water-column-sonar-processing 25.1.4__py3-none-any.whl → 25.1.6__py3-none-any.whl

water_column_sonar_processing/cruise/resample_regrid.py

@@ -63,6 +63,7 @@ class ResampleRegrid:
             for channel in range(
                 len(channels)
             ):  # TODO: leaving off here, need to subset for just indices in time axis
+                gc.collect()
                 print(
                     np.nanmax(
                         input_xr.echo_range.sel(
@@ -88,6 +89,7 @@ class ResampleRegrid:
                 )  # removes nan's
                 # iterate through partitions of data with similar depths and resample
                 for select_max_depth in set_of_max_depths:
+                    gc.collect()
                     # TODO: for nan just skip and leave all nan's
                     select_indices = [
                         i
@@ -134,7 +136,7 @@ class ResampleRegrid:
             print(f"Problem finding the dynamodb table: {err}")
             raise err
         print("Done interpolating data.")
-        return regrid_resample
+        return regrid_resample.values.copy()
 
     #################################################################
     def resample_regrid(
@@ -226,21 +228,11 @@ class ResampleRegrid:
                 min_echo_range = np.nanmin(np.float32(cruise_df["MIN_ECHO_RANGE"]))
                 max_echo_range = np.nanmax(np.float32(cruise_df["MAX_ECHO_RANGE"]))
 
-                print("Creating empty ndarray for Sv data.")  # Note: cruise dims (depth, time, frequency)
-                output_zarr_store_shape = output_zarr_store.Sv.shape
-                end_ping_time_index - start_ping_time_index
-                output_zarr_store_height = output_zarr_store_shape[0]
-                output_zarr_store_width = end_ping_time_index - start_ping_time_index
-                output_zarr_store_depth = output_zarr_store_shape[2]
-                cruise_sv_subset = np.empty(
-                    shape=(output_zarr_store_height, output_zarr_store_width, output_zarr_store_depth)
-                )
-                cruise_sv_subset[:, :, :] = np.nan
-
+                # Note: cruise dims (depth, time, frequency)
                 all_cruise_depth_values = zarr_manager.get_depth_values(
                     min_echo_range=min_echo_range,
                     max_echo_range=max_echo_range
-                ) # (5262,) and
+                )
 
                 print(" ".join(list(input_xr_zarr_store.Sv.dims)))
                 if set(input_xr_zarr_store.Sv.dims) != {
@@ -282,7 +274,9 @@ class ResampleRegrid:
                 print(f"start_ping_time_index: {start_ping_time_index}, end_ping_time_index: {end_ping_time_index}")
                 #########################################################################
                 # write Sv values to cruise-level-model-store
-                output_zarr_store.Sv[:, start_ping_time_index:end_ping_time_index, :] = regrid_resample.values
+
+                for fff in range(regrid_resample.shape[-1]):
+                    output_zarr_store.Sv[:, start_ping_time_index:end_ping_time_index, fff] = regrid_resample[:, :, fff]
                 #########################################################################
                 # TODO: add the "detected_seafloor_depth/" to the
                 #  L2 cruise dataarrays

water_column_sonar_processing/model/zarr_manager.py

@@ -91,7 +91,7 @@ class ZarrManager:
             chunks=Constants.SPATIOTEMPORAL_CHUNK_SIZE.value,
             dtype=np.dtype(Coordinates.TIME_DTYPE.value),
             compressor=self.__compressor,
-            fill_value=np.nan,  # TODO: do i want nan's?
+            fill_value=np.nan,
             overwrite=self.__overwrite,
         )
 

{water_column_sonar_processing-25.1.4.dist-info → water_column_sonar_processing-25.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: water_column_sonar_processing
-Version: 25.1.4
+Version: 25.1.6
 Summary: 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
@@ -136,7 +136,7 @@ https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scroll
 # Tag a Release
 Step 1 --> increment the semantic version in the zarr_manager.py "metadata" & the "pyproject.toml"
 ```commandline
-git tag -a v25.1.4 -m "Releasing version v25.1.4"
+git tag -a v25.1.6 -m "Releasing version v25.1.6"
 git push origin --tags
 ```
 

{water_column_sonar_processing-25.1.4.dist-info → water_column_sonar_processing-25.1.6.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=ZsFQTDA0gXfQHlxDsXBGD1qQ0ipmx4kS81DcY6ml5Ew,7767
 water_column_sonar_processing/cruise/datatree_manager.py,sha256=Qy4dZCW8_q31lbjxbMsx3JtBS4BvQT17_2P0QD1RQcY,639
-water_column_sonar_processing/cruise/resample_regrid.py,sha256=wnog-qwFXRH20AYRD_3BXUgP-TN5ZnyPHpFws3527Mk,14533
+water_column_sonar_processing/cruise/resample_regrid.py,sha256=lEFBXVxh0l-LvLKbvM8XNrS7cPBpPr4g7SNikWMU16o,14049
 water_column_sonar_processing/geometry/__init__.py,sha256=GIzzc-_7pwEwbOkGpc4i_fmjWI5ymllXqzdHq_d3Rio,299
 water_column_sonar_processing/geometry/elevation_manager.py,sha256=eq9w691WJknPwWYkvO3giKTPleIxCVc2tMGR0e8ZRxQ,4267
 water_column_sonar_processing/geometry/geometry_manager.py,sha256=nz5T1vCDWHYIfQ853EqKYHDetTul7jRWS3y8Evep8QU,10855
@@ -18,7 +18,7 @@ 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=qsS6rKObJlFXKyzRuT1bk2_qW1YagW-Fg_AkQ1U_KRs,14213
 water_column_sonar_processing/model/__init__.py,sha256=FXaCdbPqxp0ogmZm9NplRirqpgMiYs1iRYgJbFbbX2Y,65
-water_column_sonar_processing/model/zarr_manager.py,sha256=wAO_8jcKIEonTNH12Fzzdirz0XLS7qgwOJGrmcVALR8,15678
+water_column_sonar_processing/model/zarr_manager.py,sha256=YOoUBaSo_63lPY0BbTRodAjBQ33r1UY81RAZ98hBE5E,15652
 water_column_sonar_processing/processing/__init__.py,sha256=tdpSfwnY6lbAS_yBTu4aG0SjPgCKqh6LAFvIj_t3j3U,168
 water_column_sonar_processing/processing/batch_downloader.py,sha256=qXoruHdbgzAolmroK6eRn9bWgeHFgaVQLwhJ6X5oHRE,6299
 water_column_sonar_processing/processing/raw_to_zarr.py,sha256=Sn0_zBT7yYP6abbSTlQBPA6iZSBxeVqPYYSgoroiBEU,17599
@@ -27,8 +27,8 @@ water_column_sonar_processing/utility/cleaner.py,sha256=bNbs-hopWxtKAFBK0Eu18xdR
 water_column_sonar_processing/utility/constants.py,sha256=UtzFkvH5VE7eb8PzeKUDVt-nX6SOdlHtkul1zycF_Z0,2146
 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-25.1.4.dist-info/LICENSE,sha256=lz4IpJ5_adG3S0ali-WaIpQFVTnEAOucMDQPECUVEYw,1110
-water_column_sonar_processing-25.1.4.dist-info/METADATA,sha256=vI9oh0A7AwlM3jQSKWNw3CdPR_yz4yHiynYuKbzNYH0,5959
-water_column_sonar_processing-25.1.4.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-water_column_sonar_processing-25.1.4.dist-info/top_level.txt,sha256=aRYU4A7RNBlNrL4vzjytFAir3BNnmOgsvIGKKA36tg4,30
-water_column_sonar_processing-25.1.4.dist-info/RECORD,,
+water_column_sonar_processing-25.1.6.dist-info/LICENSE,sha256=lz4IpJ5_adG3S0ali-WaIpQFVTnEAOucMDQPECUVEYw,1110
+water_column_sonar_processing-25.1.6.dist-info/METADATA,sha256=cMqKrx6xaDmiDsNoTsIfdQpherR4uf_6rolTvgGmw-0,5959
+water_column_sonar_processing-25.1.6.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+water_column_sonar_processing-25.1.6.dist-info/top_level.txt,sha256=aRYU4A7RNBlNrL4vzjytFAir3BNnmOgsvIGKKA36tg4,30
+water_column_sonar_processing-25.1.6.dist-info/RECORD,,