water-column-sonar-processing 0.0.7__py3-none-any.whl → 0.0.8__py3-none-any.whl

water_column_sonar_processing/processing/raw_to_zarr.py

@@ -0,0 +1,349 @@
+import gc
+import os
+import echopype as ep
+import numcodecs
+import numpy as np
+from numcodecs import Blosc
+from datetime import datetime
+from pathlib import Path # , PurePath
+
+from src.water_column_sonar_processing.aws import DynamoDBManager, S3Manager
+from src.water_column_sonar_processing.geometry.geometry_manager import GeometryManager
+from src.water_column_sonar_processing.utility import Cleaner
+
+TEMPDIR = "/tmp"
+
+
+# This code is getting copied from echofish-aws-raw-to-zarr-lambda
+class RawToZarr:
+    #######################################################
+    def __init__(
+            self,
+            # output_bucket_access_key,
+            # output_bucket_secret_access_key,
+            # # overwrite_existing_zarr_store,
+    ):
+        # TODO: revert to Blosc.BITSHUFFLE, troubleshooting misc error
+        self.__compressor = Blosc(cname="zstd", clevel=2)  # shuffle=Blosc.NOSHUFFLE
+        self.__overwrite = True
+        self.__num_threads = numcodecs.blosc.get_nthreads()
+        # self.input_bucket_name = os.environ.get("INPUT_BUCKET_NAME")
+        # self.output_bucket_name = os.environ.get("OUTPUT_BUCKET_NAME")
+        # self.__table_name = table_name
+        # # self.__overwrite_existing_zarr_store = overwrite_existing_zarr_store
+
+    ############################################################################
+    ############################################################################
+    def __zarr_info_to_table(
+            self,
+            output_bucket_name,
+            table_name,
+            ship_name,
+            cruise_name,
+            sensor_name,
+            file_name,
+            zarr_path,
+            min_echo_range,
+            max_echo_range,
+            num_ping_time_dropna,
+            start_time,
+            end_time,
+            frequencies,
+            channels
+    ):
+        print('Writing Zarr information to DynamoDB table.')
+        dynamodb_manager = DynamoDBManager()
+
+        # The problem is that these values were never populated
+        # and so when the query looks for values that aren't there
+        # they fail
+        dynamodb_manager.update_item(
+            table_name=table_name,
+            key={
+                'FILE_NAME': {'S': file_name},  # Partition Key
+                'CRUISE_NAME': {'S': cruise_name},  # Sort Key
+            },
+            expression_attribute_names={
+                '#CH': 'CHANNELS',
+                '#ET': 'END_TIME',
+                # "#ED": "ERROR_DETAIL",
+                '#FR': 'FREQUENCIES',
+                '#MA': 'MAX_ECHO_RANGE',
+                '#MI': 'MIN_ECHO_RANGE',
+                '#ND': 'NUM_PING_TIME_DROPNA',
+                "#PS": "PIPELINE_STATUS",
+                "#PT": "PIPELINE_TIME",
+                "#SE": "SENSOR_NAME",
+                "#SH": "SHIP_NAME",
+                '#ST': 'START_TIME',
+                '#ZB': 'ZARR_BUCKET',
+                '#ZP': 'ZARR_PATH',
+            },
+            expression_attribute_values={
+                ":ch": {"L": [{"S": i} for i in channels]},
+                ":et": {"S": end_time},
+                # ":ed": {"S": ""},
+                ":fr": {"L": [{"N": str(i)} for i in frequencies]},
+                ":ma": {"N": str(np.round(max_echo_range, 4))},
+                ":mi": {"N": str(np.round(min_echo_range, 4))},
+                ":nd": {"N": str(num_ping_time_dropna)},
+                ":ps": {"S": "PROCESSING_RESAMPLE_AND_WRITE_TO_ZARR_STORE"},
+                ":pt": {"S": datetime.now().isoformat(timespec="seconds") + "Z"},
+                ":se": {"S": sensor_name},
+                ":sh": {"S": ship_name},
+                ":st": {"S": start_time},
+                ":zb": {"S": output_bucket_name},
+                ":zp": { "S": zarr_path },
+            },
+            update_expression=(
+                "SET "
+                "#CH = :ch, "
+                "#ET = :et, "
+                # "#ED = :ed, "
+                "#FR = :fr, "
+                "#MA = :ma, "
+                "#MI = :mi, "
+                "#ND = :nd, "
+                "#PS = :ps, "
+                "#PT = :pt, "
+                "#SE = :se, "
+                "#SH = :sh, "
+                "#ST = :st, "
+                "#ZB = :zb, "
+                "#ZP = :zp"
+            ),
+        )
+
+    ############################################################################
+    ############################################################################
+    ############################################################################
+    def __upload_files_to_output_bucket(
+            self,
+            output_bucket_name,
+            local_directory,
+            object_prefix,
+    ):
+        # Note: this will be passed credentials if using NODD
+        s3_manager = S3Manager()
+        print('Uploading files using thread pool executor.')
+        all_files = []
+        for subdir, dirs, files in os.walk(local_directory):
+            for file in files:
+                local_path = os.path.join(subdir, file)
+                s3_key = os.path.join(object_prefix, local_path)
+                all_files.append([local_path, s3_key])
+        # all_files
+        all_uploads = s3_manager.upload_files_with_thread_pool_executor(
+            output_bucket_name=output_bucket_name,
+            all_files=all_files,
+        )
+        return all_uploads
+
+    ############################################################################
+    def raw_to_zarr(
+            self,
+            table_name,
+            output_bucket_name,
+            ship_name,
+            cruise_name,
+            sensor_name,
+            raw_file_name,
+    ):
+        print(f'Opening raw: {raw_file_name} and creating zarr store.')
+        geometry_manager = GeometryManager()
+        cleaner = Cleaner()
+        cleaner.delete_local_files(file_types=["*.zarr", "*.json"]) # TODO: include bot and raw?ß
+        try:
+            gc.collect()
+            print('Opening raw file with echopype.')
+            # s3_file_path = f"s3://{bucket_name}/data/raw/{ship_name}/{cruise_name}/{sensor_name}/{file_name}"
+            # s3_file_path = Path(f"s3://noaa-wcsd-pds/data/raw/{ship_name}/{cruise_name}/{sensor_name}/{file_name}")
+            echodata = ep.open_raw(
+                raw_file=raw_file_name,
+                sonar_model=sensor_name,
+                include_bot=True,
+                use_swap=True,
+                # max_chunk_size=100,
+                # storage_options={'anon': True } # 'endpoint_url': self.endpoint_url} # this was creating problems
+            )
+            print('Compute volume backscattering strength (Sv) from raw data.')
+            ds_sv = ep.calibrate.compute_Sv(echodata)
+            print('Done computing volume backscattering strength (Sv) from raw data.')
+            frequencies = echodata.environment.frequency_nominal.values
+            #################################################################
+            # Get GPS coordinates
+            gps_data, lat, lon = geometry_manager.read_echodata_gps_data(
+                echodata=echodata,
+                output_bucket_name=output_bucket_name,
+                ship_name=ship_name,
+                cruise_name=cruise_name,
+                sensor_name=sensor_name,
+                file_name=raw_file_name,
+                write_geojson=True
+            )
+            # gps_data, lat, lon = self.__get_gps_data(echodata=echodata)
+            #################################################################
+            # Technically the min_echo_range would be 0 m.
+            # TODO: this var name is supposed to represent minimum resolution of depth measurements
+            # TODO revert this so that smaller diffs can be used
+            # The most minimum the resolution can be is as small as 0.25 meters
+            min_echo_range = np.maximum(
+                0.25,
+                np.nanmin(np.diff(ds_sv.echo_range.values))
+            )
+            max_echo_range = float(np.nanmax(ds_sv.echo_range))
+            #
+            num_ping_time_dropna = lat[~np.isnan(lat)].shape[0]  # symmetric to lon
+            #
+            start_time = np.datetime_as_string(ds_sv.ping_time.values[0], unit='ms') + "Z"
+            end_time = np.datetime_as_string(ds_sv.ping_time.values[-1], unit='ms') + "Z"
+            channels = list(ds_sv.channel.values)
+            #
+            #################################################################
+            # Create the zarr store
+            store_name = f"{Path(raw_file_name).stem}.zarr"
+            ds_sv.to_zarr(store=store_name)
+            #################################################################
+            # TODO: do i still need this?
+            # print('Note: Adding GeoJSON inside Zarr store')
+            # self.__write_geojson_to_file( # Was trying to write geojson to the L1 zarr store
+            #     store_name=store_name,
+            #     data=gps_data
+            # )
+            #################################################################
+            output_zarr_prefix = f"level_1/{ship_name}/{cruise_name}/{sensor_name}/"
+            self.__zarr_info_to_table(
+                output_bucket_name=output_bucket_name,
+                table_name=table_name,
+                ship_name=ship_name,
+                cruise_name=cruise_name,
+                sensor_name=sensor_name,
+                file_name=raw_file_name,
+                zarr_path=os.path.join(output_zarr_prefix, store_name),
+                min_echo_range=min_echo_range,
+                max_echo_range=max_echo_range,
+                num_ping_time_dropna=num_ping_time_dropna,
+                start_time=start_time,
+                end_time=end_time,
+                frequencies=frequencies,
+                channels=channels
+            )
+            ###################################################################
+            #######################################################################
+            self.__upload_files_to_output_bucket(
+                output_bucket_name=output_bucket_name,
+                local_directory=store_name,
+                object_prefix=output_zarr_prefix
+            )
+            #######################################################################
+            # # TODO: verify count of objects matches
+            # s3_objects = self.__s3.list_objects(
+            #     bucket_name=self.__output_bucket,
+            #     prefix=f"{zarr_prefix}/{os.path.splitext(input_file_name)[0]}.zarr/",
+            #     access_key_id=self.__output_bucket_access_key,
+            #     secret_access_key=self.__output_bucket_secret_access_key
+            # )
+            #######################################################################
+            # self.__update_processing_status(
+            #     file_name=input_file_name,
+            #     cruise_name=cruise_name,
+            #     pipeline_status='SUCCESS_RAW_TO_ZARR'
+            # )
+            #######################################################################
+            # self.__publish_done_message(input_message)
+            print('here')
+        except Exception as err:
+            print(f'Exception encountered creating local Zarr store with echopype: {err}')
+            raise RuntimeError(f"Problem creating local Zarr store, {err}")
+        finally:
+            cleaner.delete_local_files(file_types=["*.raw", "*.bot", "*.zarr", "*.json"])
+        print('Done creating local zarr store.')
+
+    ############################################################################
+    # TODO: does this get called?
+    # def execute(self, input_message):
+    #     ship_name = input_message['shipName']
+    #     cruise_name = input_message['cruiseName']
+    #     sensor_name = input_message['sensorName']
+    #     input_file_name = input_message['fileName']
+    #     #
+    #     try:
+    #         self.__update_processing_status(
+    #             file_name=input_file_name,
+    #             cruise_name=cruise_name,
+    #             pipeline_status="PROCESSING_RAW_TO_ZARR"
+    #         )
+    #         #######################################################################
+    #         store_name = f"{os.path.splitext(input_file_name)[0]}.zarr"
+    #         output_zarr_prefix = f"level_1/{ship_name}/{cruise_name}/{sensor_name}"
+    #         bucket_key = f"data/raw/{ship_name}/{cruise_name}/{sensor_name}/{input_file_name}"
+    #         zarr_prefix = os.path.join("level_1", ship_name, cruise_name, sensor_name)
+    #         #
+    #         os.chdir(TEMPDIR)  # Lambdas require use of temp directory
+    #         #######################################################################
+    #         #######################################################################
+    #         # Check if zarr store already exists
+    #         s3_objects = self.__s3.list_objects(
+    #             bucket_name=self.__output_bucket,
+    #             prefix=f"{zarr_prefix}/{os.path.splitext(input_file_name)[0]}.zarr/",
+    #             access_key_id=self.__output_bucket_access_key,
+    #             secret_access_key=self.__output_bucket_secret_access_key
+    #         )
+    #         if len(s3_objects) > 0:
+    #             print('Zarr store data already exists in s3, deleting existing and continuing.')
+    #             self.__s3.delete_objects(
+    #                 bucket_name=self.__output_bucket,
+    #                 objects=s3_objects,
+    #                 access_key_id=self.__output_bucket_access_key,
+    #                 secret_access_key=self.__output_bucket_secret_access_key
+    #             )
+    #         #######################################################################
+    #         # self.__delete_all_local_raw_and_zarr_files()
+    #         Cleaner.delete_local_files(file_types=["*.raw*", "*.zarr"])
+    #         self.__s3.download_file(
+    #             bucket_name=self.__input_bucket,
+    #             key=bucket_key,
+    #             file_name=input_file_name
+    #         )
+    #         self.__create_local_zarr_store(
+    #             raw_file_name=input_file_name,
+    #             cruise_name=cruise_name,
+    #             sensor_name=sensor_name,
+    #             output_zarr_prefix=output_zarr_prefix,
+    #             store_name=store_name
+    #         )
+    #         #######################################################################
+    #         self.__upload_files_to_output_bucket(store_name, output_zarr_prefix)
+    #         #######################################################################
+    #         # # TODO: verify count of objects matches
+    #         # s3_objects = self.__s3.list_objects(
+    #         #     bucket_name=self.__output_bucket,
+    #         #     prefix=f"{zarr_prefix}/{os.path.splitext(input_file_name)[0]}.zarr/",
+    #         #     access_key_id=self.__output_bucket_access_key,
+    #         #     secret_access_key=self.__output_bucket_secret_access_key
+    #         # )
+    #         #######################################################################
+    #         self.__update_processing_status(
+    #             file_name=input_file_name,
+    #             cruise_name=cruise_name,
+    #             pipeline_status='SUCCESS_RAW_TO_ZARR'
+    #         )
+    #         #######################################################################
+    #         self.__publish_done_message(input_message)
+    #         #######################################################################
+    #     # except Exception as err:
+    #     #     print(f'Exception encountered: {err}')
+    #     # self.__update_processing_status(
+    #     #     file_name=input_file_name,
+    #     #     cruise_name=cruise_name,
+    #     #     pipeline_status='FAILURE_RAW_TO_ZARR',
+    #     #     error_message=str(err),
+    #     # )
+    #     finally:
+    #         self.__delete_all_local_raw_and_zarr_files()
+    #######################################################################
+
+    ############################################################################
+
+################################################################################
+############################################################################

water_column_sonar_processing/utility/cleaner.py

@@ -7,6 +7,7 @@ import shutil
 class Cleaner:
     @staticmethod
     def delete_local_files(file_types=["*.raw*", "*.model"]):  # '*.json'
+        # TODO: add .zarr to this
         print("Deleting all local raw and model files")
         for i in file_types:
             for j in glob.glob(i):

water_column_sonar_processing/utility/constants.py

@@ -3,7 +3,11 @@ from enum import Enum, Flag, unique
 
 @unique
 class Constants(Flag):
-    TILE_SIZE = 512
+    TILE_SIZE = 2048
+    # Average https://noaa-wcsd-zarr-pds.s3.us-east-1.amazonaws.com/level_2/Henry_B._Bigelow/HB0902/EK60/HB0902.zarr/time/927
+    # chunk size is ~1.3 kB, HB0902 cruise takes ~30 seconds to load all time/lat/lon data
+    # NOTE: larger value here will speed up the TurfJS download of data in the UI
+    SPATIOTEMPORAL_CHUNK_SIZE = int(1e5) # 2**17
 
 
 class Coordinates(Enum):
@@ -33,7 +37,7 @@ class Coordinates(Enum):
     # TODO: create test for reading out timestamps in Xarray
 
     FREQUENCY = "frequency"
-    FREQUENCY_DTYPE = "int"
+    FREQUENCY_DTYPE = "uint"
     FREQUENCY_UNITS = "Hz"
     FREQUENCY_LONG_NAME = "Transducer frequency"
     FREQUENCY_STANDARD_NAME = "sound_frequency"

{water_column_sonar_processing-0.0.7.dist-info → water_column_sonar_processing-0.0.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: water_column_sonar_processing
-Version: 0.0.7
+Version: 0.0.8
 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
@@ -11,26 +11,27 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: aiobotocore~=2.9.0
-Requires-Dist: aiohttp~=3.10.10
-Requires-Dist: boto3==1.33.13
-Requires-Dist: botocore~=1.33.13
+Requires-Dist: aiobotocore==2.15.2
+Requires-Dist: boto3==1.35.36
+Requires-Dist: botocore==1.35.36
 Requires-Dist: echopype==0.9.0
 Requires-Dist: fiona==1.10.1
 Requires-Dist: geopandas==1.0.1
-Requires-Dist: mock~=5.1.0
-Requires-Dist: moto~=5.0.18
+Requires-Dist: mock==5.1.0
+Requires-Dist: moto[all]==5.0.21
+Requires-Dist: moto[server]==5.0.21
 Requires-Dist: numcodecs==0.13.1
 Requires-Dist: numpy==1.26.4
 Requires-Dist: pandas==2.2.3
-Requires-Dist: pytest~=8.3.3
+Requires-Dist: pyarrow==18.1.0
 Requires-Dist: python-dotenv==1.0.0
 Requires-Dist: requests==2.32.3
-Requires-Dist: s3fs==2024.10.0
+Requires-Dist: s3fs==2023.12.1
 Requires-Dist: scipy==1.14.1
+Requires-Dist: setuptools==75.6.0
 Requires-Dist: shapely==2.0.3
 Requires-Dist: typing-extensions==4.10.0
-Requires-Dist: xarray==2022.12.0
+Requires-Dist: xarray==2024.10.0
 Requires-Dist: zarr==2.18.3
 
 # Water Column Sonar Processing
@@ -85,6 +86,8 @@ Processing tool for converting L0 data to L1 and L2 as well as generating geospa
 ```commandline
 pytest --disable-warnings
 ```
+or
+> pytest --cache-clear --cov=src tests/ --cov-report=xml
 
 # Instructions
 Following this tutorial:
@@ -122,3 +125,10 @@ https://plugins.jetbrains.com/plugin/20574-ruff
 
 # Colab Test
 https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scrollTo=AayVyvpBdfIZ
+
+# Test Coverage
+20241124
+8 failed, 32 passed, 3 skipped, 1 warning in 6.92s
+20241125
+5 failed, 35 passed, 3 skipped, 1 warning in 9.71s
+3 failed, 38 passed, 3 skipped, 1 warning in 7.24s

water_column_sonar_processing-0.0.8.dist-info/RECORD

@@ -0,0 +1,32 @@
+water_column_sonar_processing/__init__.py,sha256=Ipl74g4btRHNYqgJ4Ro957HQC4YXBoIrGhgMmBPP0Uw,290
+water_column_sonar_processing/process.py,sha256=mb8_UpcOTy7RAAMlv-nF5hZG5zFoMsFxlT4OyvrpObk,5455
+water_column_sonar_processing/aws/__init__.py,sha256=u5J-TOEVgAQsMdc5LMo1igUESRclzV8gf-b0jUaJ9Gg,277
+water_column_sonar_processing/aws/dynamodb_manager.py,sha256=sZHn-hgCt3K3w0x5BcXfF5jLMt_F11dAtQHJToij9nU,10008
+water_column_sonar_processing/aws/s3_manager.py,sha256=ctNWMkgqMlwbwmXHgwKEV8otLwIjr-dHX6bQ2rOw1ug,14718
+water_column_sonar_processing/aws/s3fs_manager.py,sha256=thVJPQKhbvF1g-Ue3BYgwazFOFDYOICIEJx4zkXBQ1E,2381
+water_column_sonar_processing/aws/sns_manager.py,sha256=Dp9avG5VSugSWPR1dZ-askuAw1fCZkNUHbOUP65iR-k,1867
+water_column_sonar_processing/aws/sqs_manager.py,sha256=NSUrWmnSC8h8Gf7gT0U8zFaQQ-yX89h0Q0mDLKGqp2Y,1597
+water_column_sonar_processing/cruise/__init__.py,sha256=H5hW0JMORuaFvQk_R31B4VL8RnRyKeanOOiWmqEMZJk,156
+water_column_sonar_processing/cruise/create_empty_zarr_store.py,sha256=ev5jMZiwLyY1zrIAQhAw9X55eD3rxMrW5PpotjlOxDE,7382
+water_column_sonar_processing/cruise/resample_regrid.py,sha256=aCbY84wtQma7GK9QooMqXzrJuIpC8IPUp1cRwN8ZOoA,12368
+water_column_sonar_processing/geometry/__init__.py,sha256=_ol5nI8AL30pYXeAh5rtP7YmQggitPC6LA_kuTfPJ0Q,231
+water_column_sonar_processing/geometry/geometry_manager.py,sha256=xN1zyD_4Apry69BNcm5GtBKPpbHaPc_TYRYYFXjtwMc,10577
+water_column_sonar_processing/geometry/geometry_simplification.py,sha256=im1HG9nfYIerQv3w-PUHzphw2B7aGgnsA3Zcdy2oTmA,3016
+water_column_sonar_processing/geometry/pmtile_generation.py,sha256=Hh7UP8_mSC4_vw0F-LEv0DCT0FBYzbuNWZ0bITdg3gI,12458
+water_column_sonar_processing/index/__init__.py,sha256=izEObsKiOoIJ0kZCFhvaYsBd6Ga71XJxnogjrNInw68,68
+water_column_sonar_processing/index/index_manager.py,sha256=k_OOpU8FNQ5pz4HZkr1xGLakLbuyeBm8LZcFVqjU2cQ,11254
+water_column_sonar_processing/model/__init__.py,sha256=FXaCdbPqxp0ogmZm9NplRirqpgMiYs1iRYgJbFbbX2Y,65
+water_column_sonar_processing/model/zarr_manager.py,sha256=hKikypzqqxGPUpjkSrf_RweHihaBuAxIQyOichf4Vhs,13637
+water_column_sonar_processing/processing/__init__.py,sha256=UwdB3BnoUxy4q3k9-ZjBF6KzmCWVDcqbcArTeHgmvGA,118
+water_column_sonar_processing/processing/cruise_sampler.py,sha256=d5_rwk9ucCGxNnL4gjDoY12fN6t9jOwJJenftGV4dGE,15931
+water_column_sonar_processing/processing/raw_to_zarr.py,sha256=W5BswuiHSnHj6jhVY_31qHo6OQHbYEvP2cqBliIqVZQ,16154
+water_column_sonar_processing/utility/__init__.py,sha256=nyqPobcvwftr6T4MNxNtQtfbWzW9Kgpbp6JO7Gr5IZI,206
+water_column_sonar_processing/utility/cleaner.py,sha256=bNbs-hopWxtKAFBK0Eu18xdRErZCGZvtla3j-1bTwQw,619
+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
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{water_column_sonar_processing-0.0.7.dist-info → water_column_sonar_processing-0.0.8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
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+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

water_column_sonar_processing-0.0.7.dist-info/RECORD

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