Merge branch 'Parse-sonar-model-from-.raw-for-EK60,-EK80' into parse-…

…remaining-sonar-models-from-raws

docs/source/contributing.md

@@ -81,7 +81,23 @@ One can replace `conda` with `mamba` in the above commands when creating the env
 
 Currently, test data are stored in a private Google Drive folder and
 made available via the [`cormorack/http`](https://hub.docker.com/r/cormorack/http)
-Docker image on Docker hub.
+Docker image on Docker hub. There’s no need to pull directly from Docker Hub, as the scripts below will handle that for you. For Linux Users: If you run into an issue where accessing the Docker daemon requires sudo privileges, which may not suit your environment, you can adjust your settings to allow non-root access to Docker:
+
+```shell
+sudo groupadd docker
+```
+
+Add the current user to the Docker group
+```shell
+sudo gpasswd -a $USER docker
+```
+
+Restart the docker daemon
+```shell
+sudo service docker restart
+```
+
+You might also need to restart your computer if the steps above don't resolve the issue.
 The image is rebuilt daily when new test data are added.
 If your tests require adding new test data, ping the maintainers (@leewujung, @ctuguinay)
 to get them added to the the Google Drive.

echopype/convert/__init__.py

@@ -14,8 +14,8 @@
 from .parse_azfp import ParseAZFP
 from .parse_azfp6 import ParseAZFP6
 from .parse_base import ParseBase
-from .parse_ek60 import ParseEK60
-from .parse_ek80 import ParseEK80
+from .parse_ek60 import ParseEK60, is_EK60
+from .parse_ek80 import ParseEK80, is_EK80
 from .set_groups_ad2cp import SetGroupsAd2cp
 from .set_groups_azfp import SetGroupsAZFP
 from .set_groups_azfp6 import SetGroupsAZFP6

echopype/convert/parse_ek60.py

@@ -1,8 +1,11 @@
 import numpy as np
 
+
 from .parse_base import ParseEK
 from .utils.ek_raw_io import RawSimradFile
 
+
+
 class ParseEK60(ParseEK):
     """Class for converting data from Simrad EK60 echosounders."""
 
@@ -18,16 +21,34 @@ def __init__(
         super().__init__(file, bot_file, idx_file, storage_options, sonar_model)
 
 
+
 def is_ER60(raw_file, storage_options):
     """Check if a raw data file is from Simrad EK60 echosounder."""
     with RawSimradFile(raw_file, "r", storage_options=storage_options) as fid:
         config_datagram = fid.read(1)
         config_datagram["timestamp"] = np.datetime64(
             config_datagram["timestamp"].replace(tzinfo=None), "[ns]"
         )
-
+        # Return True if the sounder name matches "ER60"
         try:
-            # Return True if the sounder name matches "ER60" or "EK60"
             return config_datagram["sounder_name"] in {"ER60"}
         except KeyError:
-            return False
+            return False
+
+
+
+def is_EK60(raw_file, storage_options):
+
+    """Check if a raw data file is from Simrad EK60 echosounder."""
+    with RawSimradFile(raw_file, "r", storage_options=storage_options) as fid:
+        config_datagram = fid.read(1)
+        config_datagram["timestamp"] = np.datetime64(
+            config_datagram["timestamp"].replace(tzinfo=None), "[ns]"
+        )
+
+        try:
+            # Return True if the sounder name matches "EK60"
+            return config_datagram["sounder_name"] in {"EK60"}
+        except KeyError:
+            return False
+

echopype/convert/parse_ek80.py

@@ -1,4 +1,7 @@
+import numpy as np
+
 from .parse_base import ParseEK
+from .utils.ek_raw_io import RawSimradFile
 
 
 class ParseEK80(ParseEK):
@@ -15,3 +18,15 @@ def __init__(
     ):
         super().__init__(file, bot_file, idx_file, storage_options, sonar_model)
         self.environment = {}  # dictionary to store environment data
+
+
+def is_EK80(raw_file, storage_options):
+    """Check if a raw data file is from Simrad EK80 echosounder."""
+    with RawSimradFile(raw_file, "r", storage_options=storage_options) as fid:
+        config_datagram = fid.read(1)
+        config_datagram["timestamp"] = np.datetime64(
+            config_datagram["timestamp"].replace(tzinfo=None), "[ns]"
+        )
+
+        # Return True if "configuration" exists in config_datagram
+        return "configuration" in config_datagram

echopype/tests/convert/test_convert_ek60.py

@@ -1,12 +1,12 @@
 import warnings
-
+import glob
 import numpy as np
 import pandas as pd
 from scipy.io import loadmat
 import pytest
 
 from echopype import open_raw
-from echopype.convert import ParseEK60
+from echopype.convert import ParseEK60, is_EK60
 
 
 @pytest.fixture
@@ -264,3 +264,31 @@ def test_converting_ek60_raw_with_missing_channel_power():
     # Check that all empty power channels do not exist in the EchoData Beam group
     for _, empty_power_channel_name in empty_power_chs.items():
         assert empty_power_channel_name not in ed["Sonar/Beam_group1"]["channel"]
+
+
+def test_is_EK60_ek60_files():
+    """Check that EK60 files are identified as EK60"""
+    # Collect all .raw files in the ek60 directory
+    ek60_files = glob.glob("echopype/test_data/ek60/*.raw")
+
+    # Check that each file in ek60 is identified as EK60
+    for test_file_path in ek60_files:
+        assert is_EK60(test_file_path, storage_options={}) == True
+
+def test_is_EK60_er60_files():
+    """Check that ER60 files are identified as EK60"""
+    # Collect all .raw files in the ek60 directory (assuming ER60 files are also here)
+    er60_files = glob.glob("echopype/test_data/ek60/*.raw")
+
+    # Check that each file in ek60 is identified as EK60
+    for test_file_path in er60_files:
+        assert is_EK60(test_file_path, storage_options={}) == True
+
+def test_is_EK60_non_ek60_files():
+    """Check that non-EK60 files are not identified as EK60"""
+    # Collect all .raw files in the ek80 directory (non-EK60 files)
+    ek80_files = glob.glob("echopype/test_data/ek80/*.raw")
+
+    # Check that each file in ek80 is not identified as EK60
+    for test_file_path in ek80_files:
+        assert is_EK60(test_file_path, storage_options={}) == False

echopype/tests/convert/test_convert_ek80.py

@@ -1,13 +1,13 @@
 import shutil
-
+import glob
 import pytest
 import numpy as np
 import pandas as pd
 from scipy.io import loadmat
 
 from echopype import open_raw, open_converted
 from echopype.testing import TEST_DATA_FOLDER
-from echopype.convert.parse_ek80 import ParseEK80
+from echopype.convert.parse_ek80 import ParseEK80, is_EK80
 from echopype.convert.set_groups_ek80 import WIDE_BAND_TRANS, PULSE_COMPRESS, FILTER_IMAG, FILTER_REAL, DECIMATION
 
 
@@ -531,3 +531,21 @@ def test_parse_ek80_with_invalid_env_datagrams():
         env_var = ed["Environment"][var]
         assert env_var.notnull().all() and env_var.dtype == np.float64
 
+
+def test_is_EK80_ek80_files():
+    """Test that EK80 files are identified as EK80."""
+    # Collect all .raw files in the ek80 directory
+    ek80_files = glob.glob("echopype/test_data/ek80/*.raw")
+
+    # Check that each file in ek80 is identified as EK80
+    for test_file_path in ek80_files:
+        assert is_EK80(test_file_path, storage_options={}) == True
+
+def test_is_EK80_non_ek80_files():
+    """Test that non-EK80 files are not identified as EK80."""
+    # Collect all .raw files in the ek60 directory (non-EK80 files)
+    ek60_files = glob.glob("echopype/test_data/ek60/*.raw")
+
+    # Check that each file in ek60 is not identified as EK80
+    for test_file_path in ek60_files:
+        assert is_EK80(test_file_path, storage_options={}) == False