water-column-sonar-processing 0.0.12__py3-none-any.whl → 0.0.13__py3-none-any.whl

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/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.dist-info → water_column_sonar_processing-0.0.13.dist-info}/METADATA

@@ -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.dist-info → water_column_sonar_processing-0.0.13.dist-info}/RECORD

@@ -9,7 +9,7 @@ water_column_sonar_processing/aws/sqs_manager.py,sha256=NSUrWmnSC8h8Gf7gT0U8zFaQ
 water_column_sonar_processing/cruise/__init__.py,sha256=H5hW0JMORuaFvQk_R31B4VL8RnRyKeanOOiWmqEMZJk,156
 water_column_sonar_processing/cruise/create_empty_zarr_store.py,sha256=1IehrlhMAS5XAl7DLdQI4jIMSY9ZNLiW4YdcBEwYkbc,7679
 water_column_sonar_processing/cruise/experiment_datatree.py,sha256=K6Uq_36Rygw5oFF8zWavEwb1x8D27lJv5G3j0B59agE,243
-water_column_sonar_processing/cruise/resample_regrid.py,sha256=WFWxP083X4VpH9x50Om4nxSEUwTsjKjdejQz3Nh8CLs,12822
+water_column_sonar_processing/cruise/resample_regrid.py,sha256=XpGRs8nWspWuVoXBEV6VNVJSMlr3_IjnKlN1dK6dEA4,14292
 water_column_sonar_processing/geometry/__init__.py,sha256=_ol5nI8AL30pYXeAh5rtP7YmQggitPC6LA_kuTfPJ0Q,231
 water_column_sonar_processing/geometry/geometry_manager.py,sha256=nz5T1vCDWHYIfQ853EqKYHDetTul7jRWS3y8Evep8QU,10855
 water_column_sonar_processing/geometry/geometry_simplification.py,sha256=im1HG9nfYIerQv3w-PUHzphw2B7aGgnsA3Zcdy2oTmA,3016
@@ -17,7 +17,7 @@ water_column_sonar_processing/geometry/pmtile_generation.py,sha256=7Lm08Jr6YaM4n
 water_column_sonar_processing/index/__init__.py,sha256=izEObsKiOoIJ0kZCFhvaYsBd6Ga71XJxnogjrNInw68,68
 water_column_sonar_processing/index/index_manager.py,sha256=YS6y_THfGAZpjfBZOj5n8O1aY_BnBYS781eNHfhpip0,11239
 water_column_sonar_processing/model/__init__.py,sha256=FXaCdbPqxp0ogmZm9NplRirqpgMiYs1iRYgJbFbbX2Y,65
-water_column_sonar_processing/model/zarr_manager.py,sha256=ph0sU-aJQM5TkbyyArDHqXLpeiIki_ce6WN_Z7RVxxw,15053
+water_column_sonar_processing/model/zarr_manager.py,sha256=LoL8vOnEl2r_Jhu4l30p6AgfUZg1tW5aBydHx_BZAZg,15068
 water_column_sonar_processing/processing/__init__.py,sha256=UwdB3BnoUxy4q3k9-ZjBF6KzmCWVDcqbcArTeHgmvGA,118
 water_column_sonar_processing/processing/cruise_sampler.py,sha256=hadPrnH5nz7_oG_4pND7YbMFH6NMR9d6p3xAXedtKU8,15927
 water_column_sonar_processing/processing/raw_to_zarr.py,sha256=agbb2A0BWf7D4b5u-mYOBN_VyjRVjOdQM2aeRGBweWw,17617
@@ -26,8 +26,8 @@ water_column_sonar_processing/utility/cleaner.py,sha256=bNbs-hopWxtKAFBK0Eu18xdR
 water_column_sonar_processing/utility/constants.py,sha256=EbzsorvYKadsPjuutRjQKKByGibhFm0Gw6D-Sp2ZD3I,2143
 water_column_sonar_processing/utility/pipeline_status.py,sha256=O-0SySqdRGJ6bs3zQe1NV9vkOpmsRM7zj5QoHgzYioY,4395
 water_column_sonar_processing/utility/timestamp.py,sha256=bO0oir7KxxoEHPGRkz9FCBfOligkocUyRiWRzAq8fnU,361
-water_column_sonar_processing-0.0.12.dist-info/LICENSE,sha256=lz4IpJ5_adG3S0ali-WaIpQFVTnEAOucMDQPECUVEYw,1110
-water_column_sonar_processing-0.0.12.dist-info/METADATA,sha256=813ibpVKvkucEfCFlJVHeUfKIC8n1_Pt_Di4k6OebrQ,4960
-water_column_sonar_processing-0.0.12.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-water_column_sonar_processing-0.0.12.dist-info/top_level.txt,sha256=aRYU4A7RNBlNrL4vzjytFAir3BNnmOgsvIGKKA36tg4,30
-water_column_sonar_processing-0.0.12.dist-info/RECORD,,
+water_column_sonar_processing-0.0.13.dist-info/LICENSE,sha256=lz4IpJ5_adG3S0ali-WaIpQFVTnEAOucMDQPECUVEYw,1110
+water_column_sonar_processing-0.0.13.dist-info/METADATA,sha256=MUkVn5e1wkAFUAYpk25V02yNCeYNmwBsyib788i2ibg,5087
+water_column_sonar_processing-0.0.13.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+water_column_sonar_processing-0.0.13.dist-info/top_level.txt,sha256=aRYU4A7RNBlNrL4vzjytFAir3BNnmOgsvIGKKA36tg4,30
+water_column_sonar_processing-0.0.13.dist-info/RECORD,,