Move deployments and postprocessing into sailship function and make d…

…ata directory a parameter instead of hardcoded

virtual_ship/argo_deployments.py

@@ -16,7 +16,7 @@
 )
 
 
-def argo_deployments(config, argo_time):
+def argo_deployments(config, argo_time, data_dir: str):
     """
     Deploy argo floats.
 
@@ -28,7 +28,7 @@ def argo_deployments(config, argo_time):
 
     if len(config.argo_deploylocations) > 0:
 
-        fieldset = create_argo_fieldset(config)
+        fieldset = create_argo_fieldset(config, data_dir)
 
         # Define the new Kernel that mimics Argo vertical movement
         def ArgoVerticalMovement(particle, fieldset, time):
@@ -148,19 +148,18 @@ class ArgoParticle(JITParticle):
         )
 
 
-def create_argo_fieldset(config):
+def create_argo_fieldset(config, data_dir: str):
     """
     Create a fieldset from netcdf files for argo floats, return fieldset with negative depth values.
 
     :param config: The cruise configuration.
     :returns: The fieldset.
     """
-    datadirname = os.path.dirname(__file__)
     filenames = {
-        "U": os.path.join(datadirname, "argodata_UV.nc"),
-        "V": os.path.join(datadirname, "argodata_UV.nc"),
-        "S": os.path.join(datadirname, "argodata_S.nc"),
-        "T": os.path.join(datadirname, "argodata_T.nc"),
+        "U": os.path.join(data_dir, "argodata_UV.nc"),
+        "V": os.path.join(data_dir, "argodata_UV.nc"),
+        "S": os.path.join(data_dir, "argodata_S.nc"),
+        "T": os.path.join(data_dir, "argodata_T.nc"),
     }
     variables = {"U": "uo", "V": "vo", "S": "so", "T": "thetao"}
     dimensions = {

virtual_ship/drifter_deployments.py

@@ -8,7 +8,7 @@
 from parcels import AdvectionRK4, FieldSet, JITParticle, ParticleSet, Variable
 
 
-def drifter_deployments(config, drifter_time):
+def drifter_deployments(config, drifter_time, data_dir: str):
     """
     Deploy drifters.
 
@@ -17,7 +17,7 @@ def drifter_deployments(config, drifter_time):
     """
     if len(config.drifter_deploylocations) > 0:
 
-        fieldset = create_drifter_fieldset(config)
+        fieldset = create_drifter_fieldset(config, data_dir)
 
         # Create particle to sample water underway
         class DrifterParticle(JITParticle):
@@ -74,18 +74,17 @@ def CheckError(particle, fieldset, time):
         )
 
 
-def create_drifter_fieldset(config):
+def create_drifter_fieldset(config, data_dir: str):
     """
     Create a fieldset from netcdf files for drifters, returns fieldset with negative depth values.
 
     :param config: The cruise configuration.
     :returns: The fieldset.
     """
-    datadirname = os.path.dirname(__file__)
     filenames = {
-        "U": os.path.join(datadirname, "drifterdata_UV.nc"),
-        "V": os.path.join(datadirname, "drifterdata_UV.nc"),
-        "T": os.path.join(datadirname, "drifterdata_T.nc"),
+        "U": os.path.join(data_dir, "drifterdata_UV.nc"),
+        "V": os.path.join(data_dir, "drifterdata_UV.nc"),
+        "T": os.path.join(data_dir, "drifterdata_T.nc"),
     }
     variables = {"U": "uo", "V": "vo", "T": "thetao"}
     dimensions = {

virtual_ship/sailship.py

@@ -7,6 +7,10 @@
 import pyproj
 from parcels import Field, FieldSet, JITParticle, ParticleSet, Variable
 from shapely.geometry import Point, Polygon
+from .drifter_deployments import drifter_deployments
+from .argo_deployments import argo_deployments
+from .postprocess import postprocess
+from .costs import costs
 
 
 def sailship(config):
@@ -16,8 +20,12 @@ def sailship(config):
     :param config: The cruise configuration.
     :returns: drifter_time, argo_time, total_time
     """
+    # hardcoding this until we refactor more
+    DATA_DIR = "data"
+    data_dir = DATA_DIR
+
     # Create fieldset and retreive final schip route as sample_lons and sample_lats
-    fieldset = create_fieldset(config)
+    fieldset = create_fieldset(config, data_dir)
 
     sample_lons, sample_lats = shiproute(config)
     print("Arrived in region of interest, starting to gather data.")
@@ -243,23 +251,36 @@ def SampleT(particle, fieldset, time):
         )
     print("Cruise has ended. Please wait for drifters and/or Argo floats to finish.")
 
-    return drifter_time, argo_time, total_time
+    # simulate drifter deployments
+    drifter_deployments(config, drifter_time, data_dir)
+
+    # simulate argo deployments
+    argo_deployments(config, argo_time, data_dir)
+
+    # convert CTD data to CSV
+    postprocess()
+
+    print("All data has been gathered and postprocessed, returning home.")
+
+    cost = costs(config, total_time)
+    print(
+        f"This cruise took {timedelta(seconds=total_time)} and would have cost {cost:,.0f} euros."
+    )
 
 
-def create_fieldset(config):
+def create_fieldset(config, data_dir: str):
     """
     Create fieldset from netcdf files and adds bathymetry data for CTD cast, returns fieldset with negative depth values.
 
     :param config: The cruise configuration.
     :returns: The fieldset.
     :raises ValueError: If downloaded data is not as expected.
     """
-    datadirname = os.path.dirname(__file__)
     filenames = {
-        "U": os.path.join(datadirname, "studentdata_UV.nc"),
-        "V": os.path.join(datadirname, "studentdata_UV.nc"),
-        "S": os.path.join(datadirname, "studentdata_S.nc"),
-        "T": os.path.join(datadirname, "studentdata_T.nc"),
+        "U": os.path.join(data_dir, "studentdata_UV.nc"),
+        "V": os.path.join(data_dir, "studentdata_UV.nc"),
+        "S": os.path.join(data_dir, "studentdata_S.nc"),
+        "T": os.path.join(data_dir, "studentdata_T.nc"),
     }
     variables = {"U": "uo", "V": "vo", "S": "so", "T": "thetao"}
     dimensions = {
@@ -286,7 +307,7 @@ def create_fieldset(config):
     fieldset.add_constant("maxtime", fieldset.U.grid.time_full[-1])
 
     # add bathymetry data to the fieldset for CTD cast
-    bathymetry_file = os.path.join(datadirname, "GLO-MFC_001_024_mask_bathy.nc")
+    bathymetry_file = os.path.join(data_dir, "GLO-MFC_001_024_mask_bathy.nc")
     bathymetry_variables = ("bathymetry", "deptho")
     bathymetry_dimensions = {"lon": "longitude", "lat": "latitude"}
     bathymetry_field = Field.from_netcdf(

virtual_ship/virtual_ship_configuration.py

@@ -18,7 +18,7 @@ def __init__(self, json_file):
         :param json_file: Path to the JSON file to init from.
         :raises ValueError: If JSON file not valid.
         """
-        with open(os.path.join(os.path.dirname(__file__), json_file), "r") as file:
+        with open(json_file, "r") as file:
             json_input = json.loads(file.read())
             for key in json_input:
                 setattr(self, key, json_input[key])

virtualship.py

@@ -1,17 +1,6 @@
-from datetime import timedelta
 from virtual_ship.virtual_ship_configuration import VirtualShipConfiguration
-from virtual_ship.costs import costs
 from virtual_ship.sailship import sailship
-from virtual_ship.drifter_deployments import drifter_deployments
-from virtual_ship.argo_deployments import argo_deployments
-from virtual_ship.postprocess import postprocess
 
-if __name__ == '__main__':
-    config = VirtualShipConfiguration('student_input.json')
-    drifter_time, argo_time, total_time = sailship(config)
-    drifter_deployments(config, drifter_time)
-    argo_deployments(config, argo_time)
-    postprocess()
-    print("All data has been gathered and postprocessed, returning home.")
-    cost = costs(config, total_time)
-    print(f"This cruise took {timedelta(seconds=total_time)} and would have cost {cost:,.0f} euros.")
+if __name__ == "__main__":
+    config = VirtualShipConfiguration("student_input.json")
+    sailship(config)