via `minio <https://minio.io>`_.
 will execute all tests. The entire test suite can be a bit slow, taking up to 40 minutes
 or more. If your changes impact only some of the subpackages (``convert``, ``calibrate``,
 ``preprocess``, etc), you can run ``run-test.py`` with only a subset of tests by passing
-as an argument a comma-separated list of the modules that have changed. For example:
+as an argument a comma-separated list of the modules that have changed or also run only particular test
+files by passing a comma-separated list of test files that you want to run. For example:
 
 .. code-block:: bash
 
     python .ci_helpers/run-test.py --local --pytest-args="-vv" echopype/calibrate/calibrate_ek.py,echopype/preprocess/noise_est.py
 
 will run only tests associated with the ``calibrate`` and ``preprocess`` subpackages.
+
+.. code-block:: bash
+
+    python .ci_helpers/run-test.py --local --pytest-args="-vv"  echopype/tests/convert/test_convert_azfp.py,echopype/tests/clean/test_noise.py
+
+will run only the tests in the ``test_convert_azfp.py`` and ``test_noise.py`` files.
 For ``run-test.py`` usage information, use the ``-h`` argument:
 ``python .ci_helpers/run-test.py -h``
 

echopype/calibrate/api.py

@@ -153,7 +153,7 @@ def compute_Sv(echodata: EchoData, **kwargs) -> xr.Dataset:
         - for EK60 echosounder, allowed parameters include:
           `"sa_correction"`, `"gain_correction"`, `"equivalent_beam_angle"`
         - for AZFP echosounder, allowed parameters include:
-          `"EL"`, `"DS"`, `"TVR"`, `"VTX"`, `"equivalent_beam_angle"`, `"Sv_offset"`
+          `"EL"`, `"DS"`, `"TVR"`, `"VTX0"`, `"equivalent_beam_angle"`, `"Sv_offset"`
 
         Passing in calibration parameters for other echosounders
         are not currently supported.
@@ -242,7 +242,7 @@ def compute_TS(echodata: EchoData, **kwargs):
         - for EK60 echosounder, allowed parameters include:
           `"sa_correction"`, `"gain_correction"`, `"equivalent_beam_angle"`
         - for AZFP echosounder, allowed parameters include:
-          `"EL"`, `"DS"`, `"TVR"`, `"VTX"`, `"equivalent_beam_angle"`, `"Sv_offset"`
+          `"EL"`, `"DS"`, `"TVR"`, `"VTX0"`, `"equivalent_beam_angle"`, `"Sv_offset"`
 
         Passing in calibration parameters for other echosounders
         are not currently supported.

echopype/calibrate/cal_params.py

@@ -29,7 +29,7 @@
         "impedance_transceiver",  # z_er
         "receiver_sampling_frequency",
     ),
-    "AZFP": ("EL", "DS", "TVR", "VTX", "equivalent_beam_angle", "Sv_offset"),
+    "AZFP": ("EL", "DS", "TVR", "VTX0", "equivalent_beam_angle", "Sv_offset"),
 }
 
 EK80_DEFAULT_PARAMS = {
@@ -352,7 +352,7 @@ def get_cal_params_AZFP(beam: xr.DataArray, vend: xr.DataArray, user_dict: dict)
                 out_dict[p] = beam[p]  # has only channel dim
 
             # Params from Vendor_specific group
-            elif p in ["EL", "DS", "TVR", "VTX", "Sv_offset"]:
+            elif p in ["EL", "DS", "TVR", "VTX0", "Sv_offset"]:
                 out_dict[p] = vend[p]  # these params only have the channel dimension
 
     return out_dict

echopype/calibrate/calibrate_azfp.py

@@ -63,7 +63,7 @@ def _cal_power_samples(self, cal_type, **kwargs):
         # TODO: take care of dividing by zero encountered in log10
         spreading_loss = 20 * np.log10(self.range_meter)
         absorption_loss = 2 * self.env_params["sound_absorption"] * self.range_meter
-        SL = self.cal_params["TVR"] + 20 * np.log10(self.cal_params["VTX"])  # eq.(2)
+        SL = self.cal_params["TVR"] + 20 * np.log10(self.cal_params["VTX0"])  # eq.(2)
 
         # scaling factor (slope) in Fig.G-1, units Volts/dB], see p.84
         a = self.cal_params["DS"]

echopype/calibrate/range.py

@@ -60,7 +60,7 @@ def compute_range_AZFP(echodata: EchoData, env_params: Dict, cal_type: str) -> x
     # Notation below follows p.86 of user manual
     N = vend["number_of_samples_per_average_bin"]  # samples per bin
     f = vend["digitization_rate"]  # digitization rate
-    L = vend["lockout_index"]  # number of lockout samples
+    L = vend["lock_out_index"]  # number of lockout samples
 
     # keep this in ref of AZFP matlab code,
     # set to 1 since we want to calculate from raw data

echopype/clean/__init__.py

@@ -1,10 +1,15 @@
-from .api import estimate_noise, remove_noise
-from .api import get_impulse_noise_mask, get_transient_noise_mask, get_attenuation_mask
+from .api import (
+    estimate_noise,
+    get_attenuation_mask,
+    get_impulse_noise_mask,
+    get_transient_noise_mask,
+    remove_noise,
+)
 
 __all__ = [
     "estimate_noise",
     "remove_noise",
     "get_impulse_noise_mask",
     "get_transient_noise_mask",
-    "get_attenuation_mask"
+    "get_attenuation_mask",
 ]