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‎docs/tutorials/Argo_float_tutorial.ipynb‎

Lines changed: 123 additions & 64 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,15 @@
1515
"metadata": {},
1616
"outputs": [],
1717
"source": [
18-
"from parcels import FieldSet, ParticleSet, JITParticle, Variable, AdvectionRK4, ScipyParticle, StatusCode\n",
18+
"from parcels import (\n",
19+
" FieldSet,\n",
20+
" ParticleSet,\n",
21+
" JITParticle,\n",
22+
" Variable,\n",
23+
" AdvectionRK4,\n",
24+
" ScipyParticle,\n",
25+
" StatusCode,\n",
26+
")\n",
1927
"import numpy as np\n",
2028
"import math\n",
2129
"import xarray as xr\n",
@@ -62,15 +70,19 @@
6270
"outputs": [],
6371
"source": [
6472
"# Execute the code below to create what's in Parcels called a `FieldSet` object\n",
65-
"filename = 'global-analysis-forecast-phy-001-024_1641284158025.nc'\n",
66-
"variables = {'U': 'uo', # dictionary with names of the variables in the netcdf file\n",
67-
" 'V': 'vo',\n",
68-
" 'S': 'so',\n",
69-
" 'T': 'thetao'}\n",
70-
"dimensions = {'lon': 'longitude', # dictionary with names of the dimensions in the netcdf file\n",
71-
" 'lat': 'latitude',\n",
72-
" 'depth': 'depth',\n",
73-
" 'time': 'time'}\n",
73+
"filename = \"global-analysis-forecast-phy-001-024_1641284158025.nc\"\n",
74+
"variables = {\n",
75+
" \"U\": \"uo\", # dictionary with names of the variables in the netcdf file\n",
76+
" \"V\": \"vo\",\n",
77+
" \"S\": \"so\",\n",
78+
" \"T\": \"thetao\",\n",
79+
"}\n",
80+
"dimensions = {\n",
81+
" \"lon\": \"longitude\", # dictionary with names of the dimensions in the netcdf file\n",
82+
" \"lat\": \"latitude\",\n",
83+
" \"depth\": \"depth\",\n",
84+
" \"time\": \"time\",\n",
85+
"}\n",
7486
"\n",
7587
"fieldset = FieldSet.from_netcdf(filename, variables, dimensions)\n",
7688
"fieldset.mindepth = fieldset.U.depth[0] # uppermost layer in the hydrodynamic data"
@@ -111,26 +123,44 @@
111123
}
112124
],
113125
"source": [
114-
"fieldset.computeTimeChunk() # first load the data in memory\n",
126+
"fieldset.computeTimeChunk() # first load the data in memory\n",
115127
"\n",
116128
"fig, ax = plt.subplots(1, 2, sharex=True, sharey=True)\n",
117-
"p0 = ax[0].pcolormesh(fieldset.U.lon, fieldset.U.lat, fieldset.U.data[0,0,:,:], vmin=-1.5, vmax=1.5, cmap=cmocean.cm.balance)\n",
118-
"p1 = ax[1].pcolormesh(fieldset.V.lon, fieldset.V.lat, fieldset.V.data[0,0,:,:], vmin=-1.5, vmax=1.5, cmap=cmocean.cm.balance)\n",
119-
"ax[0].set_title('zonal velocity')\n",
120-
"ax[1].set_title('meridional velocity')\n",
121-
"ax[0].set_ylabel('latitude [°N]')\n",
122-
"ax[0].set_xlabel('longitude [°E]')\n",
123-
"ax[1].set_xlabel('longitude [°E]')\n",
129+
"p0 = ax[0].pcolormesh(\n",
130+
" fieldset.U.lon,\n",
131+
" fieldset.U.lat,\n",
132+
" fieldset.U.data[0, 0, :, :],\n",
133+
" vmin=-1.5,\n",
134+
" vmax=1.5,\n",
135+
" cmap=cmocean.cm.balance,\n",
136+
")\n",
137+
"p1 = ax[1].pcolormesh(\n",
138+
" fieldset.V.lon,\n",
139+
" fieldset.V.lat,\n",
140+
" fieldset.V.data[0, 0, :, :],\n",
141+
" vmin=-1.5,\n",
142+
" vmax=1.5,\n",
143+
" cmap=cmocean.cm.balance,\n",
144+
")\n",
145+
"ax[0].set_title(\"zonal velocity\")\n",
146+
"ax[1].set_title(\"meridional velocity\")\n",
147+
"ax[0].set_ylabel(\"latitude [°N]\")\n",
148+
"ax[0].set_xlabel(\"longitude [°E]\")\n",
149+
"ax[1].set_xlabel(\"longitude [°E]\")\n",
124150
"ax[1].yaxis.set_tick_params(left=False, right=True, labelleft=False, labelright=True)\n",
125151
"ax[0].grid()\n",
126152
"ax[1].grid()\n",
127-
"cb = fig.colorbar(p1, ax=ax, orientation='horizontal')\n",
128-
"cb.set_label('[m/s]')\n",
153+
"cb = fig.colorbar(p1, ax=ax, orientation=\"horizontal\")\n",
154+
"cb.set_label(\"[m/s]\")\n",
129155
"gd = fieldset.U.grid\n",
130-
"fig.suptitle(f\"velocity at depth {gd.depth[0]:.2f} m, {gd.timeslices[0][0].astype('datetime64[m]')}\")\n",
156+
"fig.suptitle(\n",
157+
" f\"velocity at depth {gd.depth[0]:.2f} m, {gd.timeslices[0][0].astype('datetime64[m]')}\"\n",
158+
")\n",
131159
"plt.show()\n",
132160
"\n",
133-
"print(f\"The dimensions of the data are:\\nlon: {gd.xdim}\\nlat: {gd.ydim}\\ndepth: {gd.zdim}\\ntime: {len(gd.time_full)} ({gd.tdim} loaded)\")"
161+
"print(\n",
162+
" f\"The dimensions of the data are:\\nlon: {gd.xdim}\\nlat: {gd.ydim}\\ndepth: {gd.zdim}\\ntime: {len(gd.time_full)} ({gd.tdim} loaded)\"\n",
163+
")"
134164
]
135165
},
136166
{
@@ -183,10 +213,14 @@
183213
" elif particle.cycle_phase == 3:\n",
184214
" # Phase 3: Rising with vertical_speed until at surface\n",
185215
" particle_ddepth -= vertical_speed * particle.dt\n",
186-
" particle.cycle_age += particle.dt # solve issue of not updating cycle_age during ascent\n",
216+
" particle.cycle_age += (\n",
217+
" particle.dt\n",
218+
" ) # solve issue of not updating cycle_age during ascent\n",
187219
" if particle.depth <= fieldset.mindepth:\n",
188220
" particle.depth = fieldset.mindepth\n",
189-
" particle.temp = math.nan # reset temperature to NaN at end of sampling cycle\n",
221+
" particle.temp = (\n",
222+
" math.nan\n",
223+
" ) # reset temperature to NaN at end of sampling cycle\n",
190224
" particle.salt = math.nan # idem\n",
191225
" particle.cycle_phase = 4\n",
192226
" else:\n",
@@ -226,11 +260,11 @@
226260
"source": [
227261
"# Define the ArgoParticle class\n",
228262
"variables = [\n",
229-
" Variable('cycle_phase', dtype=np.int32, initial=0.0),\n",
230-
" Variable('cycle_age', dtype=np.float32, initial=0.0),\n",
231-
" Variable('drift_age', dtype=np.float32, initial=0.0),\n",
232-
" Variable('temp', dtype=np.float32, initial=np.nan),\n",
233-
" Variable('salt', dtype=np.float32, initial=np.nan),\n",
263+
" Variable(\"cycle_phase\", dtype=np.int32, initial=0.0),\n",
264+
" Variable(\"cycle_age\", dtype=np.float32, initial=0.0),\n",
265+
" Variable(\"drift_age\", dtype=np.float32, initial=0.0),\n",
266+
" Variable(\"temp\", dtype=np.float32, initial=np.nan),\n",
267+
" Variable(\"salt\", dtype=np.float32, initial=np.nan),\n",
234268
"]\n",
235269
"ArgoParticle = JITParticle.add_variables(variables)"
236270
]
@@ -248,10 +282,14 @@
248282
"metadata": {},
249283
"outputs": [],
250284
"source": [
251-
"# Define the ParticleSet \n",
285+
"# Define the ParticleSet\n",
252286
"argoset = ParticleSet(\n",
253-
" fieldset=fieldset, pclass=ArgoParticle, lon=[-37.09499], lat=[6.73472],\n",
254-
" depth=fieldset.mindepth, time=np.datetime64('2019-07-25T11:14:00')\n",
287+
" fieldset=fieldset,\n",
288+
" pclass=ArgoParticle,\n",
289+
" lon=[-37.09499],\n",
290+
" lat=[6.73472],\n",
291+
" depth=fieldset.mindepth,\n",
292+
" time=np.datetime64(\"2019-07-25T11:14:00\"),\n",
255293
")"
256294
]
257295
},
@@ -271,10 +309,16 @@
271309
"outputs": [],
272310
"source": [
273311
"argoset.execute(\n",
274-
" [ArgoVerticalMovement, AdvectionRK4, KeepAtSurface], # list of kernels to be executed\n",
312+
" [\n",
313+
" ArgoVerticalMovement,\n",
314+
" AdvectionRK4,\n",
315+
" KeepAtSurface,\n",
316+
" ], # list of kernels to be executed\n",
275317
" runtime=timedelta(days=31),\n",
276318
" dt=timedelta(minutes=5),\n",
277-
" output_file=argoset.ParticleFile(name=\"argo_float\", outputdt=timedelta(minutes=5), chunks=(1,500)),\n",
319+
" output_file=argoset.ParticleFile(\n",
320+
" name=\"argo_float\", outputdt=timedelta(minutes=5), chunks=(1, 500)\n",
321+
" ),\n",
278322
")"
279323
]
280324
},
@@ -303,19 +347,19 @@
303347
],
304348
"source": [
305349
"# Plot the trajectory of the Argo float you've just simulated\n",
306-
"ds_argo = xr.open_zarr('argo_float.zarr')\n",
350+
"ds_argo = xr.open_zarr(\"argo_float.zarr\")\n",
307351
"\n",
308352
"x = ds_argo[\"lon\"][:].squeeze()\n",
309353
"y = ds_argo[\"lat\"][:].squeeze()\n",
310354
"z = ds_argo[\"z\"][:].squeeze()\n",
311355
"\n",
312-
"fig = plt.figure(figsize=(13,10))\n",
313-
"ax = plt.axes(projection='3d')\n",
356+
"fig = plt.figure(figsize=(13, 10))\n",
357+
"ax = plt.axes(projection=\"3d\")\n",
314358
"ax.invert_zaxis()\n",
315-
"p = ax.scatter(x,y,z, c=z, s=20, marker=\"o\", cmap='viridis_r', depthshade=False)\n",
359+
"p = ax.scatter(x, y, z, c=z, s=20, marker=\"o\", cmap=\"viridis_r\", depthshade=False)\n",
316360
"cb = plt.colorbar(p, shrink=0.5)\n",
317361
"cb.ax.invert_yaxis()\n",
318-
"cb.set_label('depth [m]')"
362+
"cb.set_label(\"depth [m]\")"
319363
]
320364
},
321365
{
@@ -352,7 +396,8 @@
352396
"source": [
353397
"# Answer\n",
354398
"\n",
355-
"def ArgoVerticalMovement2(particle, fieldset, time): # -- change kernel name\n",
399+
"\n",
400+
"def ArgoVerticalMovement2(particle, fieldset, time): # -- change kernel name\n",
356401
" driftdepth = 1000 # maximum depth in m\n",
357402
" maxdepth = 2000 # maximum depth in m\n",
358403
" vertical_speed = 0.10 # sink and rise speed in m/s\n",
@@ -380,16 +425,20 @@
380425
"\n",
381426
" elif particle.cycle_phase == 3:\n",
382427
" # Phase 3: Rising with vertical_speed until at surface\n",
383-
" particle_ddepth -= vertical_speed * particle.dt/ 2.0 # ------------- make twice as slow\n",
384-
" particle.cycle_age += particle.dt \n",
428+
" particle_ddepth -= (\n",
429+
" vertical_speed * particle.dt / 2.0\n",
430+
" ) # ------------- make twice as slow\n",
431+
" particle.cycle_age += particle.dt\n",
385432
" particle.temp = fieldset.T[time, particle.depth, particle.lat, particle.lon]\n",
386433
" particle.salt = fieldset.S[time, particle.depth, particle.lat, particle.lon]\n",
387434
" if particle.depth <= fieldset.mindepth:\n",
388435
" particle.depth = fieldset.mindepth\n",
389-
" particle.temp = math.nan # reset temperature to NaN at end of sampling cycle\n",
436+
" particle.temp = (\n",
437+
" math.nan\n",
438+
" ) # reset temperature to NaN at end of sampling cycle\n",
390439
" particle.salt = math.nan # idem\n",
391440
" particle.cycle_phase = 4\n",
392-
" \n",
441+
"\n",
393442
" elif particle.cycle_phase == 4:\n",
394443
" # Phase 4: Transmitting at surface until cycletime is reached\n",
395444
" if particle.cycle_age > cycletime:\n",
@@ -407,24 +456,30 @@
407456
"\n",
408457
"\n",
409458
"argoset = ParticleSet( # ------------ redefine argoset, otherwise simulation continues from previous run\n",
410-
" fieldset=fieldset, pclass=ArgoParticle, lon=[-37.09499], lat=[6.73472],\n",
411-
" depth=fieldset.mindepth, time=np.datetime64('2019-07-25T11:14:00')\n",
459+
" fieldset=fieldset,\n",
460+
" pclass=ArgoParticle,\n",
461+
" lon=[-37.09499],\n",
462+
" lat=[6.73472],\n",
463+
" depth=fieldset.mindepth,\n",
464+
" time=np.datetime64(\"2019-07-25T11:14:00\"),\n",
412465
")\n",
413466
"argoset.execute(\n",
414467
" [ArgoVerticalMovement2, AdvectionRK4, KeepAtSurface], # ----- changed kernel\n",
415468
" runtime=timedelta(days=31),\n",
416469
" dt=timedelta(minutes=5),\n",
417-
" output_file=argoset.ParticleFile(name=\"argo_float2\", outputdt=timedelta(minutes=30), chunks=(1,500)), # -- changed filename\n",
470+
" output_file=argoset.ParticleFile(\n",
471+
" name=\"argo_float2\", outputdt=timedelta(minutes=30), chunks=(1, 500)\n",
472+
" ), # -- changed filename\n",
418473
")\n",
419474
"\n",
420475
"# Plot depth as a function of time for both the regular and slowly-ascending floats to check if your code works\n",
421-
"ds_argo2 = xr.open_zarr('argo_float2.zarr')\n",
476+
"ds_argo2 = xr.open_zarr(\"argo_float2.zarr\")\n",
422477
"fig = plt.figure()\n",
423-
"plt.plot(ds_argo.time[0,:], -ds_argo.z[0,:], 'k', label='original')\n",
424-
"plt.plot(ds_argo2.time[0,:], -ds_argo2.z[0,:], 'b:',label='edited')\n",
478+
"plt.plot(ds_argo.time[0, :], -ds_argo.z[0, :], \"k\", label=\"original\")\n",
479+
"plt.plot(ds_argo2.time[0, :], -ds_argo2.z[0, :], \"b:\", label=\"edited\")\n",
425480
"plt.legend()\n",
426481
"plt.grid()\n",
427-
"plt.ylabel('depth [m]')\n",
482+
"plt.ylabel(\"depth [m]\")\n",
428483
"plt.show()"
429484
]
430485
},
@@ -446,31 +501,35 @@
446501
],
447502
"source": [
448503
"# Plots of the vertical temperature and salinity profile, which were recorded during the ascents to the surface.\n",
449-
"fig = plt.figure(figsize=(12,6))\n",
450-
"fig.suptitle(f'Temperature, salinity and time during phase 3')\n",
504+
"fig = plt.figure(figsize=(12, 6))\n",
505+
"fig.suptitle(f\"Temperature, salinity and time during phase 3\")\n",
451506
"\n",
452-
"days = (ds_argo.time[0,:]-ds_argo.time[0,0]).data.astype('timedelta64[m]').astype('int')/1440\n",
453-
"tids3 = ~ds_argo.temp[0,:].isnull().compute() # time indices during cycle phase 3 (ascent)\n",
507+
"days = (ds_argo.time[0, :] - ds_argo.time[0, 0]).data.astype(\"timedelta64[m]\").astype(\n",
508+
" \"int\"\n",
509+
") / 1440\n",
510+
"tids3 = (\n",
511+
" ~ds_argo.temp[0, :].isnull().compute()\n",
512+
") # time indices during cycle phase 3 (ascent)\n",
454513
"\n",
455514
"ax1 = fig.add_subplot(131)\n",
456-
"ax1.plot(ds_argo.temp[0,:],-ds_argo.z[0,:], 'k')\n",
515+
"ax1.plot(ds_argo.temp[0, :], -ds_argo.z[0, :], \"k\")\n",
457516
"ax1.grid()\n",
458-
"ax1.set_xlabel('temperature [°C]')\n",
459-
"ax1.set_ylabel('depth [m]')\n",
517+
"ax1.set_xlabel(\"temperature [°C]\")\n",
518+
"ax1.set_ylabel(\"depth [m]\")\n",
460519
"\n",
461520
"ax2 = fig.add_subplot(132, sharey=ax1)\n",
462-
"ax2.plot(ds_argo.salt[0,:], -ds_argo.z[0,:], 'k')\n",
521+
"ax2.plot(ds_argo.salt[0, :], -ds_argo.z[0, :], \"k\")\n",
463522
"ax2.grid()\n",
464523
"ax2.yaxis.set_tick_params(left=False, labelleft=False)\n",
465-
"ax2.set_xlabel('salinity [g/kg]')\n",
524+
"ax2.set_xlabel(\"salinity [g/kg]\")\n",
466525
"\n",
467526
"ax3 = fig.add_subplot(133, sharey=ax1)\n",
468-
"ax3.plot(days[tids3], -ds_argo.z[0,tids3], 'k-o', ms=4)\n",
527+
"ax3.plot(days[tids3], -ds_argo.z[0, tids3], \"k-o\", ms=4)\n",
469528
"ax3.yaxis.tick_right()\n",
470-
"ax3.yaxis.label_position = 'right'\n",
529+
"ax3.yaxis.label_position = \"right\"\n",
471530
"ax3.grid()\n",
472-
"ax3.set_xlabel('days from launch')\n",
473-
"ax3.set_ylabel('depth [m]', rotation=270)\n",
531+
"ax3.set_xlabel(\"days from launch\")\n",
532+
"ax3.set_ylabel(\"depth [m]\", rotation=270)\n",
474533
"plt.show()"
475534
]
476535
}

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