Seperate instruments (#35)

* wip drifters * drifters instrument. just missing test * drifter test * Remove old drifter file and fix errors * codetools * outputdf wherever i forgot to use it * added todo list * ctd instrument * CTDtest * use new ctd instrument in sailship * fix typo * codetools * use new parcels api for particle class * add ctd to init * comments * first try adcp * adcp test * use adcp instrument in sailship * cleanup * instrument ship s t * use ship st in sailship * cleanup * refactor sailship ctd cast * cleanup * large cleanup * add checks that all drifter and argo floats are deployed * comments * docstrings and other codetools fixes * rename SamplePoint to Spacetime and move them one dir up * rm todo * run pydocstyle on tests * fix some names * Update virtual_ship/instruments/ctd.py Co-authored-by: Erik van Sebille <[email protected]> * removed comment about ctd * fix incorrect docstring * renamed ship_st to ship_underwater_st * remove sailship create fieldset commented out function * ship underway st docstring improvement * minor docstring change * minor docstring change --------- Co-authored-by: Erik van Sebille <[email protected]>
OceanParcels · Jun 5, 2024 · fcb36d7 · fcb36d7
1 parent 92d0838
commit fcb36d7
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Showing 22 changed files with 740 additions and 452 deletions.
diff --git a/codetools.sh b/codetools.sh
@@ -20,7 +20,7 @@ flake8 ./$PACKAGE ./$TESTS
 echo "--------------"
 echo "pydocstyle"
 echo "--------------"
-pydocstyle ./$PACKAGE
+pydocstyle ./$PACKAGE ./$TESTS
 
 echo "--------------"
 echo "sort-all"

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,7 +1,14 @@
+"""Test configuration that is ran for every test."""
+
 import pytest
 
 
-# Set the working directory for each test to the directory of that test.
 @pytest.fixture(autouse=True)
 def change_test_dir(request, monkeypatch):
+    """
+    Set the working directory for each test to the directory of that test.
+
+    :param request: -
+    :param monkeypatch: -
+    """
     monkeypatch.chdir(request.fspath.dirname)
diff --git a/tests/instruments/test_adcp.py b/tests/instruments/test_adcp.py
@@ -0,0 +1,33 @@
+"""Test the simulation of ADCP instruments."""
+
+import numpy as np
+from parcels import FieldSet
+
+from virtual_ship import Location, Spacetime
+from virtual_ship.instruments.adcp import simulate_adcp
+
+
+def test_simulate_adcp() -> None:
+    MAX_DEPTH = -1000
+    MIN_DEPTH = -5
+    BIN_SIZE = 24
+
+    fieldset = FieldSet.from_data(
+        {"U": 0, "V": 0},
+        {
+            "lon": 0,
+            "lat": 0,
+            "time": [np.datetime64("1950-01-01") + np.timedelta64(632160, "h")],
+        },
+    )
+
+    sample_points = [Spacetime(Location(0, 0), 0)]
+
+    simulate_adcp(
+        fieldset=fieldset,
+        out_file_name="test",
+        max_depth=MAX_DEPTH,
+        min_depth=MIN_DEPTH,
+        bin_size=BIN_SIZE,
+        sample_points=sample_points,
+    )
diff --git a/tests/instruments/test_argo.py b/tests/instruments/test_argo.py
@@ -5,14 +5,14 @@
 import numpy as np
 from parcels import FieldSet
 
-from virtual_ship.instruments import Location
+from virtual_ship import Location, Spacetime
 from virtual_ship.instruments.argo_float import ArgoFloat, simulate_argo_floats
 
 
 def test_simulate_argo_floats() -> None:
     DRIFT_DEPTH = -1000
     MAX_DEPTH = -2000
-    VERTICLE_SPEED = -0.10
+    VERTICAL_SPEED = -0.10
     CYCLE_DAYS = 10
     DRIFT_DAYS = 9
 
@@ -29,12 +29,11 @@ def test_simulate_argo_floats() -> None:
 
     argo_floats = [
         ArgoFloat(
-            location=Location(latitude=0, longitude=0),
-            deployment_time=0,
+            spacetime=Spacetime(location=Location(latitude=0, longitude=0), time=0),
             min_depth=min_depth,
             max_depth=MAX_DEPTH,
             drift_depth=DRIFT_DEPTH,
-            vertical_speed=VERTICLE_SPEED,
+            vertical_speed=VERTICAL_SPEED,
             cycle_days=CYCLE_DAYS,
             drift_days=DRIFT_DAYS,
         )

diff --git a/tests/instruments/test_ctd.py b/tests/instruments/test_ctd.py
@@ -0,0 +1,38 @@
+"""Test the simulation of CTD instruments."""
+
+from datetime import timedelta
+
+import numpy as np
+from parcels import FieldSet
+
+from virtual_ship import Location, Spacetime
+from virtual_ship.instruments.ctd import CTD, simulate_ctd
+
+
+def test_simulate_ctds() -> None:
+    fieldset = FieldSet.from_data(
+        {"U": 0, "V": 0, "T": 0, "S": 0, "bathymetry": 100},
+        {
+            "lon": 0,
+            "lat": 0,
+            "time": [np.datetime64("1950-01-01") + np.timedelta64(632160, "h")],
+        },
+    )
+
+    min_depth = -fieldset.U.depth[0]
+    max_depth = -fieldset.U.depth[-1]
+
+    ctds = [
+        CTD(
+            spacetime=Spacetime(location=Location(latitude=0, longitude=0), time=0),
+            min_depth=min_depth,
+            max_depth=max_depth,
+        )
+    ]
+
+    simulate_ctd(
+        ctds=ctds,
+        fieldset=fieldset,
+        out_file_name="test",
+        outputdt=timedelta(seconds=10),
+    )
diff --git a/tests/instruments/test_drifters.py b/tests/instruments/test_drifters.py
@@ -0,0 +1,36 @@
+"""Test the simulation of drifters."""
+
+from datetime import timedelta
+
+import numpy as np
+from parcels import FieldSet
+
+from virtual_ship import Location, Spacetime
+from virtual_ship.instruments.drifter import Drifter, simulate_drifters
+
+
+def test_simulate_drifters() -> None:
+    fieldset = FieldSet.from_data(
+        {"U": 0, "V": 0, "T": 0},
+        {
+            "lon": 0,
+            "lat": 0,
+            "time": [np.datetime64("1950-01-01") + np.timedelta64(632160, "h")],
+        },
+    )
+
+    min_depth = -fieldset.U.depth[0]
+
+    drifters = [
+        Drifter(
+            spacetime=Spacetime(location=Location(latitude=0, longitude=0), time=0),
+            min_depth=min_depth,
+        )
+    ]
+
+    simulate_drifters(
+        drifters=drifters,
+        fieldset=fieldset,
+        out_file_name="test",
+        outputdt=timedelta(minutes=5),
+    )
diff --git a/tests/instruments/test_ship_underwater_st.py b/tests/instruments/test_ship_underwater_st.py
@@ -0,0 +1,29 @@
+"""Test the simulation of ship salinity temperature measurements."""
+
+import numpy as np
+from parcels import FieldSet
+
+from virtual_ship import Location, Spacetime
+from virtual_ship.instruments.ship_underwater_st import simulate_ship_underwater_st
+
+
+def test_simulate_ship_underwater_st() -> None:
+    DEPTH = -2
+
+    fieldset = FieldSet.from_data(
+        {"U": 0, "V": 0, "S": 0, "T": 0},
+        {
+            "lon": 0,
+            "lat": 0,
+            "time": [np.datetime64("1950-01-01") + np.timedelta64(632160, "h")],
+        },
+    )
+
+    sample_points = [Spacetime(Location(0, 0), 0)]
+
+    simulate_ship_underwater_st(
+        fieldset=fieldset,
+        out_file_name="test",
+        depth=DEPTH,
+        sample_points=sample_points,
+    )
diff --git a/tests/sailship_config.json b/tests/sailship_config.json
@@ -19,13 +19,13 @@
         "bin_size_m": 24
       },
     "CTD_locations": [
-      [-23.071289, 63.743631]
+      [-23.081289, 63.743631]
     ],
     "CTD_settings": {
         "max_depth": "max"
       },
     "drifter_deploylocations": [
-
+      [-23.081289, 63.743631]
     ],
     "argo_deploylocations": [
       [-23.081289, 63.743631]

diff --git a/tests/test_sailship.py b/tests/test_sailship.py
@@ -8,20 +8,28 @@
 
 
 def test_sailship() -> None:
+    adcp_fieldset = FieldSet.from_data(
+        {"U": 0, "V": 0},
+        {"lon": 0, "lat": 0},
+    )
+
+    ship_underwater_st_fieldset = FieldSet.from_data(
+        {"U": 0, "V": 0, "S": 0, "T": 0},
+        {"lon": 0, "lat": 0},
+    )
+
     ctd_fieldset = FieldSet.from_data(
         {"U": 0, "V": 0, "S": 0, "T": 0, "bathymetry": 0},
         {"lon": 0, "lat": 0},
     )
-    ctd_fieldset.add_constant("maxtime", ctd_fieldset.U.grid.time_full[-1])
-    ctd_fieldset.add_constant("mindepth", -ctd_fieldset.U.depth[0])
-    ctd_fieldset.add_constant("max_depth", -ctd_fieldset.U.depth[-1])
 
     drifter_fieldset = FieldSet.from_data(
+        {"U": 0, "V": 0, "T": 0},
         {
-            "U": 0,
-            "V": 0,
+            "lon": 0,
+            "lat": 0,
+            "time": [np.datetime64("1950-01-01") + np.timedelta64(632160, "h")],
         },
-        {"lon": 0, "lat": 0},
     )
 
     argo_float_fieldset = FieldSet.from_data(
@@ -35,6 +43,8 @@ def test_sailship() -> None:
 
     config = VirtualShipConfiguration(
         "sailship_config.json",
+        adcp_fieldset=adcp_fieldset,
+        ship_underwater_st_fieldset=ship_underwater_st_fieldset,
         ctd_fieldset=ctd_fieldset,
         drifter_fieldset=drifter_fieldset,
         argo_float_fieldset=argo_float_fieldset,

diff --git a/virtual_ship/__init__.py b/virtual_ship/__init__.py
@@ -1,5 +1,7 @@
 """Code for the Virtual Ship Classroom, where Marine Scientists can combine Copernicus Marine Data with an OceanParcels ship to go on a virtual expedition."""
 
 from . import instruments, sailship
+from .location import Location
+from .spacetime import Spacetime
 
-__all__ = ["instruments", "sailship"]
+__all__ = ["Location", "Spacetime", "instruments", "sailship"]
diff --git a/virtual_ship/costs.py b/virtual_ship/costs.py
@@ -1,19 +1,23 @@
 """costs function."""
 
+from datetime import timedelta
 
-def costs(config, total_time):
+from .virtual_ship_configuration import VirtualShipConfiguration
+
+
+def costs(config: VirtualShipConfiguration, total_time: timedelta):
     """
     Calculate the cost of the virtual ship (in US$).
 
     :param config: The cruise configuration.
-    :param total_time: Time cruised in seconds.
+    :param total_time: Time cruised.
     :returns: The calculated cost of the cruise.
     """
     ship_cost_per_day = 30000
     drifter_deploy_cost = 2500
     argo_deploy_cost = 15000
 
-    ship_cost = ship_cost_per_day / 24 * total_time // 3600
+    ship_cost = ship_cost_per_day / 24 * total_time.total_seconds() // 3600
     argo_cost = len(config.argo_deploylocations) * argo_deploy_cost
     drifter_cost = len(config.drifter_deploylocations) * drifter_deploy_cost