Log filter v2

src/virtualship/expedition/do_expedition.py

@@ -32,6 +32,10 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
     :param expedition_dir: The base directory for the expedition.
     :param input_data: Input data folder (override used for testing).
     """
+    print("\n╔═════════════════════════════════════════════════╗")
+    print("║          VIRTUALSHIP EXPEDITION STATUS          ║")
+    print("╚═════════════════════════════════════════════════╝")
+
     if isinstance(expedition_dir, str):
         expedition_dir = Path(expedition_dir)
 
@@ -57,6 +61,8 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
         input_data=input_data,
     )
 
+    print("\n---- WAYPOINT VERIFICATION ----")
+
     # verify schedule is valid
     schedule.verify(ship_config.ship_speed_knots, input_data)
 
@@ -83,6 +89,8 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
         shutil.rmtree(expedition_dir.joinpath("results"))
     os.makedirs(expedition_dir.joinpath("results"))
 
+    print("\n----- EXPEDITION SUMMARY ------")
+
     # calculate expedition cost in US$
     assert schedule.waypoints[0].time is not None, (
         "First waypoint has no time. This should not be possible as it should have been verified before."
@@ -91,20 +99,26 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
     cost = expedition_cost(schedule_results, time_past)
     with open(expedition_dir.joinpath("results", "cost.txt"), "w") as file:
         file.writelines(f"cost: {cost} US$")
-    print(f"This expedition took {time_past} and would have cost {cost:,.0f} US$.")
+    print(f"\nExpedition duration: {time_past}\nExpedition cost: US$ {cost:,.0f}.")
+
+    print("\n--- MEASUREMENT SIMULATIONS ---")
 
     # simulate measurements
-    print("Simulating measurements. This may take a while..")
+    print("\nSimulating measurements. This may take a while...\n")
     simulate_measurements(
         expedition_dir,
         ship_config,
         input_data,
         schedule_results.measurements_to_simulate,
     )
-    print("Done simulating measurements.")
+    print("\nAll measurement simulations are complete.")
 
-    print("Your expedition has concluded successfully!")
-    print("Your measurements can be found in the results directory.")
+    print("\n----- EXPEDITION RESULTS ------")
+    print("\nYour expedition has concluded successfully!")
+    print(
+        f"Your measurements can be found in the '{expedition_dir}/results' directory."
+    )
+    print("\n------------- END -------------\n")
 
 
 def _load_input_data(

src/virtualship/expedition/schedule.py

@@ -139,7 +139,7 @@ def verify(
         # check if all waypoints are in water
         # this is done by picking an arbitrary provided fieldset and checking if UV is not zero
 
-        print("Verifying all waypoints are on water..")
+        print("\nVerifying all waypoints are on water...")
 
         # get all available fieldsets
         available_fieldsets = []
@@ -178,7 +178,7 @@ def verify(
                 raise ScheduleError(
                     f"The following waypoints are on land: {['#' + str(wp_i) + ' ' + str(wp) for (wp_i, wp) in land_waypoints]}"
                 )
-            print("Good, all waypoints are on water.")
+            print("... Good, all waypoints are on water.")
 
         # check that ship will arrive on time at each waypoint (in case no unexpected event happen)
         time = self.waypoints[0].time

src/virtualship/expedition/simulate_measurements.py

@@ -36,7 +36,6 @@ def simulate_measurements(
         expedition_dir = Path(expedition_dir)
 
     if len(measurements.ship_underwater_sts) > 0:
-        print("Simulating onboard salinity and temperature measurements.")
         if ship_config.ship_underwater_st_config is None:
             raise RuntimeError("No configuration for ship underwater ST provided.")
         if input_data.ship_underwater_st_fieldset is None:
@@ -49,7 +48,6 @@ def simulate_measurements(
         )
 
     if len(measurements.adcps) > 0:
-        print("Simulating onboard ADCP.")
         if ship_config.adcp_config is None:
             raise RuntimeError("No configuration for ADCP provided.")
         if input_data.adcp_fieldset is None:
@@ -64,7 +62,6 @@ def simulate_measurements(
         )
 
     if len(measurements.ctds) > 0:
-        print("Simulating CTD casts.")
         if ship_config.ctd_config is None:
             raise RuntimeError("No configuration for CTD provided.")
         if input_data.ctd_fieldset is None:
@@ -77,7 +74,6 @@ def simulate_measurements(
         )
 
     if len(measurements.ctd_bgcs) > 0:
-        print("Simulating BGC CTD casts.")
         if ship_config.ctd_bgc_config is None:
             raise RuntimeError("No configuration for CTD_BGC provided.")
         if input_data.ctd_bgc_fieldset is None:
@@ -90,7 +86,6 @@ def simulate_measurements(
         )
 
     if len(measurements.drifters) > 0:
-        print("Simulating drifters")
         if ship_config.drifter_config is None:
             raise RuntimeError("No configuration for drifters provided.")
         if input_data.drifter_fieldset is None:
@@ -105,7 +100,6 @@ def simulate_measurements(
         )
 
     if len(measurements.argo_floats) > 0:
-        print("Simulating argo floats")
         if ship_config.argo_float_config is None:
             raise RuntimeError("No configuration for argo floats provided.")
         if input_data.argo_float_fieldset is None:
@@ -119,7 +113,6 @@ def simulate_measurements(
         )
 
     if len(measurements.xbts) > 0:
-        print("Simulating XBTs")
         if ship_config.xbt_config is None:
             raise RuntimeError("No configuration for XBTs provided.")
         if input_data.xbt_fieldset is None:

src/virtualship/instruments/__init__.py

@@ -1,5 +1,13 @@
 """Measurement instrument that can be used with Parcels."""
 
-from . import adcp, argo_float, ctd, drifter, ship_underwater_st, xbt
+from . import adcp, argo_float, ctd, ctd_bgc, drifter, ship_underwater_st, xbt
 
-__all__ = ["adcp", "argo_float", "ctd", "drifter", "ship_underwater_st", "xbt"]
+__all__ = [
+    "adcp",
+    "argo_float",
+    "ctd",
+    "ctd_bgc",
+    "drifter",
+    "ship_underwater_st",
+    "xbt",
+]

src/virtualship/instruments/adcp.py

@@ -5,7 +5,9 @@
 import numpy as np
 from parcels import FieldSet, ParticleSet, ScipyParticle, Variable
 
+from ..log_filter import Filter, external_logger
 from ..spacetime import Spacetime
+from ..utils import RotatePrint
 
 # we specifically use ScipyParticle because we have many small calls to execute
 # there is some overhead with JITParticle and this ends up being significantly faster
@@ -41,6 +43,8 @@ def simulate_adcp(
     :param num_bins: How many samples to take in the complete range between max_depth and min_depth.
     :param sample_points: The places and times to sample at.
     """
+    rotator = RotatePrint("Simulating onboard ADCP...")
+
     sample_points.sort(key=lambda p: p.time)
 
     bins = np.linspace(max_depth, min_depth, num_bins)
@@ -60,19 +64,33 @@ def simulate_adcp(
     # outputdt set to infinite as we just want to write at the end of every call to 'execute'
     out_file = particleset.ParticleFile(name=out_path, outputdt=np.inf)
 
-    for point in sample_points:
-        particleset.lon_nextloop[:] = point.location.lon
-        particleset.lat_nextloop[:] = point.location.lat
-        particleset.time_nextloop[:] = fieldset.time_origin.reltime(
-            np.datetime64(point.time)
-        )
-
-        # perform one step using the particleset
-        # dt and runtime are set so exactly one step is made.
-        particleset.execute(
-            [_sample_velocity],
-            dt=1,
-            runtime=1,
-            verbose_progress=False,
-            output_file=out_file,
-        )
+    # filter out Parcels logging messages
+    for handler in external_logger.handlers:
+        handler.addFilter(Filter())
+
+    # try/finally to ensure filter is always removed even if .execute fails (to avoid filter being appled universally)
+    # also suits starting and ending the rotator for custom log message
+    try:
+        rotator.start()
+
+        for point in sample_points:
+            particleset.lon_nextloop[:] = point.location.lon
+            particleset.lat_nextloop[:] = point.location.lat
+            particleset.time_nextloop[:] = fieldset.time_origin.reltime(
+                np.datetime64(point.time)
+            )
+
+            # perform one step using the particleset
+            # dt and runtime are set so exactly one step is made.
+            particleset.execute(
+                [_sample_velocity],
+                dt=1,
+                runtime=1,
+                verbose_progress=False,
+                output_file=out_file,
+            )
+
+    finally:
+        rotator.stop()
+        for handler in external_logger.handlers:
+            handler.removeFilter(handler.filters[0])

src/virtualship/instruments/argo_float.py

@@ -15,6 +15,7 @@
     Variable,
 )
 
+from ..log_filter import Filter, external_logger
 from ..spacetime import Spacetime
 
 
@@ -131,6 +132,7 @@ def simulate_argo_floats(
     :param outputdt: Interval which dictates the update frequency of file output during simulation
     :param endtime: Stop at this time, or if None, continue until the end of the fieldset.
     """
+    print("Simulating argo floats...")
     DT = 10.0  # dt of Argo float simulation integrator
 
     if len(argo_floats) == 0:
@@ -171,16 +173,26 @@ def simulate_argo_floats(
     else:
         actual_endtime = np.timedelta64(endtime)
 
-    # execute simulation
-    argo_float_particleset.execute(
-        [
-            _argo_float_vertical_movement,
-            AdvectionRK4,
-            _keep_at_surface,
-            _check_error,
-        ],
-        endtime=actual_endtime,
-        dt=DT,
-        output_file=out_file,
-        verbose_progress=True,
-    )
+    # filter out Parcels logging messages
+    for handler in external_logger.handlers:
+        handler.addFilter(Filter())
+
+    # try/finally to ensure filter is always removed even if .execute fails (to avoid filter being appled universally)
+    try:
+        argo_float_particleset.execute(
+            [
+                _argo_float_vertical_movement,
+                AdvectionRK4,
+                _keep_at_surface,
+                _check_error,
+            ],
+            endtime=actual_endtime,
+            dt=DT,
+            output_file=out_file,
+            verbose_progress=True,
+        )
+
+    finally:
+        print("... [COMPLETED]")
+        for handler in external_logger.handlers:
+            handler.removeFilter(handler.filters[0])

src/virtualship/instruments/ctd.py

@@ -7,7 +7,9 @@
 import numpy as np
 from parcels import FieldSet, JITParticle, ParticleSet, Variable
 
+from ..log_filter import Filter, external_logger
 from ..spacetime import Spacetime
+from ..utils import RotatePrint
 
 
 @dataclass
@@ -68,6 +70,8 @@ def simulate_ctd(
     :param outputdt: Interval which dictates the update frequency of file output during simulation
     :raises ValueError: Whenever provided CTDs, fieldset, are not compatible with this function.
     """
+    rotator = RotatePrint("Simulating CTD casts...")
+
     WINCH_SPEED = 1.0  # sink and rise speed in m/s
     DT = 10.0  # dt of CTD simulation integrator
 
@@ -121,14 +125,27 @@ def simulate_ctd(
     # define output file for the simulation
     out_file = ctd_particleset.ParticleFile(name=out_path, outputdt=outputdt)
 
-    # execute simulation
-    ctd_particleset.execute(
-        [_sample_salinity, _sample_temperature, _ctd_cast],
-        endtime=fieldset_endtime,
-        dt=DT,
-        verbose_progress=False,
-        output_file=out_file,
-    )
+    # filter out Parcels logging messages
+    for handler in external_logger.handlers:
+        handler.addFilter(Filter())
+
+    # try/finally to ensure filter is always removed even if .execute fails (to avoid filter being appled universally)
+    # also suits starting and ending the rotator for custom log message
+    try:
+        rotator.start()
+
+        ctd_particleset.execute(
+            [_sample_salinity, _sample_temperature, _ctd_cast],
+            endtime=fieldset_endtime,
+            dt=DT,
+            verbose_progress=False,
+            output_file=out_file,
+        )
+
+    finally:
+        rotator.stop()
+        for handler in external_logger.handlers:
+            handler.removeFilter(handler.filters[0])
 
     # there should be no particles left, as they delete themselves when they resurface
     if len(ctd_particleset.particledata) != 0:

src/virtualship/instruments/ctd_bgc.py

@@ -7,7 +7,9 @@
 import numpy as np
 from parcels import FieldSet, JITParticle, ParticleSet, Variable
 
+from ..log_filter import Filter, external_logger
 from ..spacetime import Spacetime
+from ..utils import RotatePrint
 
 
 @dataclass
@@ -68,6 +70,8 @@ def simulate_ctd_bgc(
     :param outputdt: Interval which dictates the update frequency of file output during simulation
     :raises ValueError: Whenever provided BGC CTDs, fieldset, are not compatible with this function.
     """
+    rotator = RotatePrint("Simulating BGC CTD casts...")
+
     WINCH_SPEED = 1.0  # sink and rise speed in m/s
     DT = 10.0  # dt of CTD simulation integrator
 
@@ -127,14 +131,27 @@ def simulate_ctd_bgc(
     # define output file for the simulation
     out_file = ctd_bgc_particleset.ParticleFile(name=out_path, outputdt=outputdt)
 
-    # execute simulation
-    ctd_bgc_particleset.execute(
-        [_sample_o2, _sample_chlorophyll, _ctd_bgc_cast],
-        endtime=fieldset_endtime,
-        dt=DT,
-        verbose_progress=False,
-        output_file=out_file,
-    )
+    # filter out Parcels logging messages
+    for handler in external_logger.handlers:
+        handler.addFilter(Filter())
+
+    # try/finally to ensure filter is always removed even if .execute fails (to avoid filter being appled universally)
+    # also suits starting and ending the rotator for custom log message
+    try:
+        rotator.start()
+
+        ctd_bgc_particleset.execute(
+            [_sample_o2, _sample_chlorophyll, _ctd_bgc_cast],
+            endtime=fieldset_endtime,
+            dt=DT,
+            verbose_progress=False,
+            output_file=out_file,
+        )
+
+    finally:
+        rotator.stop()
+        for handler in external_logger.handlers:
+            handler.removeFilter(handler.filters[0])
 
     # there should be no particles left, as they delete themselves when they resurface
     if len(ctd_bgc_particleset.particledata) != 0: