water-column-sonar-processing 0.0.12__tar.gz → 0.0.13__tar.gz

{water_column_sonar_processing-0.0.12 → water_column_sonar_processing-0.0.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: water_column_sonar_processing
-Version: 0.0.12
+Version: 0.0.13
 Summary: A processing tool for water column sonar data.
 Author-email: Rudy Klucik <rudy.klucik@noaa.gov>
 Project-URL: Homepage, https://github.com/CI-CMG/water-column-sonar-processing
@@ -131,9 +131,12 @@ https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scroll
 3 failed, 38 passed, 3 skipped, 1 warning in 7.24s
 
 # Tag a Release
+Step 1 --> increment the semantic version in the zarr_manager.py "metadata" & the "pyproject.toml"
+```commandline
+git tag "v0.0.13" -a
+```
+Step 3 --> enter description
 ```commandline
-git tag "v0.0.12" -a
-# enter description
 git push origin --tags
 ```
 

{water_column_sonar_processing-0.0.12 → water_column_sonar_processing-0.0.13}/README.md

@@ -95,9 +95,12 @@ https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scroll
 3 failed, 38 passed, 3 skipped, 1 warning in 7.24s
 
 # Tag a Release
+Step 1 --> increment the semantic version in the zarr_manager.py "metadata" & the "pyproject.toml"
+```commandline
+git tag "v0.0.13" -a
+```
+Step 3 --> enter description
 ```commandline
-git tag "v0.0.12" -a
-# enter description
 git push origin --tags
 ```
 

{water_column_sonar_processing-0.0.12 → water_column_sonar_processing-0.0.13}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "water_column_sonar_processing"
-version = "0.0.12"
+version = "0.0.13"
 authors = [
   { name="Rudy Klucik", email="rudy.klucik@noaa.gov" },
 ]

{water_column_sonar_processing-0.0.12 → water_column_sonar_processing-0.0.13}/tests/conftest.py

@@ -16,13 +16,17 @@ HB0707_RAW = pooch.create(
         #https://noaa-wcsd-pds.s3.amazonaws.com/data/raw/Henry_B._Bigelow/HB0707/EK60/D20070711-T182032.raw
         # TODO: add bottom files
         "D20070712-T124906.raw": "sha256:44f9b2402a8d6d51c69235d1e33c3e4ab570fc541e9f269009924378bf4d97a2", # 250 m, 158 MB
+        "D20070712-T124906.bot": "sha256:9eebd8b85a514f3df6b7c4ba127967302dfea7c5e9fb47c22e3182ad1a93c78f",
         "D20070712-T152416.raw": "sha256:94a937eefd6ae5763c27c9ba1e4769b2b76fcc2d840e7db6c2e0edd925d6f70f", # 1000 m, 200 MB
+        "D20070712-T152416.bot": "sha256:65b16cff596502889f841e58061217660e066b07fb732ccf211f1c6e46ee8210",
     },
 )
 
 def fetch_raw_files():
     HB0707_RAW.fetch(fname="D20070712-T124906.raw", progressbar=True)
-    file_name = HB0707_RAW.fetch(fname="D20070712-T152416.raw", progressbar=True)
+    HB0707_RAW.fetch(fname="D20070712-T124906.bot", progressbar=True)
+    HB0707_RAW.fetch(fname="D20070712-T152416.raw", progressbar=True)
+    file_name = HB0707_RAW.fetch(fname="D20070712-T152416.bot", progressbar=True)
     return Path(file_name).parent #joinpath(Path(file_path).stem)
 
 @pytest.fixture(scope="session")

{water_column_sonar_processing-0.0.12 → water_column_sonar_processing-0.0.13}/water_column_sonar_processing/cruise/resample_regrid.py

@@ -188,10 +188,10 @@ class ResampleRegrid:
             for file_name in all_file_names:
                 gc.collect()
                 file_name_stem = Path(file_name).stem
-                # file_name_stem = "D20070724-T151330"
                 print(f"Processing file: {file_name_stem}.")
-                # if f"{file_name_stem}.raw" not in list(cruise_df['FILE_NAME']):
-                #     raise Exception(f"Raw file file_stem not found in dynamodb.")
+
+                if f"{file_name_stem}.raw" not in list(cruise_df['FILE_NAME']):
+                    raise Exception(f"Raw file file_stem not found in dynamodb.")
 
                 # status = PipelineStatus['LEVEL_1_PROCESSING']
                 # TODO: filter rows by enum success, filter the dataframe just for enums >= LEVEL_1_PROCESSING
@@ -296,6 +296,26 @@ class ResampleRegrid:
                 output_zarr_store.longitude[
                     start_ping_time_index:end_ping_time_index
                 ] = geospatial.dropna()["longitude"].values
+
+                #########################################################################
+                # TODO: add the "detected_seafloor_depth/" to the
+                #  L2 cruise dataarrays
+                # TODO: make bottom optional if 'detected_seafloor_depth' in input_xr.variables:
+                # TODO: Only checking the first channel for now. Need to average across all channels
+                #  in the future. See https://github.com/CI-CMG/water-column-sonar-processing/issues/11
+                # detected_seafloor_depths = input_xr.detected_seafloor_depth.values[0, :] # note can include nans?
+                detected_seafloor_depth = input_xr.detected_seafloor_depth.values
+                detected_seafloor_depth[detected_seafloor_depth == 0.] = np.nan
+                detected_seafloor_depths = np.nanmean(detected_seafloor_depth, 0)
+                detected_seafloor_depths[detected_seafloor_depths == 0.] = np.nan
+                print(f"min depth measured: {np.nanmin(detected_seafloor_depths)}")
+                print(f"max depth measured: {np.nanmax(detected_seafloor_depths)}")
+                #available_indices = np.argwhere(np.isnan(geospatial['latitude'].values))
+                output_zarr_store.bottom[
+                    start_ping_time_index:end_ping_time_index
+                ] = detected_seafloor_depths
+                #########################################################################
+                #########################################################################
         except Exception as err:
             print(f"Problem interpolating the data: {err}")
             raise err

{water_column_sonar_processing-0.0.12 → water_column_sonar_processing-0.0.13}/water_column_sonar_processing/model/zarr_manager.py

@@ -246,7 +246,7 @@ class ZarrManager:
         #
         root.attrs["processing_software_name"] = Coordinates.PROJECT_NAME.value
         root.attrs["processing_software_version"] = (
-            "0.0.12"  # TODO: get programmatically, echopype>utils>prov.py
+            "0.0.13"  # TODO: get programmatically, echopype>utils>prov.py
         )
         root.attrs["processing_software_time"] = Timestamp.get_timestamp()
         #
@@ -288,7 +288,7 @@ class ZarrManager:
     ):
         # Mounts a Zarr store using pythons Zarr implementation. The mounted store
         #  will have read/write privileges so that store can be updated.
-        print("Opening Zarr store with Zarr.")
+        print("Opening L2 Zarr store with Zarr for writing.")
         try:
             s3fs_manager = S3FSManager(endpoint_url=endpoint_url)
             root = f"{output_bucket_name}/level_2/{ship_name}/{cruise_name}/{sensor_name}/{cruise_name}.zarr"

{water_column_sonar_processing-0.0.12 → water_column_sonar_processing-0.0.13}/water_column_sonar_processing.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: water_column_sonar_processing
-Version: 0.0.12
+Version: 0.0.13
 Summary: A processing tool for water column sonar data.
 Author-email: Rudy Klucik <rudy.klucik@noaa.gov>
 Project-URL: Homepage, https://github.com/CI-CMG/water-column-sonar-processing
@@ -131,9 +131,12 @@ https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scroll
 3 failed, 38 passed, 3 skipped, 1 warning in 7.24s
 
 # Tag a Release
+Step 1 --> increment the semantic version in the zarr_manager.py "metadata" & the "pyproject.toml"
+```commandline
+git tag "v0.0.13" -a
+```
+Step 3 --> enter description
 ```commandline
-git tag "v0.0.12" -a
-# enter description
 git push origin --tags
 ```