LiveSurvey Class

config_files/live_initialization_config.yml

@@ -0,0 +1,65 @@
+# This YAML file is a configuration file for all
+# initialization parameters used for the `LiveSurvey`
+# class in Echopop
+
+---
+  #####################################################################################################################
+  # Biological data processing#
+  ########################
+  biology:
+    # Length-binning
+    # NOTE: start : end : number
+    length_distribution:
+      bins: [2, 80, 40]
+    # Station separation
+    # NOTE: if `separate_stations` is True, `['list']` is required for `station_id`
+    stations:
+      separate_stations: True
+      station_id: ["length", "specimen"]
+    # Trawl identifier
+    catch:
+      partition: codend
+
+  #####################################################################################################################
+  # Geospatial settings#
+  ########################
+  geospatial:
+    inpfc:                                  # INPFC northern latitude limits and labels
+      latitude_max: [36.0, 40.5, 43.0,
+                    45.7667, 48.50, 55.0]
+      stratum_names: [1, 2, 3, 4, 5, 6]
+    griddify:
+      # Coordinate bounds
+      bounds:
+        latitude: [32.75, 55.50]
+        longitude: [-135.25, -117.00]
+      # x/y (or E-W/N-S) grid resolution in nmi
+      grid_resolution:
+        x_distance: 25.0
+        y_distance: 25.0
+    projection: epsg:4326                   # EPSG integer code for geodetic parameter dataset
+  # TODO: Remember to convert this back to a string
+  # NOTE: `link_biology_acoustics` defines how biological and acoustic data are linked with one another. This
+  # comprises True/False statements that denote the desired association. All values set to "True" will be output.
+  # `global`        --> NASC associated with sigma_bs calculated from all survey data
+  # `INPFC`         --> NASC for each INPFC stratum associated with matched stratum-specific sigma_bs
+  # `closest_haul`  --> NASC associated with sigma_bs calculated from the closest (spatially) trawls
+  # `weighted_haul` --> NASC associated with sigma_bs calculated from all survey data weighted by distance from haul coordinates
+    link_biology_acoustics: INPFC
+
+  #####################################################################################################################
+  # Acoustics settings#
+  ########################
+  acoustics:
+    # Acoustic transmit frequency (Hz or kHz)
+    transmit:
+      frequency: 38.0
+      units: kHz
+    # Target strength (TS) - length (L) regression: TS=m*log10(L)+b
+    TS_length_regression_parameters:
+      pacific_hake:                         # corresponding species text code
+        number_code: 22500                  # species number code
+        TS_L_slope: 20.0                    # the 'm' or 'slope' parameter
+        TS_L_intercept: -68.0               # the 'b' or 'y-intercept'
+        length_units: cm                    # units for L used in regression/relationship
+...

config_files/live_survey_year_2019_config.yml

@@ -0,0 +1,54 @@
+# This YAML file is a configuration file specifying
+# input filenames & some process parameter settings.
+# Relative file paths defined below are concatenated
+# with the data_root_dir path also set below.
+
+---
+##############################################################################
+# Parameters
+
+ship_id: R/V Shimada
+survey_year: 2024           # survey year being considered
+species:
+  text_code: pacific_hake    # target species for the survey year -- species name
+  number_code: 22500         # target species for the survey year -- numeric code
+##############################################################################
+# Directory path that contains all input data needed
+
+data_root_dir: C:/Users/Brandyn/Documents/GitHub/EchoPro_data/live_2019_files
+database_directory: C:/Users/Brandyn/Documents/GitHub/EchoPro_data/live_2019_files/database
+
+##############################################################################
+# Input data directories
+input_directories:
+  acoustics:
+    directory: acoustics/
+    database_name: acoustics.db
+    extension: zarr
+  biology:
+    directory: biology/
+    # directory: s3://sh2407-upload/data/Echopop-biology/
+    database_name: biology.db
+    extension: csv
+    file_name_formats:
+      catch: "{DATE:YYYYMM}_{HAUL}_{FILE_ID:catch_perc}"
+      length: "{DATE:YYYYMM}_{SPECIES_CODE}_{HAUL}_{FILE_ID:lf}"
+      specimen: "{DATE:YYYYMM}_{SPECIES_CODE}_{HAUL}_{FILE_ID:spec}"
+      trawl_info: "{DATE:YYYYMM}_{HAUL}_{FILE_ID:operation_info}"
+    file_index:
+      catch: [haul_num]
+      length: [haul_num, species_id]
+      specimen: [haul_num, species_id]
+      trawl_info: []
+    file_ids:
+      catch: catch_perc
+      length: lf
+      specimen: spec
+      trawl_info: operation_info
+  coastline:
+    directory: coastline/
+    coastline_name: ne_10m_land
+  grid:
+    database_name: grid.db
+
+...

echopop/__init__.py

@@ -3,4 +3,4 @@
 
 __all__ = ["Survey", "operations"]
 
-from _echopop_version import version as __version__  # noqa
+# from _echopop_version import version as __version__  # noqa

echopop/biology.py

@@ -75,7 +75,7 @@ def fit_length_weight_relationship(
                 np.polyfit(np.log10(df["length"]), np.log10(df["weight"]), 1),
                 index=["rate", "initial"],
             ),
-            include_groups=False,
+            # include_groups=False,
         )
         .reset_index()
     )

echopop/live/__init__.py

@@ -0,0 +1,5 @@
+from echopop.utils import operations
+
+__all__ = ["operations"]
+
+# from _echopop_version import version as __version__  # noqa