def get_datafiles_in_flist(file_): """ read flist1.txt, flist2.txt, gridcur_ts_hdr2.cur and download the netcdf datafiles from server if required helper function that reads each line of the file_ and gets an files that are defined by [FILE] or [File] from the server NOTE: reading the text file and getting the names of the datafiles on the fly works fine. It maybe simpler to define a dict containing all files required by these tests including the files listed in flist1.txt, flist2.txt ..currently this is the only place where this needs to be done """ flist = get_datafile(file_) with open(flist, 'r') as fh: while True: line = fh.readline() if len(line) == 0: break elif line[:6].lower() == '[file]': # read filename and download it from server if it required get_datafile(os.path.join(os.path.split(flist)[0], line[6:].strip())) return flist
def CurrentsAndWinds(timeStep, start_time, duration, weatheringSteps, mapfile, uncertain, data_path, curr_path, wind_path, map_path, reFloatHalfLife, windFile, currFile, tidalFile, num_elements, depths, lat, lon, output_path, wind_scale, save_nc, timestep_outputs, weatherers, td): print 'initializing the model:' model = Model(time_step=timeStep, start_time=start_time, duration=duration) print 'adding the map:' print (data_path, map_path, mapfile) mapfile = get_datafile(os.path.join(data_path, map_path, mapfile)) model.map = MapFromBNA(mapfile, refloat_halflife=reFloatHalfLife) print 'adding a renderer' model.outputters += Renderer(mapfile, output_path, size=(800, 600), output_timestep=timedelta(hours=timestep_outputs)) if save_nc: nc_outputter = NetCDFOutput('currentsAndWinds_example.nc', which_data='standard', output_timestep=timedelta(hours=timestep_outputs)) model.outputters += nc_outputter print 'adding a wind mover:' wind_file = get_datafile(os.path.join(data_path, wind_path, windFile)) wind = GridWindMover(wind_file) wind.wind_scale = wind_scale model.movers += wind print 'adding a current mover: ' curr_file = get_datafile(os.path.join(data_path, curr_path, currFile)) model.movers += GridCurrentMover(curr_file, num_method='RK4') if td: random_mover = RandomMover(diffusion_coef=10000) model.movers += random_mover print 'adding spill' model.spills += point_line_release_spill(num_elements=num_elements, start_position=(lon, lat, 0), release_time=start_time, end_release_time=start_time + duration) return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2012, 9, 15, 12, 0) mapfile = get_datafile(os.path.join(base_dir, './LongIslandSoundMap.BNA')) gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours # # the image output renderer # global renderer # one hour timestep model = Model(start_time=start_time, duration=timedelta(hours=48), time_step=3600, map=gnome_map, uncertain=True, cache_enabled=True) netcdf_file = os.path.join(base_dir, 'script_long_island.nc') scripting.remove_netcdf(netcdf_file) print 'adding outputters' model.outputters += Renderer(mapfile, images_dir, size=(800, 600)) model.outputters += NetCDFOutput(netcdf_file, which_data='all') print 'adding a spill' spill = point_line_release_spill(num_elements=1000, start_position=(-72.419992, 41.202120, 0.0), release_time=start_time) model.spills += spill print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=500000, uncertain_factor=2) print 'adding a wind mover:' series = np.zeros((5, ), dtype=datetime_value_2d) series[0] = (start_time, (10, 45)) series[1] = (start_time + timedelta(hours=18), (10, 90)) series[2] = (start_time + timedelta(hours=30), (10, 135)) series[3] = (start_time + timedelta(hours=42), (10, 180)) series[4] = (start_time + timedelta(hours=54), (10, 225)) wind = Wind(timeseries=series, units='m/s') model.movers += WindMover(wind) print 'adding a cats mover:' curr_file = get_datafile(os.path.join(base_dir, r"./LI_tidesWAC.CUR")) tide_file = get_datafile(os.path.join(base_dir, r"./CLISShio.txt")) c_mover = CatsMover(curr_file, tide=Tide(tide_file)) model.movers += c_mover model.environment += c_mover.tide print 'viewport is:', [ o.viewport for o in model.outputters if isinstance(o, Renderer) ] return model
def allWeatherers(timeStep, start_time, duration, weatheringSteps, map, uncertain, data_path, curr_path, wind_path, map_path, reFloatHalfLife, windFile, currFile, tidalFile, num_elements, depths, lat, lon, output_path, wind_scale, save_nc, timestep_outputs, weatherers, td): print 'initializing the model:' model = Model(time_step=timeStep, start_time=start_time, duration=duration) print 'adding the map:' map_folder = os.path.join(data_path, map_path) if not(os.path.exists(map_folder)): print('The map folder is incorrectly set:', map_folder) mapfile = get_datafile( os.path.join(map_folder,map) ) model.map = MapFromBNA(mapfile, refloat_halflife=reFloatHalfLife) print 'adding a renderer' model.outputters += Renderer(mapfile, output_path, size=(800, 600), output_timestep=timedelta(hours=1)) if save_nc: nc_outputter = NetCDFOutput(netcdf_file, which_data='most', output_timestep=timedelta(hours=1)) model.outputters += nc_outputter print 'adding a wind mover:' wind_file = get_datafile(os.path.join(data_path, wind_path, windFile)) wind = GridWindMover(wind_file) wind.wind_scale = wind_scale model.movers += wind print 'adding a current mover: ' curr_file = get_datafile(os.path.join(data_path, curr_path, currFile)) model.movers += GridCurrentMover(curr_file, num_method='RK4') if td: random_mover = RandomMover(diffusion_coef=10000) model.movers += random_mover print 'adding spill' model.spills += point_line_release_spill(num_elements=num_elements, start_position=(lon, lat, 0), release_time=start_time, end_release_time=start_time + duration) print 'adding weatherers' water = Water(280.92) wind = constant_wind(20.0, 117, 'knots') waves = Waves(wind, water) model.weatherers += Evaporation(water, wind) model.weatherers += Emulsification(waves) model.weatherers += NaturalDispersion(waves, water) return model
def make_model(coor, yr, month, day, period=46, dt=900 ,opt='SUNTANS', images_dir=os.getcwd()+"/images"): ''' Run multiple GNOME; yr,month,day---oil spill start time; period---oil spill simulation duration; dt--oil spill time step in second ''' print "initializing the model" base_dir=os.getcwd() #start_time = datetime(2014,8,21,0) start_time = datetime(yr,month,day,0) model = Model(start_time = start_time, duration = timedelta(hours=period), time_step =dt, uncertain = False, ) mapfile = os.path.join(base_dir, './coast.bna') print "adding the map" gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours print "adding renderer" model.outputters += Renderer(mapfile, images_dir, size=(1800, 1600)) print "adding a wind mover from a time-series" ## this is wind wind_file=get_datafile(os.path.join(base_dir, 'wind.WND')) wind = Wind(filename=wind_file) w_mover = WindMover(wind) model.movers += w_mover print "adding a current mover:" ## this is currents curr_file = get_datafile(os.path.join(base_dir, 'current_'+opt+'.txt')) model.movers += GridCurrentMover(curr_file) #model.movers += RandomMover(1000) ## ## Add some spills (sources of elements) ## print "adding 13 points in a cluster that has some small initial separation as the source of spill" for i in range(len(coor)): xcoor,ycoor=nctools.utmToLatLng(15,coor[i][0],coor[i][1],northernHemisphere=True) model.spills += point_line_release_spill(num_elements=1, start_position = (ycoor,xcoor, 0.0), release_time = start_time, ) print "adding netcdf output" netcdf_output_file = os.path.join(base_dir,'GNOME_'+opt+'.nc') scripting.remove_netcdf(netcdf_output_file) model.outputters += NetCDFOutput(netcdf_output_file, which_data='all') return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2015, 9, 24, 1, 1) # 1 day of data in file # 1/2 hr in seconds model = Model(start_time=start_time, duration=timedelta(hours=48), time_step=900) mapfile = get_datafile(os.path.join(base_dir, 'columbia_river.bna')) print 'adding the map' model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds # draw_ontop can be 'uncertain' or 'forecast' # 'forecast' LEs are in black, and 'uncertain' are in red # default is 'forecast' LEs draw on top renderer = Renderer(mapfile, images_dir, image_size=(600, 1200)) renderer.graticule.set_DMS(True) # renderer.viewport = ((-123.35, 45.6), (-122.68, 46.13)) # renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0)) print 'adding outputters' model.outputters += renderer print 'adding a spill' # for now subsurface spill stays on initial layer # - will need diffusion and rise velocity # - wind doesn't act # - start_position = (-76.126872, 37.680952, 5.0), spill1 = point_line_release_spill(num_elements=1000, start_position=(-122.625, 45.609, 0.0), release_time=start_time) model.spills += spill1 print 'adding a RandomMover:' # model.movers += RandomMover(diffusion_coef=50000) print 'adding a wind mover:' model.movers += constant_wind_mover(0.5, 0, units='m/s') print 'adding a current mover:' curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc')) # uncertain_time_delay in hours # vec_field = TriVectorField('COOPSu_CREOFS24.nc') # u_mover = UGridCurrentMover(vec_field) c_mover = GridCurrentMover(curr_file) # c_mover.uncertain_cross = 0 # default is .25 # model.movers += u_mover model.movers += c_mover model.save return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'creating the maps' mapfile = get_datafile(os.path.join(base_dir, 'LowerMississippiMap.bna')) gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours print 'initializing the model' start_time = datetime(2012, 9, 15, 12, 0) # default to now, rounded to the nearest hour model = Model(time_step=600, start_time=start_time, duration=timedelta(days=1), map=gnome_map, uncertain=True) print 'adding outputters' model.outputters += Renderer(mapfile, images_dir, image_size=(800, 600)) netcdf_file = os.path.join(base_dir, 'script_lower_mississippi.nc') scripting.remove_netcdf(netcdf_file) model.outputters += NetCDFOutput(netcdf_file, which_data='all') print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=10000) print 'adding a wind mover:' series = np.zeros((5, ), dtype=datetime_value_2d) series[0] = (start_time, (2, 45)) series[1] = (start_time + timedelta(hours=18), (2, 90)) series[2] = (start_time + timedelta(hours=30), (2, 135)) series[3] = (start_time + timedelta(hours=42), (2, 180)) series[4] = (start_time + timedelta(hours=54), (2, 225)) w_mover = WindMover(Wind(timeseries=series, units='m/s')) model.movers += w_mover print 'adding a cats mover:' curr_file = get_datafile(os.path.join(base_dir, 'LMiss.CUR')) c_mover = CatsMover(curr_file) # but do need to scale (based on river stage) c_mover.scale = True c_mover.scale_refpoint = (-89.699944, 29.494558) # based on stage height 10ft (range is 0-18) c_mover.scale_value = 1.027154 model.movers += c_mover print 'adding a spill' spill = point_line_release_spill(num_elements=1000, start_position=(-89.699944, 29.494558, 0.0), release_time=start_time) model.spills += spill return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2012, 9, 15, 12, 0) mapfile = get_datafile(os.path.join(base_dir, 'LongIslandSoundMap.BNA')) gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours # # the image output renderer # global renderer # one hour timestep model = Model(start_time=start_time, duration=timedelta(hours=48), time_step=3600, map=gnome_map, uncertain=True, cache_enabled=True) print 'adding outputters' model.outputters += Renderer(mapfile, images_dir, size=(800, 600)) netcdf_file = os.path.join(base_dir, 'script_long_island.nc') scripting.remove_netcdf(netcdf_file) model.outputters += NetCDFOutput(netcdf_file, which_data='all') print 'adding a spill' spill = point_line_release_spill(num_elements=1000, start_position=(-72.419992, 41.202120, 0.0), release_time=start_time) model.spills += spill print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=500000, uncertain_factor=2) print 'adding a wind mover:' series = np.zeros((5, ), dtype=datetime_value_2d) series[0] = (start_time, (10, 45)) series[1] = (start_time + timedelta(hours=18), (10, 90)) series[2] = (start_time + timedelta(hours=30), (10, 135)) series[3] = (start_time + timedelta(hours=42), (10, 180)) series[4] = (start_time + timedelta(hours=54), (10, 225)) wind = Wind(timeseries=series, units='m/s') model.movers += WindMover(wind) print 'adding a cats mover:' curr_file = get_datafile(os.path.join(base_dir, 'LI_tidesWAC.CUR')) tide_file = get_datafile(os.path.join(base_dir, 'CLISShio.txt')) c_mover = CatsMover(curr_file, tide=Tide(tide_file)) model.movers += c_mover model.environment += c_mover.tide print 'viewport is:', [o.viewport for o in model.outputters if isinstance(o, Renderer)] return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2015, 9, 24, 1, 1) # 1 day of data in file # 1/2 hr in seconds model = Model(start_time=start_time, duration=timedelta(hours = 48), time_step=900) mapfile = get_datafile(os.path.join(base_dir, 'columbia_river.bna')) print 'adding the map' model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds # draw_ontop can be 'uncertain' or 'forecast' # 'forecast' LEs are in black, and 'uncertain' are in red # default is 'forecast' LEs draw on top renderer = Renderer(mapfile, images_dir, image_size=(600, 1200)) renderer.graticule.set_DMS(True) # renderer.viewport = ((-123.35, 45.6), (-122.68, 46.13)) # renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0)) print 'adding outputters' model.outputters += renderer print 'adding a spill' # for now subsurface spill stays on initial layer # - will need diffusion and rise velocity # - wind doesn't act # - start_position = (-76.126872, 37.680952, 5.0), spill1 = point_line_release_spill(num_elements=5000, start_position=(-122.625, 45.609, 0.0), release_time=start_time) model.spills += spill1 print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=5000) print 'adding a wind mover:' # model.movers += constant_wind_mover(8, 90, units='m/s') print 'adding a current mover:' curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc')) # uncertain_time_delay in hours c_mover = GridCurrentMover(curr_file) c_mover.uncertain_cross = 0 # default is .25 model.movers += c_mover return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'creating the maps' mapfile = get_datafile(os.path.join(base_dir, 'LowerMississippiMap.bna')) gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours print 'initializing the model' start_time = datetime(2012, 9, 15, 12, 0) # default to now, rounded to the nearest hour model = Model(time_step=600, start_time=start_time, duration=timedelta(days=1), map=gnome_map, uncertain=True) print 'adding outputters' model.outputters += Renderer(mapfile, images_dir, size=(800, 600)) netcdf_file = os.path.join(base_dir, 'script_lower_mississippi.nc') scripting.remove_netcdf(netcdf_file) model.outputters += NetCDFOutput(netcdf_file, which_data='all') print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=10000) print 'adding a wind mover:' series = np.zeros((5, ), dtype=datetime_value_2d) series[0] = (start_time, (2, 45)) series[1] = (start_time + timedelta(hours=18), (2, 90)) series[2] = (start_time + timedelta(hours=30), (2, 135)) series[3] = (start_time + timedelta(hours=42), (2, 180)) series[4] = (start_time + timedelta(hours=54), (2, 225)) w_mover = WindMover(Wind(timeseries=series, units='m/s')) model.movers += w_mover print 'adding a cats mover:' curr_file = get_datafile(os.path.join(base_dir, 'LMiss.CUR')) c_mover = CatsMover(curr_file) # but do need to scale (based on river stage) c_mover.scale = True c_mover.scale_refpoint = (-89.699944, 29.494558) # based on stage height 10ft (range is 0-18) c_mover.scale_value = 1.027154 model.movers += c_mover print 'adding a spill' spill = point_line_release_spill(num_elements=1000, start_position=(-89.699944, 29.494558, 0.0), release_time=start_time) model.spills += spill return model
def test_exception(): """ bogus file to raise an exception """ bogus = os.path.join(here, 'bogus.txt') with pytest.raises(HTTPError): get_datafile(bogus)
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2006, 3, 31, 20, 0) model = Model(start_time=start_time, duration=timedelta(days=3), time_step=30 * 60, uncertain=True) print 'adding the map' mapfile = get_datafile(os.path.join(base_dir, 'coastSF.bna')) model.map = MapFromBNA(mapfile, refloat_halflife=1) # seconds renderer = Renderer(mapfile, images_dir, image_size=(800, 600), draw_ontop='forecast') renderer.viewport = ((-124.5, 37.), (-120.5, 39)) print 'adding outputters' model.outputters += renderer netcdf_file = os.path.join(base_dir, 'script_sf_bay.nc') scripting.remove_netcdf(netcdf_file) model.outputters += NetCDFOutput(netcdf_file, which_data='all') print 'adding a spill' spill = point_line_release_spill( num_elements=1000, start_position=(-123.57152, 37.369436, 0.0), release_time=start_time, substance=NonWeatheringSubstance(windage_range=(0.01, .04)) #element_type=floating(windage_range=(0.01, # 0.04) # ) ) model.spills += spill # print 'adding a RandomMover:' # r_mover = gnome.movers.RandomMover(diffusion_coef=50000) # model.movers += r_mover print 'adding a grid wind mover:' wind_file = get_datafile(os.path.join(base_dir, 'WindSpeedDirSubset.nc')) topology_file = get_datafile( os.path.join(base_dir, 'WindSpeedDirSubsetTop.dat')) w_mover = GridWindMover(wind_file, topology_file) # w_mover.uncertain_time_delay = 6 # w_mover.uncertain_duration = 6 w_mover.uncertain_speed_scale = 1 w_mover.uncertain_angle_scale = 0.2 # default is .4 w_mover.wind_scale = 2 model.movers += w_mover return model
def test_move_tri_tide(self): """ test move for a triangular grid (first time in file) """ time = datetime.datetime(2014, 6, 9, 0) self.cm.model_time = time_utils.date_to_sec(time) self.cm.uncertain = True time_grid_file = get_datafile(os.path.join(cur_dir, 'PQBayCur.nc4' )) topology_file = get_datafile(os.path.join(cur_dir, 'PassamaquoddyTOP.dat' )) tide_file = get_datafile(os.path.join(tide_dir, 'EstesHead.txt' )) yeardata_path = os.path.join(os.path.dirname(gnome.__file__), 'data/yeardata/') self.shio = cy_shio_time.CyShioTime(tide_file) self.ccm.set_shio(self.shio) self.ccm.text_read(time_grid_file, topology_file) self.shio.set_shio_yeardata_path(yeardata_path) self.cm.ref[:]['long'] = -66.991344 # for Passamaquoddy self.cm.ref[:]['lat'] = 45.059316 #self.check_move() self.check_move_certain_uncertain(self.ccm.uncertain_time_delay) actual = np.empty((self.cm.num_le, ), dtype=world_point) actual[:]['lat'] = -.000440779 actual[:]['long'] = .00016611 tol = 1e-5 msg = r"{0} move is not within a tolerance of {1}" np.testing.assert_allclose( self.cm.delta['lat'], actual['lat'], tol, tol, msg.format('ches_bay', tol), 0, ) np.testing.assert_allclose( self.cm.delta['long'], actual['long'], tol, tol, msg.format('ches_bay', tol), 0, ) #check that certain and uncertain are the same if uncertainty is time delayed #self.ccm.uncertain_time_delay = 3 self.ccm.uncertain_time_delay = 10800 # cython expects time_delay in seconds self.check_move_certain_uncertain(self.ccm.uncertain_time_delay)
def test_callback_add_mover(): 'Test callback after add mover' units = 'meter per second' model = Model() model.start_time = datetime(2012, 1, 1, 0, 0) model.duration = timedelta(hours=10) model.time_step = timedelta(hours=1) # start_loc = (1.0, 2.0, 0.0) # random non-zero starting points # add Movers model.movers += SimpleMover(velocity=(1., -1., 0.)) series = np.array((model.start_time, (10, 45)), dtype=datetime_value_2d).reshape((1, )) model.movers += WindMover(Wind(timeseries=series, units=units)) # this should create a Wind object new_wind = Wind(timeseries=series, units=units) model.environment += new_wind assert new_wind in model.environment assert len(model.environment) == 2 tide_file = get_datafile(os.path.join(tides_dir, 'CLISShio.txt')) tide_ = Tide(filename=tide_file) d_file = get_datafile(os.path.join(lis_dir, 'tidesWAC.CUR')) model.movers += CatsMover(d_file, tide=tide_) model.movers += CatsMover(d_file) for mover in model.movers: assert mover.active_start == inf_datetime.InfDateTime('-inf') assert mover.active_stop == inf_datetime.InfDateTime('inf') if hasattr(mover, 'wind'): assert mover.wind in model.environment if hasattr(mover, 'tide'): if mover.tide is not None: assert mover.tide in model.environment # Add a mover with user defined active_start / active_stop values # - these should not be updated active_on = model.start_time + timedelta(hours=1) active_off = model.start_time + timedelta(hours=4) custom_mover = SimpleMover(velocity=(1., -1., 0.), active_start=active_on, active_stop=active_off) model.movers += custom_mover assert model.movers[custom_mover.id].active_start == active_on assert model.movers[custom_mover.id].active_stop == active_off
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2006, 3, 31, 20, 0) model = Model(start_time=start_time, duration=timedelta(days=3), time_step=30 * 60, uncertain=True) print 'adding the map' mapfile = get_datafile(os.path.join(base_dir, './coastSF.bna')) model.map = MapFromBNA(mapfile, refloat_halflife=1) # seconds renderer = Renderer(mapfile, images_dir, size=(800, 600), draw_ontop='forecast') renderer.viewport = ((-124.5, 37.), (-120.5, 39)) print 'adding outputters' model.outputters += renderer netcdf_file = os.path.join(base_dir, 'script_sf_bay.nc') scripting.remove_netcdf(netcdf_file) model.outputters += NetCDFOutput(netcdf_file, which_data='all') print 'adding a spill' spill = point_line_release_spill(num_elements=1000, start_position=(-123.57152, 37.369436, 0.0), release_time=start_time, element_type=floating(windage_range=(0.01, 0.04) ) ) model.spills += spill # print 'adding a RandomMover:' # r_mover = gnome.movers.RandomMover(diffusion_coef=50000) # model.movers += r_mover print 'adding a grid wind mover:' wind_file = get_datafile(os.path.join(base_dir, r"./WindSpeedDirSubset.nc") ) topology_file = get_datafile(os.path.join(base_dir, r"./WindSpeedDirSubsetTop.dat")) w_mover = GridWindMover(wind_file, topology_file) #w_mover.uncertain_time_delay = 6 #w_mover.uncertain_duration = 6 w_mover.uncertain_speed_scale = 1 w_mover.uncertain_angle_scale = 0.2 # default is .4 w_mover.wind_scale = 2 model.movers += w_mover return model
def test_callback_add_mover(): """ Test callback after add mover """ units = 'meter per second' model = Model() model.time_step = timedelta(hours=1) model.duration = timedelta(hours=10) model.start_time = datetime(2012, 1, 1, 0, 0) # start_loc = (1.0, 2.0, 0.0) # random non-zero starting points # add Movers model.movers += SimpleMover(velocity=(1., -1., 0.)) series = np.array((model.start_time, (10, 45)), dtype=datetime_value_2d).reshape((1, )) model.movers += WindMover(Wind(timeseries=series, units=units)) tide_file = get_datafile(os.path.join(os.path.dirname(__file__), r"sample_data", 'tides', 'CLISShio.txt')) tide_ = Tide(filename=tide_file) d_file = get_datafile(os.path.join(datadir, r"long_island_sound/tidesWAC.CUR")) model.movers += CatsMover(d_file, tide=tide_) model.movers += CatsMover(d_file) for mover in model.movers: assert mover.active_start == inf_datetime.InfDateTime('-inf') assert mover.active_stop == inf_datetime.InfDateTime('inf') if isinstance(mover, WindMover): assert mover.wind.id in model.environment if isinstance(mover, CatsMover): if mover.tide is not None: assert mover.tide.id in model.environment # Add a mover with user defined active_start / active_stop values # - these should not be updated active_on = model.start_time + timedelta(hours=1) active_off = model.start_time + timedelta(hours=4) custom_mover = SimpleMover(velocity=(1., -1., 0.), active_start=active_on, active_stop=active_off) model.movers += custom_mover assert model.movers[custom_mover.id].active_start == active_on assert model.movers[custom_mover.id].active_stop == active_off
def test_move_curv(self): """ test move for a curvilinear grid (first time in file) """ time = datetime.datetime(2006, 3, 31, 21) self.cm.model_time = date_to_sec(time) self.cm.uncertain = True time_grid_file = get_datafile(os.path.join(winds_dir, 'WindSpeedDirSubset.nc')) topology_file = get_datafile(os.path.join(winds_dir, 'WindSpeedDirSubsetTop.dat')) self.gcm.text_read(time_grid_file, topology_file) self.cm.ref[:]['long'] = -122.934656 # for NWS off CA self.cm.ref[:]['lat'] = 38.27594 #self.check_move() self.check_move_certain_uncertain(self.gcm.uncertain_time_delay) actual = np.empty((self.cm.num_le, ), dtype=world_point) actual[:]['lat'] = 0.0009890068148185598 actual[:]['long'] = 0.0012165959734995123 actual[:]['z'] = 0. tol = 1e-5 msg = '{0} move is not within a tolerance of {1}' np.testing.assert_allclose( self.cm.delta['lat'], actual['lat'], tol, tol, msg.format('WindSpeedDirSubset.nc', tol), 0, ) np.testing.assert_allclose( self.cm.delta['long'], actual['long'], tol, tol, msg.format('WindSpeedDirSubset.nc', tol), 0, ) #check that certain and uncertain are the same if uncertainty is time delayed #self.gcm.uncertain_time_delay = 3 self.gcm.uncertain_time_delay = 10800 # cython expects time_delay in seconds self.check_move_certain_uncertain(self.gcm.uncertain_time_delay) # np.testing.assert_equal(self.cm.delta, actual, # "test_move_curv() failed", 0) np.all(self.cm.delta['z'] == 0)
def test_catsmover_update(): curr_file = get_datafile(os.path.join(lis_dir, 'tidesWAC.CUR')) td_file = get_datafile(os.path.join(lis_dir, 'CLISShio.txt')) c_mv = movers.CatsMover(curr_file, tide=environment.Tide(td_file)) c_dict = movers_schema.CatsMover().serialize(c_mv.to_dict()) dict_ = movers_schema.CatsMover().deserialize(c_dict) # now let's say we want to update the Tide object, which is not part of the serialization tide = environment.Tide(td_file) dict_.update({'tide': tide}) c_mv.from_dict(dict_) assert c_mv.tide.id == tide.id
def make_model(timeStep,start_time, duration, weatheringSteps, map, uncertain, data_path, reFloatHalfLife, windFile, currFile, tidalFile, num_elements, depths, lat, lon, output_path, evaporation): #initalizing the model print 'initializing the model:' # model = Model(time_step = timeStep, start_time= start_time, duration=duration, uncertain = uncertain) model = Model(time_step = timeStep, start_time= start_time, duration=duration) #adding the map print 'adding the map:' print 'pinche path', data_path mapfile = get_datafile(os.path.join(data_path, map)) model.map = MapFromBNA(mapfile, refloat_halflife = reFloatHalfLife) #model.map = GnomeMap() print 'adding a renderer' # renderer is a class that writes map images for GNOME results model.outputters += Renderer(mapfile, output_path, size=(800, 600), output_timestep=timedelta(hours=1)) ##scripting.remove_netcdf(netcdf_file) #nc_outputter = NetCDFOutput(netcdf_file, which_data='most', output_timestep=timedelta(hours=1)) #model.outputters += nc_outputter #adding the movers print 'adding a wind mover:' wind_file = get_datafile(os.path.join(data_path, windFile)) wind = GridWindMover(wind_file) wind.wind_scale = 2 model.movers += wind print 'adding a current mover: ' curr_file = get_datafile(os.path.join(data_path,currFile)) model.movers+= GridCurrentMover(curr_file, num_method='RK4') #random_mover = RandomMover(diffusion_coef=10000) #in cm/sdfd #model.movers += random_mover if evaporation: #wind for evaporation print'adding evaporation' wind = constant_wind(1, 0, 'knots') water = Water(temperature=300.0, salinity=35.0) model.weatherers += Evaporation(wind=wind, water=water) # print 'adding a spill' # for i in depths: # model.spills+= point_line_release_spill(num_elements=num_elements, start_position=(lon,lat,i), release_time=start_time) model.spills+= point_line_release_spill(num_elements=num_elements, start_position=(lon,lat,0), release_time=start_time, end_release_time=start_time+timedelta(days=93)) return model
def test_exception(): """ bogus file to raise an exception - do this if we have an internet connection before testing it """ bogus = os.path.join(here, 'bogus.txt') try: with pytest.raises(HTTPError): get_datafile(bogus) except URLError, u: 'no internet connection' return
def make_model(images_dir=os.path.join(base_dir, "images")): print "initializing the model" start_time = datetime(2006, 3, 31, 21, 0) model = gnome.model.Model( start_time=start_time, duration=timedelta(days=3), time_step=30 * 60, uncertain=True ) # 1 day of data in file # 1/2 hr in seconds mapfile = get_datafile(os.path.join(base_dir, "./coastSF.bna")) print "adding the map" model.map = gnome.map.MapFromBNA(mapfile, refloat_halflife=1) # seconds renderer = gnome.renderer.Renderer(mapfile, images_dir, size=(800, 600)) renderer.viewport = ((-124.5, 37.0), (-120.5, 39)) print "adding outputters" model.outputters += renderer netcdf_file = os.path.join(base_dir, "script_sf_bay.nc") scripting.remove_netcdf(netcdf_file) model.outputters += gnome.netcdf_outputter.NetCDFOutput(netcdf_file, all_data=True) print "adding a spill" spill = gnome.spill.PointLineSource( num_elements=1000, start_position=(-123.57152, 37.369436, 0.0), release_time=start_time, windage_range=(0.3, 0.3), ) model.spills += spill # print 'adding a RandomMover:' # r_mover = gnome.movers.RandomMover(diffusion_coef=50000) # model.movers += r_mover # print "adding a grid wind mover:" wind_file = get_datafile(os.path.join(base_dir, r"./WindSpeedDirSubset.nc")) topology_file = get_datafile(os.path.join(base_dir, r"./WindSpeedDirSubsetTop.dat")) w_mover = gnome.movers.GridWindMover(wind_file, topology_file) # w_mover.uncertain_time_delay=6 # w_mover.uncertain_duration=6 w_mover.uncertain_speed_scale = 0.5 w_mover.set_uncertain_angle(0, "rad") # default is .4 model.movers += w_mover return model
def test_exception(): """ bogus file to raise an exception - do this if we have an internet connection before testing it """ bogus = 'bogus.txt' try: with pytest.raises(HTTPError): get_datafile(bogus) except URLError: 'no internet connection' return
def make_model(images_dir=os.path.join(base_dir,"images")): print "initializing the model" start_time = datetime(2013, 7, 23, 0) model = Model(start_time = start_time, duration = timedelta(hours=47), # n+1 of data in file time_step = 900, # 4 hr in seconds uncertain = False, ) mapfile = os.path.join(base_dir, './coast.bna') print "adding the map" gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours print "adding renderer" model.outputters += Renderer(mapfile, images_dir, size=(1800, 1600)) print "adding a wind mover from a time-series" ## this is wind wind_file=get_datafile(os.path.join(base_dir, 'wind.WND')) wind = Wind(filename=wind_file) w_mover = WindMover(wind) model.movers += w_mover print "adding a current mover:" ## this is currents curr_file = get_datafile(os.path.join(base_dir, 'current.txt')) model.movers += GridCurrentMover(curr_file) ## ## Add some spills (sources of elements) ## print "adding 13 points in a cluster that has some small initial separation as the source of spill" for i in range(len(coor)): aaa=utmToLatLng(14,coor[i][0],coor[i][1],northernHemisphere=True) model.spills += point_line_release_spill(num_elements=1, start_position = (aaa[1],aaa[0], 0.0), release_time = start_time, ) print "adding netcdf output" netcdf_output_file = os.path.join(base_dir,'GNOME_output.nc') scripting.remove_netcdf(netcdf_output_file) model.outputters += NetCDFOutput(netcdf_output_file, which_data='all') return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2012, 10, 25, 0, 1) # start_time = datetime(2015, 12, 18, 06, 01) # 1 day of data in file # 1/2 hr in seconds model = Model(start_time=start_time, duration=timedelta(hours=6), time_step=900) mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna')) print 'adding the map' '''TODO: sort out MapFromBna's map_bounds parameter... it does nothing right now, and the spill is out of bounds''' model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds # draw_ontop can be 'uncertain' or 'forecast' # 'forecast' LEs are in black, and 'uncertain' are in red # default is 'forecast' LEs draw on top renderer = Renderer(mapfile, images_dir, image_size=(1024, 768)) # renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75)) # renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0)) print 'adding outputters' model.outputters += renderer print 'adding a spill' # for now subsurface spill stays on initial layer # - will need diffusion and rise velocity # - wind doesn't act # - start_position = (-76.126872, 37.680952, 5.0), spill1 = point_line_release_spill(num_elements=1000, start_position=(-74.15, 40.5, 0.0), release_time=start_time) model.spills += spill1 print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=50000) print 'adding a wind mover:' model.movers += constant_wind_mover(4, 270, units='m/s') print 'adding a current mover:' # url is broken, fix and include the following section # url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml') # # cf = roms_field('nos.tbofs.fields.n000.20160406.t00z_sgrid.nc') # cf = GridCurrent.from_netCDF(url) # renderer.add_grid(cf.grid) # renderer.delay = 25 # u_mover = PyCurrentMover(cf, default_num_method='Euler') # model.movers += u_mover # return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2015, 9, 24, 3, 0) # 1 day of data in file # 1/2 hr in seconds model = Model(start_time=start_time, duration=timedelta(hours = 48), time_step=3600) mapfile = get_datafile(os.path.join(base_dir, 'Perfland.bna')) print 'adding the map' model.map = MapFromBNA(mapfile, refloat_halflife=1, raster_size=1024*1024) # seconds # draw_ontop can be 'uncertain' or 'forecast' # 'forecast' LEs are in black, and 'uncertain' are in red # default is 'forecast' LEs draw on top renderer = Renderer(mapfile, images_dir, image_size=(800, 600), output_timestep=timedelta(hours=1), timestamp_attrib={'size': 'medium', 'color':'uncert_LE'}) renderer.set_timestamp_attrib(format='%a %c') renderer.graticule.set_DMS(True) # renderer.viewport = ((-124.25, 47.5), (-122.0, 48.70)) print 'adding outputters' model.outputters += renderer print 'adding a spill' # for now subsurface spill stays on initial layer # - will need diffusion and rise velocity # - wind doesn't act # - start_position = (-76.126872, 37.680952, 5.0), spill1 = point_line_release_spill(num_elements=5000, start_position=(0.0, 0.0, 0.0), release_time=start_time) model.spills += spill1 print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=50000) print 'adding a wind mover:' model.movers += constant_wind_mover(13, 270, units='m/s') print 'adding a current mover:' # curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc')) # # # uncertain_time_delay in hours # c_mover = GridCurrentMover(curr_file) # c_mover.uncertain_cross = 0 # default is .25 # # model.movers += c_mover return model
def make_db(): from py.test import config # Only run database setup on master (in case of xdist/multiproc mode) if not hasattr(config, 'slaveinput'): try: from gnome.db.oil_library.initializedb import initialize_sql, \ load_database oillib_file = get_datafile(os.path.join(data_dir, 'OilLib.smaller')) sqlalchemy_url = 'sqlite:///{0}'.format(db_file) settings = {'sqlalchemy.url': sqlalchemy_url, 'oillib.file': oillib_file} initialize_sql(settings) load_database(settings) except ImportError, ie: print '\nWarning: Required modules for database unit-testing not found.' dependant_modules = ('sqlalchemy', 'zope.sqlalchemy', 'transaction') print ie print 'Also may need:', print '\t {0}\n'.format([m for m in dependant_modules if not m in sys.modules])
def test_get_datafile(): """ downloads CLISShio.txt to make sure get_datafile works as expected Uses testdata['CatsMover']['tide'] as test file. If it exists, it moves it '*.renamed'. It then trys to download file and if it fails for any reason (most likely internet connection is missing), then copy the file back from '*.renamed' to testdata['CatsMover']['tide'] At the end also, move the renamed file back """ file_ = testdata['CatsMover']['tide'] renamed = None if os.path.exists(file_): renamed = file_ + '.renamed' shutil.move(file_, renamed) num_calls = 0 while num_calls < 2: # do this twice to make sure it still works as expected after file has # been downloaded in 1st call try: r_file = get_datafile(file_) assert os.path.exists(r_file) except: if renamed is not None: shutil.move(renamed, file_) reason = ("Most likely urllib2.HTTPError exception in " "get_datafile(). Check internet connectivity.") pytest.xfail(reason=reason) return num_calls += 1 # do not delete file_ if renamed is not None: shutil.move(renamed, file_)
def test_get_datafile(): """ downloads CLISShio.txt to make sure get_datafile works as expected removes the file sample_data/CLISShio.txt after downloading it to leave it in clean _state """ file_ = os.path.join(here, r'sample_data/CLISShio.txt') if os.path.exists(file_): os.remove(file_) for i in range(2): # do this twice to make sure it still works as expected after file has been downloaded in 1st call try: r_file = get_datafile(file_) except: return assert os.path.exists(r_file) # clean up file_ that was downloaded just for this test os.remove(file_)
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2013, 1, 1, 1) # data starts at 1:00 instead of 0:00 model = Model(start_time=start_time, duration=timedelta(days=1), time_step=900, uncertain=False) try: mapfile = get_datafile(os.path.join(base_dir, './pearl_harbor.bna')) except HTTPError: print ('Could not download Pearl Harbor data from server - ' 'returning empty model') return model print 'adding the map' model.map = MapFromBNA(mapfile, refloat_halflife=1) # hours # # Add the outputters -- render to images, and save out as netCDF # print 'adding renderer and netcdf output' model.outputters += Renderer(mapfile, images_dir, size=(800, 600)) netcdf_output_file = os.path.join(base_dir, 'pearl_harbor_output.nc') scripting.remove_netcdf(netcdf_output_file) model.outputters += NetCDFOutput(netcdf_output_file, which_data='all') # # # # Set up the movers: # # print 'adding a random mover:' model.movers += RandomMover(diffusion_coef=10000) print 'adding a wind mover:' series = np.zeros((3, ), dtype=datetime_value_2d) series[0] = (start_time, (4, 180)) series[1] = (start_time + timedelta(hours=12), (2, 270)) series[2] = (start_time + timedelta(hours=24), (4, 180)) w_mover = WindMover(Wind(timeseries=series, units='knots')) model.movers += w_mover model.environment += w_mover.wind print 'adding a current mover:' # this is CH3D currents curr_file = os.path.join(base_dir, r"./ch3d2013.nc") topology_file = os.path.join(base_dir, r"./PearlHarborTop.dat") model.movers += GridCurrentMover(curr_file, topology_file) # # # # Add a spill (sources of elements) # # print 'adding spill' model.spills += point_line_release_spill(num_elements=1000, start_position=(-157.97064, 21.331524, 0.0), release_time=start_time) return model
def __init__(self): wind_file = get_datafile(os.path.join(datadir, r"delaware_bay/ConstantWind.WND")) # self.ossm = cy_ossm_time.CyOSSMTime(wind_file,file_contains=basic_types.ts_format.magnitude_direction) wm = Wind(filename=wind_file) cats1_file = get_datafile(os.path.join(datadir, r"delaware_bay/NW30ktwinds.cur")) cats2_file = get_datafile(os.path.join(datadir, r"delaware_bay/SW30ktwinds.cur")) self.component = cy_component_mover.CyComponentMover() self.component.set_ossm(wm.ossm) # self.component.set_ossm(self.ossm) self.component.text_read(cats1_file, cats2_file) self.component.ref_point = (-75.262319, 39.142987) super(ComponentMove, self).__init__() self.ref[:] = (-75.262319, 39.142987, 0) self.component.prepare_for_model_run() self.component.prepare_for_model_step(self.model_time, self.time_step, 1, self.spill_size)
def test_move_tri(self): """ test move for a triangular grid (first time in file) """ time = datetime.datetime(2004, 12, 31, 13) self.cm.model_time = time_utils.date_to_sec(time) self.cm.uncertain = True time_grid_file = get_datafile(os.path.join(cur_dir, 'ChesBay.nc' )) topology_file = get_datafile(os.path.join(cur_dir, 'ChesBay.dat' )) self.gcm.text_read(time_grid_file, topology_file) self.cm.ref[:]['long'] = -76.149368 # for ChesBay self.cm.ref[:]['lat'] = 37.74496 #self.check_move() self.check_move_certain_uncertain(self.gcm.uncertain_time_delay) actual = np.empty((self.cm.num_le, ), dtype=world_point) actual[:]['lat'] = -.00170908 actual[:]['long'] = -.0003672 tol = 1e-5 msg = r"{0} move is not within a tolerance of {1}" np.testing.assert_allclose( self.cm.delta['lat'], actual['lat'], tol, tol, msg.format('ches_bay', tol), 0, ) np.testing.assert_allclose( self.cm.delta['long'], actual['long'], tol, tol, msg.format('ches_bay', tol), 0, ) #check that certain and uncertain are the same if uncertainty is time delayed #self.gcm.uncertain_time_delay = 3 self.gcm.uncertain_time_delay = 10800 # cython expects time_delay in seconds self.check_move_certain_uncertain(self.gcm.uncertain_time_delay)
def ug_data(): base_dir = os.path.dirname(__file__) filename = get_datafile(os.path.join(base_dir, 'sample_data', 'currents', 'ChesBay.nc')) return filename, nc.Dataset(filename)
def __init__(self): file_ = get_datafile(os.path.join(datadir, r"long_island_sound/CLISShio.txt")) self.shio = cy_shio_time.CyShioTime(file_) top_file = get_datafile(os.path.join(datadir, r"long_island_sound/tidesWAC.CUR")) yeardata_path = os.path.join(os.path.dirname(gnome.__file__), 'data/yeardata/') self.cats = cy_cats_mover.CyCatsMover() self.cats.set_shio(self.shio) self.cats.text_read(top_file) self.shio.set_shio_yeardata_path(yeardata_path) super(CatsMove, self).__init__() self.ref[:] = (-72.5, 41.17, 0) self.cats.prepare_for_model_run() self.cats.prepare_for_model_step(self.model_time, self.time_step, 1, self.spill_size)
def only_Winds(timeStep, start_time, duration, weatheringSteps, map, uncertain, data_path, curr_path, wind_path, map_path, reFloatHalfLife, windFile, currFile, tidalFile, num_elements, depths, lat, lon, output_path, wind_scale, save_nc, timestep_outputs, weatherers, td): print 'initializing the model:' model = Model(time_step=timeStep, start_time=start_time, duration=duration) print 'adding the map:' mapfile = get_datafile(os.path.join(data_path, map_path, map)) model.map = MapFromBNA(mapfile, refloat_halflife=reFloatHalfLife) print 'adding a renderer' model.outputters += Renderer(mapfile, output_path, size=(800, 600), output_timestep=timedelta(hours=timestep_outputs)) if save_nc: nc_outputter = NetCDFOutput(netcdf_file, which_data='most', output_timestep=timedelta(hours=timestep_outputs)) model.outputters += nc_outputter print 'adding a wind mover:' wind_file = get_datafile(os.path.join(data_path, wind_path, windFile)) wind = GridWindMover(wind_file) wind.wind_scale = wind_scale model.movers += wind print 'adding a spill' model.spills += point_line_release_spill(num_elements=num_elements, start_position=(lon, lat, 0), release_time=start_time, end_release_time=start_time + duration) return model
def test_move_tri(self): """ test move for a triangular grid (first time in file) """ time = datetime.datetime(2014, 6, 9, 0) self.cm.model_time = time_utils.date_to_sec(time) time_grid_file = get_datafile(os.path.join(cur_dir, 'PQBayCur.nc4')) topology_file = get_datafile(os.path.join(cur_dir, r'PassamaquoddyTOP.dat')) self.ccm.text_read(time_grid_file, topology_file) # self.ccm.export_topology(topology_file2) self.cm.ref[:]['long'] = -66.991344 # for Passamaquoddy self.cm.ref[:]['lat'] = 45.059316 self.check_move() actual = np.empty((self.cm.num_le, ), dtype=world_point) actual[:]['lat'] = .00020319 actual[:]['long'] = -.0001276599 tol = 1e-5 msg = r"{0} move is not within a tolerance of {1}" np.testing.assert_allclose( self.cm.delta['lat'], actual['lat'], tol, tol, msg.format('PQBayCur.nc4', tol), 0, ) np.testing.assert_allclose( self.cm.delta['long'], actual['long'], tol, tol, msg.format('PQBayCur.nc4', tol), 0, )
def test_move_curv(self): """ test move for a curvilinear grid (first time in file) """ time = datetime.datetime(2008, 1, 29, 17) self.cm.model_time = time_utils.date_to_sec(time) time_grid_file = get_datafile(os.path.join(cur_dir, 'ny_cg.nc')) topology_file = get_datafile(os.path.join(cur_dir, r'NYTopology.dat')) self.gcm.text_read(time_grid_file, topology_file) # self.gcm.export_topology(topology_file2) self.cm.ref[:]['long'] = -74.03988 # for NY self.cm.ref[:]['lat'] = 40.536092 self.check_move() actual = np.empty((self.cm.num_le, ), dtype=world_point) actual[:]['lat'] = .000911 actual[:]['long'] = -.001288 tol = 1e-5 msg = r"{0} move is not within a tolerance of {1}" np.testing.assert_allclose( self.cm.delta['lat'], actual['lat'], tol, tol, msg.format('ny_cg.nc', tol), 0, ) np.testing.assert_allclose( self.cm.delta['long'], actual['long'], tol, tol, msg.format('ny_cg.nc', tol), 0, )
def make_models(): print 'initializing the model' # start_time = datetime(2015, 12, 18, 06, 01) # 1 day of data in file # 1/2 hr in seconds models = [] start_time = datetime(2012, 10, 27, 0, 30) duration_hrs=23 time_step=450 num_steps = duration_hrs * 3600 / time_step names = [ 'Euler', 'Trapezoid', 'RK4', ] mapfile = get_datafile(os.path.join(base_dir, 'long_beach.bna')) print 'gen map' map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds fn = ('00_dir_roms_display.ncml.nc4') curr = GridCurrent.from_netCDF(filename=fn) models = [] for method in names: mod = Model(start_time=start_time, duration=timedelta(hours=duration_hrs), time_step=time_step) mod.map = map spill = point_line_release_spill(num_elements=1000, start_position=(-74.1, 39.7525, 0.0), release_time=start_time) mod.spills += spill mod.movers += RandomMover(diffusion_coef=100) mod.movers += PyGridCurrentMover(current=curr, default_num_method=method) images_dir = method + '-' + str(time_step / 60) + 'min-' + str(num_steps) + 'steps' renderer = Renderer(mapfile, images_dir, image_size=(1024, 768)) renderer.delay = 25 # renderer.add_grid(curr.grid) mod.outputters += renderer netCDF_fn = os.path.join(base_dir, images_dir + '.nc') mod.outputters += NetCDFOutput(netCDF_fn, which_data='all') models.append(mod) print 'returning models' return models
def test_grid_map_cats(self): """ Test a grid map - read and write out """ # triangle grid gcm3 = CyGridMap() grid_map_file = get_datafile(os.path.join(cur_dir, "BigCombinedwMap.cur")) gcm3.text_read(grid_map_file) topology_file = os.path.join(cur_dir, "BigCombinedTop.dat") gcm3.export_topology(topology_file)
def make_model(base_dir='.'): #,images_dir=os.path.join(base_dir, 'images',gdat_dir='/data/dylan/ArcticTAP/data_gnome/ROMS_h2ouv/')): print 'initializing the model' print base_dir start_time = datetime(1985, 1, 1, 13, 31) # start with generic times...this will be changed when model is run model = Model(start_time=start_time, time_step=setup.time_step) mapfile = get_datafile(os.path.join(base_dir, setup.MapFileName)) print mapfile print 'adding the map' model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds return model
def test_ucode_char_in_grid_mover_filename(mover_test): # on windows file1_ = get_datafile(os.path.join(datadir, mover_test[1])) ufile1 = create_ucode_file(file1_) # invalid unicode for windows invalid_ufile1 = create_ucode_file(file1_, valid=False) if mover_test[2] is None: file2_ = None ufile2 = None invalid_ufile2 = None else: file2_ = get_datafile(os.path.join(datadir, mover_test[2])) ufile2 = create_ucode_file(file2_) # invalid unicode for windows invalid_ufile2 = create_ucode_file(file2_, valid=False) mover_test[0](file1_, file2_) # valid unicode names should work for both systems mover_test[0](ufile1, ufile2) if sys.platform == 'win32': with pytest.raises(UnicodeEncodeError): mover_test[0](invalid_ufile1, invalid_ufile2) elif sys.platform == 'darwin': # todo: also need a test case for linux2 mover_test[0](invalid_ufile1, invalid_ufile2) print '{0}({1},{2}) passed the test'.format(mover_test[0], mover_test[1], mover_test[2]) assert True
def make_modelF(timeStep, start_time, duration, weatheringSteps, map, uncertain, data_path, curr_path, wind_path, map_path, reFloatHalfLife, windFile, currFile, num_elements, depths, lat, lon, output_path, wind_scale, save_nc, timestep_outputs, weatherers, td, dif_coef,temp_water): print 'initializing the model:' model = Model(time_step=timeStep, start_time=start_time, duration=duration, uncertain=uncertain) print 'adding the map:' mapfile = get_datafile(os.path.join(data_path, map_path, map)) model.map = MapFromBNA(mapfile, refloat_halflife=reFloatHalfLife) print 'adding a renderer' if save_nc: scripting.remove_netcdf(output_path+'/'+'output.nc') nc_outputter = NetCDFOutput(output_path+'/'+'output.nc', which_data='standard', output_timestep=timedelta(hours=timestep_outputs)) model.outputters += nc_outputter print 'adding a wind mover:' wind_file = get_datafile(os.path.join(data_path, wind_path, windFile)) wind = GridWindMover(wind_file) # wind.wind_scale = wind_scale model.movers += wind print 'adding a current mover:' curr_file = get_datafile(os.path.join(data_path, curr_path, currFile)) model.movers += GridCurrentMover(curr_file, num_method='RK4') if td: random_mover = RandomMover(diffusion_coef=dif_coef) model.movers += random_mover print 'adding spill' model.spills += point_line_release_spill(num_elements=num_elements, start_position=(lon, lat, 0), release_time=start_time, end_release_time=start_time + duration)#, substance='AD04001', amount=9600000, units='kg') if weatherers: print 'adding weatherers' water = Water(temp_water) wind = constant_wind(0.0001, 0, 'knots') waves = Waves(wind, water) model.weatherers += Evaporation(water, wind) # model.weatherers += Emulsification(waves) model.weatherers += NaturalDispersion(waves, water) return model
def make_model(base_dir='.'): #,images_dir=os.path.join(base_dir, 'images',gdat_dir='/data/dylan/ArcticTAP/data_gnome/ROMS_h2ouv/')): print 'initializing the model' print base_dir start_time = datetime(1985, 1, 1, 13, 31) # start with generic times...this will be changed when model is run model = Model(start_time=start_time, duration=timedelta(hours=96), time_step=120*60) mapfile = get_datafile(os.path.join(base_dir, 'arctic_coast3.bna')) print mapfile print 'adding the map' model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds return model
def test_ucode_char_in_filename(test_case): # on windows file_ = get_datafile(os.path.join(datadir, test_case[1])) # first check that it works with file without adding special character to filename test_case[0](filename=file_) ufile = create_ucode_file(file_) test_case[0](filename=ufile) # This should read valid unicode filenames invalid_ufile = create_ucode_file(file_, False) if sys.platform == 'win32': with pytest.raises(UnicodeEncodeError): test_case[0](filename=invalid_ufile) elif sys.platform == 'darwin': test_case[0](filename=invalid_ufile) print '{0}({1}) passed the test'.format(test_case[0], test_case[1]) assert True
def get_testdata(): ''' define all the testdata files here most of these are used in multiple modules. Some are not, but let's just define them all in one place, ie here. ''' s_data = os.path.join(base_dir, 'sample_data') lis = os.path.join(s_data, 'long_island_sound') bos = os.path.join(s_data, 'boston_data') dbay = os.path.join(s_data, 'delaware_bay') curr_dir = os.path.join(s_data, 'currents') tide_dir = os.path.join(s_data, 'tides') wind_dir = os.path.join(s_data, 'winds') testmap = os.path.join(base_dir, '../sample_data', 'MapBounds_Island.bna') bna_sample = os.path.join(s_data, 'MapBounds_2Spillable2Islands2Lakes.bna') data = dict() data['CatsMover'] = \ {'curr': get_datafile(os.path.join(lis, 'tidesWAC.CUR')), 'tide': get_datafile(os.path.join(lis, 'CLISShio.txt'))} data['ComponentMover'] = \ {'curr': get_datafile(os.path.join(dbay, 'NW30ktwinds.cur')), 'curr2': get_datafile(os.path.join(dbay, 'SW30ktwinds.cur')), 'wind': get_datafile(os.path.join(dbay, 'ConstantWind.WND'))} data['CurrentCycleMover'] = \ {'curr': get_datafile(os.path.join(curr_dir, 'PQBayCur.nc4')), 'top': get_datafile(os.path.join(curr_dir, 'PassamaquoddyTOP.dat')), 'tide': get_datafile(os.path.join(tide_dir, 'EstesHead.txt')), 'curr_bad_file': get_datafile(os.path.join(curr_dir, 'BigCombinedwMapBad.cur'))} data['GridCurrentMover'] = \ {'curr_tri': get_datafile(os.path.join(curr_dir, 'ChesBay.nc')), 'top_tri': get_datafile(os.path.join(curr_dir, 'ChesBay.dat')), 'curr_reg': get_datafile(os.path.join(curr_dir, 'test.cdf')), 'curr_curv': get_datafile(os.path.join(curr_dir, 'ny_cg.nc')), 'top_curv': get_datafile(os.path.join(curr_dir, 'NYTopology.dat')), 'ice_curr_curv': get_datafile(os.path.join(curr_dir, 'acnfs_example.nc')), 'ice_top_curv': get_datafile(os.path.join(curr_dir, 'acnfs_topo.dat')), 'ptCur': get_datafile(os.path.join(curr_dir, 'ptCurNoMap.cur')), 'grid_ts': get_datafile(os.path.join(curr_dir, 'gridcur_ts.cur')), 'series_gridCur': get_datafile(os.path.join(curr_dir, 'gridcur_ts_hdr2.cur')), 'series_curv': get_datafile(os.path.join(curr_dir, 'file_series', 'flist2.txt')), 'series_top': get_datafile(os.path.join(curr_dir, 'file_series', 'HiROMSTopology.dat'))} data['IceMover'] = \ {'ice_curr_curv': get_datafile(os.path.join(curr_dir, 'acnfs_example.nc')), 'ice_top_curv': get_datafile(os.path.join(curr_dir, 'acnfs_topo.dat'))} # get netcdf stored in fileseries flist2.txt, gridcur_ts_hdr2 get_datafile(os.path.join(curr_dir, 'file_series', 'hiog_file1.nc')) get_datafile(os.path.join(curr_dir, 'file_series', 'hiog_file2.nc')) get_datafile(os.path.join(curr_dir, 'gridcur_tsA.cur')) get_datafile(os.path.join(curr_dir, 'gridcur_tsB.cur')) data['GridWindMover'] = \ {'wind_curv': get_datafile(os.path.join(wind_dir, 'WindSpeedDirSubset.nc')), 'top_curv': get_datafile(os.path.join(wind_dir, 'WindSpeedDirSubsetTop.dat')), 'wind_rect': get_datafile(os.path.join(wind_dir, 'test_wind.cdf')), 'grid_ts': get_datafile(os.path.join(wind_dir, 'gridwind_ts.wnd'))} data['MapFromBNA'] = {'testmap': testmap} data['Renderer'] = {'bna_sample': bna_sample, 'bna_star': os.path.join(s_data, 'Star.bna')} data['GridMap'] = \ {'curr': get_datafile(os.path.join(curr_dir, 'ny_cg.nc')), 'BigCombinedwMap': get_datafile(os.path.join(curr_dir, 'BigCombinedwMap.cur')), } # following are not on server, they are part of git repo so just set the # path correctly data['timeseries'] = \ {'wind_ts': os.path.join(s_data, 'WindDataFromGnome.WND'), 'wind_ts_av': os.path.join(s_data, 'WindDataFromGnomeAv.WND'), 'wind_constant': os.path.join(s_data, 'WindDataFromGnomeConstantWind.WND'), 'wind_bad_units': os.path.join(s_data, 'WindDataFromGnome_BadUnits.WND'), 'wind_cardinal': os.path.join(s_data, 'WindDataFromGnomeCardinal.WND'), 'wind_kph': os.path.join(s_data, 'WindDataFromGnomeKPH.WND'), 'tide_shio': get_datafile(os.path.join(tide_dir, 'CLISShio.txt')), 'tide_ossm': get_datafile(os.path.join(tide_dir, 'TideHdr.FINAL')) } # data for boston model - used for testing save files/webapi data['boston_data'] = \ {'map': get_datafile(os.path.join(bos, 'MassBayMap.bna')), 'cats_curr1': get_datafile(os.path.join(bos, 'EbbTides.cur')), 'cats_shio': get_datafile(os.path.join(bos, 'EbbTidesShio.txt')), 'cats_curr2': get_datafile(os.path.join(bos, 'MerrimackMassCoast.cur')), 'cats_ossm': get_datafile(os.path.join(bos, 'MerrimackMassCoastOSSM.txt')), 'cats_curr3': get_datafile(os.path.join(bos, 'MassBaySewage.cur')), 'component_curr1': get_datafile(os.path.join(bos, "WAC10msNW.cur")), 'component_curr2': get_datafile(os.path.join(bos, "WAC10msSW.cur")) } data['nc'] = {'nc_output': get_datafile(os.path.join(s_data, 'nc', 'test_output.nc'))} data['lis'] = \ {'map': get_datafile(os.path.join(lis, 'LongIslandSoundMap.BNA')), 'cats_curr': get_datafile(os.path.join(lis, r"LI_tidesWAC.CUR")), 'cats_tide': get_datafile(os.path.join(lis, r"CLISShio.txt")) } return data
def make_model(images_dir=os.path.join(base_dir, 'images')): # create the maps: print 'creating the maps' mapfile = get_datafile(os.path.join(base_dir, './MassBayMap.bna')) gnome_map = MapFromBNA( mapfile, refloat_halflife=1, # hours raster_size=2048 * 2048 # about 4 MB ) renderer = Renderer( mapfile, images_dir, image_size=(800, 800), ) print 'initializing the model' start_time = datetime(2016, 3, 9, 15) # 1 hour in seconds # Default to now, rounded to the nearest hour model = Model(time_step=3600, start_time=start_time, duration=timedelta(days=6), map=gnome_map, uncertain=True) print 'adding outputters' model.outputters += renderer # netcdf_file = os.path.join(base_dir, 'script_boston.nc') # scripting.remove_netcdf(netcdf_file) # model.outputters += NetCDFOutput(netcdf_file, which_data='all') # model.outputters += KMZOutput(os.path.join(base_dir, 'script_boston.kmz')) print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=100000) print 'adding a wind mover:' series = np.zeros((2, ), dtype=datetime_value_2d) series[0] = (start_time, (5, 180)) series[1] = (start_time + timedelta(hours=18), (5, 180)) w = Wind(filename=os.path.join(base_dir, '22NM_WNW_PortAngelesWA.nws')) w_mover = WindMover(w) model.movers += w_mover model.environment += w_mover.wind # print 'adding a cats shio mover:' # curr_file = get_datafile(os.path.join(base_dir, r"./EbbTides.cur")) # tide_file = get_datafile(os.path.join(base_dir, r"./EbbTidesShio.txt")) # c_mover = CatsMover(curr_file, tide=Tide(tide_file)) # # this is the value in the file (default) # c_mover.scale_refpoint = (-70.8875, 42.321333) # c_mover.scale = True # c_mover.scale_value = -1 # model.movers += c_mover # # TODO: cannot add this till environment base class is created # model.environment += c_mover.tide print 'adding a spill' end_time = start_time + timedelta(hours=12) spill = point_line_release_spill(num_elements=100, start_position=(-70.911432, 42.369142, 0.0), release_time=start_time, end_release_time=end_time) model.spills += spill return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2015, 9, 24, 1, 1) # start_time = datetime(2015, 12, 18, 06, 01) # 1 day of data in file # 1/2 hr in seconds model = Model(start_time=start_time, duration=timedelta(hours=47), time_step=300) mapfile = get_datafile(os.path.join(base_dir, 'columbia_river.bna')) print 'adding the map' model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds # draw_ontop can be 'uncertain' or 'forecast' # 'forecast' LEs are in black, and 'uncertain' are in red # default is 'forecast' LEs draw on top renderer = Renderer(mapfile, images_dir, image_size=(600, 1200)) renderer.delay = 15 # renderer.viewport = ((-123.35, 45.6), (-122.68, 46.13)) # renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0)) print 'adding outputters' model.outputters += renderer print 'adding a spill' # for now subsurface spill stays on initial layer # - will need diffusion and rise velocity # - wind doesn't act # - start_position = (-76.126872, 37.680952, 5.0), spill1 = continuous_release_spill(initial_elements=10000, num_elements=400, start_position=(-122.625, 45.609, 0.0), release_time=start_time, end_position=(-122.6, 45.605, 0.0), end_release_time=start_time + timedelta(seconds=36000)) model.spills += spill1 print 'adding a RandomMover:' # model.movers += RandomMover(diffusion_coef=10000) print 'adding a wind mover:' series = [] for i in [(1, (5, 90)), (7, (5, 180)), (13, (5, 270)), (19, (5, 0)), (25, (5, 90))]: series.append((start_time + timedelta(hours=i[0]), i[1])) wind1 = WindTS.constant_wind('wind1', 0.5, 0, 'm/s') wind2 = WindTS(timeseries=series, units='knots', extrapolate=True) # wind = Wind(timeseries=series, units='knots') model.movers += PyWindMover(wind=wind1) print 'adding a current mover:' # url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml') # test = GridCurrent.from_netCDF(name='gc1', filename=url) curr_file = get_datafile('COOPSu_CREOFS24.nc') curr = GridCurrent.from_netCDF( name='gc2', filename=curr_file, ) c_mover = PyGridCurrentMover(curr, extrapolate=True, default_num_method='Trapezoid') # renderer.add_grid(curr.grid) # renderer.add_vec_prop(curr) model.movers += c_mover print 'adding a random mover' model.movers += RandomMover(diffusion_coef=1000) # curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc')) # c_mover = GridCurrentMover(curr_file) # model.movers += c_mover return model
def make_model(images_dir=os.path.join(base_dir, 'images')): # create the maps: print 'creating the maps' mapfile = get_datafile(os.path.join(base_dir, './MassBayMap.bna')) gnome_map = MapFromBNA(mapfile, refloat_halflife=1) # hours renderer = Renderer(mapfile, images_dir, size=(800, 800), projection_class=GeoProjection) print 'initializing the model' start_time = datetime(2013, 3, 12, 10, 0) # 15 minutes in seconds # Default to now, rounded to the nearest hour model = Model(time_step=900, start_time=start_time, duration=timedelta(days=1), map=gnome_map, uncertain=False) print 'adding outputters' model.outputters += renderer netcdf_file = os.path.join(base_dir, 'script_boston.nc') scripting.remove_netcdf(netcdf_file) model.outputters += NetCDFOutput(netcdf_file, which_data='all') print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=100000) print 'adding a wind mover:' series = np.zeros((2, ), dtype=datetime_value_2d) series[0] = (start_time, (5, 180)) series[1] = (start_time + timedelta(hours=18), (5, 180)) w_mover = WindMover(Wind(timeseries=series, units='m/s')) model.movers += w_mover model.environment += w_mover.wind print 'adding a cats shio mover:' curr_file = get_datafile(os.path.join(base_dir, r"./EbbTides.cur")) tide_file = get_datafile(os.path.join(base_dir, r"./EbbTidesShio.txt")) c_mover = CatsMover(curr_file, tide=Tide(tide_file)) # this is the value in the file (default) c_mover.scale_refpoint = (-70.8875, 42.321333) c_mover.scale = True c_mover.scale_value = -1 model.movers += c_mover # TODO: cannot add this till environment base class is created model.environment += c_mover.tide print 'adding a cats ossm mover:' # ossm_file = get_datafile(os.path.join(base_dir, # r"./MerrimackMassCoastOSSM.txt")) curr_file = get_datafile( os.path.join(base_dir, r"./MerrimackMassCoast.cur")) tide_file = get_datafile( os.path.join(base_dir, r"./MerrimackMassCoastOSSM.txt")) c_mover = CatsMover(curr_file, tide=Tide(tide_file)) # but do need to scale (based on river stage) c_mover.scale = True c_mover.scale_refpoint = (-70.65, 42.58333) c_mover.scale_value = 1. model.movers += c_mover model.environment += c_mover.tide print 'adding a cats mover:' curr_file = get_datafile(os.path.join(base_dir, r"MassBaySewage.cur")) c_mover = CatsMover(curr_file) # but do need to scale (based on river stage) c_mover.scale = True c_mover.scale_refpoint = (-70.78333, 42.39333) # the scale factor is 0 if user inputs no sewage outfall effects c_mover.scale_value = .04 model.movers += c_mover # pat1Angle 315; # pat1Speed 19.44; pat1SpeedUnits knots; # pat1ScaleToValue 0.138855 # # pat2Angle 225; # pat2Speed 19.44; pat2SpeedUnits knots; # pat2ScaleToValue 0.05121 # # scaleBy WindStress print "adding a component mover:" component_file1 = get_datafile(os.path.join(base_dir, r"./WAC10msNW.cur")) component_file2 = get_datafile(os.path.join(base_dir, r"./WAC10msSW.cur")) comp_mover = ComponentMover(component_file1, component_file2, w_mover.wind) # todo: callback did not work correctly below - fix! # comp_mover = ComponentMover(component_file1, # component_file2, # Wind(timeseries=series, units='m/s')) comp_mover.scale_refpoint = (-70.855, 42.275) comp_mover.pat1_angle = 315 comp_mover.pat1_speed = 19.44 comp_mover.pat1_speed_units = 1 comp_mover.pat1ScaleToValue = .138855 comp_mover.pat2_angle = 225 comp_mover.pat2_speed = 19.44 comp_mover.pat2_speed_units = 1 comp_mover.pat2ScaleToValue = .05121 model.movers += comp_mover print 'adding a spill' end_time = start_time + timedelta(hours=12) spill = point_line_release_spill(num_elements=1000, start_position=(-70.911432, 42.369142, 0.0), release_time=start_time, end_release_time=end_time) model.spills += spill return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2012, 10, 25, 0, 1) # start_time = datetime(2015, 12, 18, 06, 01) # 1 day of data in file # 1/2 hr in seconds model = Model(start_time=start_time, duration=timedelta(hours=24), time_step=900) mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna')) print 'adding the map' '''TODO: sort out MapFromBna's map_bounds parameter... it does nothing right now, and the spill is out of bounds''' model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds # draw_ontop can be 'uncertain' or 'forecast' # 'forecast' LEs are in black, and 'uncertain' are in red # default is 'forecast' LEs draw on top renderer = Renderer(mapfile, images_dir, image_size=(1024, 768)) # renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75)) # renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0)) print 'adding outputters' model.outputters += renderer print 'adding a spill' # for now subsurface spill stays on initial layer # - will need diffusion and rise velocity # - wind doesn't act # - start_position = (-76.126872, 37.680952, 5.0), spill1 = point_line_release_spill(num_elements=1000, start_position=(-74.15, 40.5, 0.0), release_time=start_time) model.spills += spill1 print 'adding a RandomMover:' # model.movers += RandomMover(diffusion_coef=50000) print 'adding a wind mover:' series = [] for i in [(1, (5, 90)), (7, (5, 180)), (13, (5, 270)), (19, (5, 0)), (25, (5, 90))]: series.append((start_time + timedelta(hours=i[0]), i[1])) wind1 = WindTS.constant_wind('wind1', 5, 270, 'knots') wind2 = WindTS(timeseries=series, units='knots', extrapolate=True) wind = Wind(timeseries=series, units='knots') model.movers += PyWindMover(wind=wind2) # model.movers += WindMover(wind) # print 'adding a current mover:' # # url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml') # # cf = roms_field('nos.tbofs.fields.n000.20160406.t00z_sgrid.nc') # cf = roms_field(url) # cf.set_appearance(on=True) # renderer.grids += [cf] # renderer.delay = 25 # u_mover = UGridCurrentMover(cf) # model.movers += u_mover # curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc')) # c_mover = GridCurrentMover(curr_file) # model.movers += c_mover return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(1985, 1, 1, 13, 31) # 1 day of data in file # 1/2 hr in seconds model = Model(start_time=start_time, duration=timedelta(days=4), time_step=7200) # mapfile = get_datafile(os.path.join(base_dir, 'ak_arctic.bna')) mapfile = get_datafile('arctic_coast3.bna') print 'adding the map' model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds print 'adding a spill' # for now subsurface spill stays on initial layer # - will need diffusion and rise velocity # - wind doesn't act # - start_position = (-76.126872, 37.680952, 5.0), # spill1 = point_line_release_spill(num_elements=10000, # start_position=(-163.75, # 69.75, # 0.0), # release_time=start_time) # spill1 = point_line_release_spill(num_elements=50000, start_position=(196.25, 69.75, 0.0), release_time=start_time) model.spills += spill1 # model.spills += spill2 print 'adding a wind mover:' # model.movers += constant_wind_mover(0.5, 0, units='m/s') print 'adding a current mover:' fn = ['arctic_avg2_0001_gnome.nc', 'arctic_avg2_0002_gnome.nc'] # fn = ['C:\\Users\\jay.hennen\\Documents\\Code\\pygnome\\py_gnome\\scripts\\script_TAP\\arctic_avg2_0001_gnome.nc', # 'C:\\Users\\jay.hennen\\Documents\\Code\\pygnome\\py_gnome\\scripts\\script_TAP\\arctic_avg2_0002_gnome.nc'] gt = {'node_lon': 'lon', 'node_lat': 'lat'} # fn='arctic_avg2_0001_gnome.nc' wind_method = 'Euler' method = 'RK2' print 'adding outputters' # draw_ontop can be 'uncertain' or 'forecast' # 'forecast' LEs are in black, and 'uncertain' are in red # default is 'forecast' LEs draw on top renderer = Renderer(mapfile, images_dir, image_size=(1024, 768)) model.outputters += renderer netcdf_file = os.path.join(base_dir, str(model.time_step / 60) + method + '.nc') scripting.remove_netcdf(netcdf_file) print 'adding movers' model.outputters += NetCDFOutput(netcdf_file, which_data='all') print 'loading entire current data' ice_aware_curr = IceAwareCurrent.from_netCDF(filename=fn, grid_topology=gt) # env1 = get_env_from_netCDF(filename) # mov = PyCurrentMover.from_netCDF(filename) ice_aware_curr.ice_velocity.variables[0].dimension_ordering = [ 'time', 'x', 'y' ] ice_aware_wind = IceAwareWind.from_netCDF( filename=fn, ice_velocity=ice_aware_curr.ice_velocity, ice_concentration=ice_aware_curr.ice_concentration, grid=ice_aware_curr.grid) curr = GridCurrent.from_netCDF(filename=fn) # GridCurrent.is_gridded() # import pprint as pp # from gnome.utilities.orderedcollection import OrderedCollection # model.environment = OrderedCollection(dtype=Environment) # model.environment.add(ice_aware_curr) # from gnome.environment import WindTS print 'loading entire wind data' # i_c_mover = PyCurrentMover(current=ice_aware_curr) # i_c_mover = PyCurrentMover(current=ice_aware_curr, default_num_method='Euler') i_c_mover = PyCurrentMover(current=ice_aware_curr, default_num_method=method, extrapolate=True) i_w_mover = PyWindMover(wind=ice_aware_wind, default_num_method=wind_method) # ice_aware_curr.grid.node_lon = ice_aware_curr.grid.node_lon[:]-360 # ice_aware_curr.grid.build_celltree() model.movers += i_c_mover model.movers += i_w_mover print 'adding an IceAwareRandomMover:' model.movers += IceAwareRandomMover( ice_concentration=ice_aware_curr.ice_concentration, diffusion_coef=1000) # renderer.add_grid(ice_aware_curr.grid) # renderer.add_vec_prop(ice_aware_curr) # curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc')) # c_mover = GridCurrentMover(curr_file) # model.movers += c_mover # model.environment.add(WindTS.constant(10, 300)) # print('Saving') # model.environment[0].ice_velocity.variables[0].serialize() # IceVelocity.deserialize(model.environment[0].ice_velocity.serialize()) # model.save('.') # from gnome.persist.save_load import load # print('Loading') # model2 = load('./Model.zip') return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2014, 6, 9, 0, 0) mapfile = get_datafile(os.path.join(base_dir, 'PassamaquoddyMap.bna')) gnome_map = MapFromBNA(mapfile, refloat_halflife=1) # hours # # the image output renderer # global renderer # one hour timestep model = Model(start_time=start_time, duration=timedelta(hours=24), time_step=360, map=gnome_map, uncertain=False, cache_enabled=True) print 'adding outputters' renderer = Renderer(mapfile, images_dir, size=(800, 600), # output_timestep=timedelta(hours=1), draw_ontop='uncertain') renderer.viewport = ((-67.15, 45.), (-66.9, 45.2)) model.outputters += renderer netcdf_file = os.path.join(base_dir, 'script_passamaquoddy.nc') scripting.remove_netcdf(netcdf_file) model.outputters += NetCDFOutput(netcdf_file, which_data='all') print 'adding a spill' spill = point_line_release_spill(num_elements=1000, start_position=(-66.991344, 45.059316, 0.0), release_time=start_time) model.spills += spill print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=30000, uncertain_factor=2) print 'adding a wind mover:' series = np.zeros((5, ), dtype=datetime_value_2d) series[0] = (start_time, (5, 90)) series[1] = (start_time + timedelta(hours=18), (5, 180)) series[2] = (start_time + timedelta(hours=30), (5, 135)) series[3] = (start_time + timedelta(hours=42), (5, 180)) series[4] = (start_time + timedelta(hours=54), (5, 225)) wind = Wind(timeseries=series, units='m/s') model.movers += WindMover(wind) print 'adding a current mover:' curr_file = get_datafile(os.path.join(base_dir, 'PQBayCur.nc4')) topology_file = get_datafile(os.path.join(base_dir, 'PassamaquoddyTOP.dat') ) tide_file = get_datafile(os.path.join(base_dir, 'EstesHead.txt')) cc_mover = CurrentCycleMover(curr_file, topology_file, tide=Tide(tide_file)) model.movers += cc_mover model.environment += cc_mover.tide print 'viewport is:', [o.viewport for o in model.outputters if isinstance(o, Renderer)] return model
def main(RootDir, Data_Dir, StartSite, RunSite, NumStarts, RunStarts, ReleaseLength, TrajectoryRunLength, StartTimeFiles, TrajectoriesPath, NumLEs, MapFileName, refloat, current_files, wind_files, diffusion_coef, model_timestep, windage_range, windage_persist, OutputTimestep): timingRecord = open(os.path.join(RootDir, "timing.txt"), "w") count = len(StartTimeFiles) * len(RunStarts) timingRecord.write("This file tracks the time to process " + str(count) + " gnome runs") # model timing release_duration = timedelta(hours=ReleaseLength) run_time = timedelta(hours=TrajectoryRunLength) # initiate model model = Model(duration=run_time, time_step=model_timestep, uncertain=False) # determine boundary for model print "Adding the map:", MapFileName mapfile = get_datafile(os.path.join(Data_Dir, MapFileName)) # model.map = MapFromBNA(mapfile, refloat_halflife=refloat) no, model map needs to inclde mudflats. later # loop through seasons for Season in StartTimeFiles: timer1 = datetime.now() SeasonName = Season[1] start_times = open(Season[0], 'r').readlines()[:NumStarts] SeasonTrajDir = os.path.join(RootDir, TrajectoriesPath, SeasonName) if not os.path.isdir(SeasonTrajDir): print "Creating directory: ", SeasonTrajDir make_dir(SeasonTrajDir) print " Season:", SeasonName # get and parse start times in this season start_dt = [] for start_time in start_times: start_time = [int(i) for i in start_time.split(',')] start_time = datetime(start_time[0], start_time[1], start_time[2], start_time[3], start_time[4]) start_dt.append(start_time) ## loop through start times for time_idx in RunStarts: timer2 = datetime.now() gc.collect() model.movers.clear() ## set the start location start_time = start_dt[time_idx] end_time = start_time + run_time model.start_time = start_time print " ", start_time, "to", end_time ## get a list of the only data files needed for the start time (less data used) ## note: requires data files in year increments #Todo: needs fixing before real run years = range(start_time.year, end_time.year + 1) years = [str(i) for i in years] wind = [s for s in wind_files if any(xs in s for xs in years)] current = [ s for s in current_files if any(xs in s for xs in years) ] #Todo: add mudflats. Does it work like this? topology = {'node_lon': 'x', 'node_lat': 'y'} ## add wind movers w_mover = PyWindMover(filename=wind) model.movers += w_mover ## add current movers current_mover = gs.GridCurrent.from_netCDF(current, grid_topology=topology) c_mover = PyCurrentMover(current=current_mover) model.movers += c_mover tideflat = Matroos_Mudflats(current, grid_topology=topology) land_map = gs.MapFromBNA(mapfile) model.map = TideflatMap(land_map, tideflat) ## add diffusion model.movers += RandomMover(diffusion_coef=diffusion_coef) ## loop through start locations timer3 = datetime.now() #Todo: can it deal with the test.location.txt file?? start_position = [float(i) for i in StartSite.split(',')] OutDir = os.path.join(RootDir, TrajectoriesPath, SeasonName, 'pos_%03i' % (RunSite + 1)) make_dir(OutDir) print " ", RunSite, time_idx print " Running: start time:", start_time, print "at start location:", start_position ## set the spill to the location spill = surface_point_line_spill( num_elements=NumLEs, start_position=(start_position[0], start_position[1], 0.0), release_time=start_time, end_release_time=start_time + release_duration, windage_range=windage_range, windage_persist=windage_persist) # print "adding netcdf output" netcdf_output_file = os.path.join( OutDir, 'pos_%03i-t%03i_%08i.nc' % (RunSite + 1, time_idx, int(start_time.strftime('%y%m%d%H'))), ) model.outputters.clear() model.outputters += NetCDFOutput( netcdf_output_file, output_timestep=timedelta(hours=OutputTimestep)) model.spills.clear() model.spills += spill model.full_run(rewind=True) timer4 = datetime.now() diff = round((timer4 - timer3).total_seconds() / 60, 2) timingRecord.write("\t\t" + str(RunSite) + " took " + str(diff) + " minutes to complete") diff = round((timer4 - timer1).total_seconds() / 3600, 2) count = len(RunStarts) timingRecord.write("\t" + str(SeasonName) + " took " + str(diff) + " hours to finish " + str(count) + " Gnome runs") #OutDir.close timingRecord.close
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2012, 9, 15, 12, 0) mapfile = get_datafile(os.path.join(base_dir, './LongIslandSoundMap.BNA')) gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours # # the image output renderer # global renderer # one hour timestep model = Model(start_time=start_time, duration=timedelta(hours=48), time_step=3600, map=gnome_map, uncertain=False, cache_enabled=False) print 'adding a spill' et = floating_weathering(substance='FUEL OIL NO.6') spill = point_line_release_spill(num_elements=1000, start_position=(-72.419992, 41.202120, 0.0), release_time=start_time, amount=1000, units='kg', element_type=et) spill.amount_uncertainty_scale = 1.0 model.spills += spill print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=500000, uncertain_factor=2) print 'adding a wind mover:' series = np.zeros((5, ), dtype=datetime_value_2d) series[0] = (start_time, (10, 45)) series[1] = (start_time + timedelta(hours=18), (10, 90)) series[2] = (start_time + timedelta(hours=30), (10, 135)) series[3] = (start_time + timedelta(hours=42), (10, 180)) series[4] = (start_time + timedelta(hours=54), (10, 225)) wind = Wind(timeseries=series, units='m/s', speed_uncertainty_scale=0.5) model.movers += WindMover(wind) print 'adding a cats mover:' curr_file = get_datafile(os.path.join(base_dir, r"./LI_tidesWAC.CUR")) tide_file = get_datafile(os.path.join(base_dir, r"./CLISShio.txt")) c_mover = CatsMover(curr_file, tide=Tide(tide_file)) model.movers += c_mover model.environment += c_mover.tide print 'adding Weatherers' water_env = Water(311.15) model.environment += water_env model.weatherers += [Evaporation(water_env, wind), Dispersion(), Burn(), Skimmer()] print 'adding outputters' model.outputters += WeatheringOutput() return model
def make_model(images_dir=os.path.join(base_dir, 'images')): # create the maps: print 'creating the maps' mapfile = get_datafile(os.path.join(base_dir, 'DelawareRiverMap.bna')) gnome_map = MapFromBNA(mapfile, refloat_halflife=1) # hours renderer = Renderer(mapfile, images_dir, image_size=(800, 800), projection_class=GeoProjection) print 'initializing the model' start_time = datetime(2012, 8, 20, 13, 0) # 15 minutes in seconds # Default to now, rounded to the nearest hour model = Model(time_step=900, start_time=start_time, duration=timedelta(days=1), map=gnome_map, uncertain=False) print 'adding outputters' model.outputters += renderer netcdf_file = os.path.join(base_dir, 'script_delaware_bay.nc') scripting.remove_netcdf(netcdf_file) model.outputters += NetCDFOutput(netcdf_file, which_data='all') print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=100000) print 'adding a wind mover:' # wind_file = get_datafile(os.path.join(base_dir, 'ConstantWind.WND')) # wind = Wind(filename=wind_file) series = np.zeros((2, ), dtype=datetime_value_2d) series[0] = (start_time, (5, 270)) series[1] = (start_time + timedelta(hours=25), (5, 270)) wind = Wind(timeseries=series, units='m/s') # w_mover = WindMover(Wind(timeseries=series, units='knots')) w_mover = WindMover(wind) model.movers += w_mover print 'adding a cats shio mover:' curr_file = get_datafile(os.path.join(base_dir, 'FloodTides.cur')) tide_file = get_datafile(os.path.join(base_dir, 'FloodTidesShio.txt')) c_mover = CatsMover(curr_file, tide=Tide(tide_file)) # this is the value in the file (default) c_mover.scale_refpoint = (-75.081667, 38.7995) c_mover.scale = True c_mover.scale_value = 1 model.movers += c_mover # TODO: cannot add this till environment base class is created model.environment += c_mover.tide print 'adding a cats mover:' curr_file = get_datafile(os.path.join(base_dir, 'Offshore.cur')) c_mover = CatsMover(curr_file) # but do need to scale (based on river stage) c_mover.scale = True c_mover.scale_refpoint = (-74.7483333, 38.898333) c_mover.scale_value = .03 model.movers += c_mover # # these are from windows they don't match Mac values... # pat1Angle 315; # pat1Speed 30; pat1SpeedUnits knots; # pat1ScaleToValue 0.314426 # # pat2Angle 225; # pat2Speed 30; pat2SpeedUnits knots; # pat2ScaleToValue 0.032882 # scaleBy WindStress print 'adding a component mover:' # if only using one current pattern # comp_mover = ComponentMover(curr_file1, None, wind) # # todo: following is not working when model is saved out - fix # comp_mover = ComponentMover(curr_file1, curr_file2, # Wind(timeseries=series, units='m/s')) # comp_mover = ComponentMover(curr_file1, curr_file2, # wind=Wind(filename=wind_file)) curr_file1 = get_datafile(os.path.join(base_dir, 'NW30ktwinds.cur')) curr_file2 = get_datafile(os.path.join(base_dir, 'SW30ktwinds.cur')) comp_mover = ComponentMover(curr_file1, curr_file2, wind) comp_mover.scale_refpoint = (-75.263166, 39.1428333) comp_mover.pat1_angle = 315 comp_mover.pat1_speed = 30 comp_mover.pat1_speed_units = 1 # comp_mover.pat1ScaleToValue = .314426 comp_mover.pat1_scale_to_value = .502035 comp_mover.pat2_angle = 225 comp_mover.pat2_speed = 30 comp_mover.pat2_speed_units = 1 # comp_mover.pat2ScaleToValue = .032882 comp_mover.pat2_scale_to_value = .021869 model.movers += comp_mover print 'adding a spill' end_time = start_time + timedelta(hours=12) spill = point_line_release_spill(num_elements=1000, release_time=start_time, # end_release_time=end_time, start_position=(-75.262319, 39.142987, 0.0), ) model.spills += spill return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(2013, 5, 18, 0) model = Model(start_time=start_time, duration=timedelta(days=8), time_step=4 * 3600, uncertain=False) mapfile = get_datafile(os.path.join(base_dir, 'mariana_island.bna')) print 'adding the map' model.map = MapFromBNA(mapfile, refloat_halflife=6) # hours # # Add the outputters -- render to images, and save out as netCDF # print 'adding renderer' model.outputters += Renderer( mapfile, images_dir, size=(800, 600), ) # draw_back_to_fore=True) # print "adding netcdf output" # netcdf_output_file = os.path.join(base_dir,'mariana_output.nc') # scripting.remove_netcdf(netcdf_output_file) # model.outputters += NetCDFOutput(netcdf_output_file, which_data='all') # # Set up the movers: # print 'adding a RandomMover:' model.movers += RandomMover(diffusion_coef=10000) print 'adding a simple wind mover:' model.movers += constant_wind_mover(5, 315, units='m/s') print 'adding a current mover:' # # this is HYCOM currents curr_file = get_datafile(os.path.join(base_dir, 'HYCOM.nc')) model.movers += GridCurrentMover(curr_file, num_method=numerical_methods.euler) # # # # Add some spills (sources of elements) # # print 'adding four spill' model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4, start_position=(145.25, 15.0, 0.0), release_time=start_time) model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4, start_position=(146.25, 15.0, 0.0), release_time=start_time) model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4, start_position=(145.75, 15.25, 0.0), release_time=start_time) model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4, start_position=(145.75, 14.75, 0.0), release_time=start_time) return model
def make_model(images_dir=os.path.join(base_dir, 'images')): print 'initializing the model' start_time = datetime(1985, 1, 1, 13, 31) # 1 day of data in file # 1/2 hr in seconds model = Model(start_time=start_time, duration=timedelta(days=4), time_step=3600 * 2) # mapfile = get_datafile(os.path.join(base_dir, 'ak_arctic.bna')) mapfile = get_datafile('arctic_coast3.bna') print 'adding the map' model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds print 'adding a spill' # for now subsurface spill stays on initial layer # - will need diffusion and rise velocity # - wind doesn't act # - start_position = (-76.126872, 37.680952, 5.0), # spill1 = point_line_release_spill(num_elements=10000, # start_position=(-163.75, # 69.75, # 0.0), # release_time=start_time) # spill1 = point_line_release_spill(num_elements=100, start_position=(196.25, 69.75, 0.0), release_time=start_time) model.spills += spill1 # model.spills += spill2 print 'adding a wind mover:' # model.movers += constant_wind_mover(0.5, 0, units='m/s') print 'adding a current mover:' fn = ['arctic_avg2_0001_gnome.nc', 'arctic_avg2_0002_gnome.nc'] gt = {'node_lon': 'lon', 'node_lat': 'lat'} # fn='arctic_avg2_0001_gnome.nc' wind_method = 'Euler' method = 'Trapezoid' print 'adding outputters' # draw_ontop can be 'uncertain' or 'forecast' # 'forecast' LEs are in black, and 'uncertain' are in red # default is 'forecast' LEs draw on top # renderer = Renderer(mapfile, images_dir, image_size=(1024, 768)) # model.outputters += renderer netcdf_file = os.path.join(base_dir, str(model.time_step / 60) + method + '.nc') scripting.remove_netcdf(netcdf_file) print 'adding movers' model.outputters += NetCDFOutput(netcdf_file, which_data='all') ice_aware_curr = IceAwareCurrent.from_netCDF(filename=fn, grid_topology=gt) ice_aware_wind = IceAwareWind.from_netCDF( filename=fn, ice_var=ice_aware_curr.ice_var, ice_conc_var=ice_aware_curr.ice_conc_var, grid=ice_aware_curr.grid, ) # i_c_mover = PyGridCurrentMover(current=ice_aware_curr) # i_c_mover = PyGridCurrentMover(current=ice_aware_curr, default_num_method='Euler') i_c_mover = PyGridCurrentMover(current=ice_aware_curr, default_num_method=method) i_w_mover = PyWindMover(wind=ice_aware_wind, default_num_method=wind_method) # ice_aware_curr.grid.node_lon = ice_aware_curr.grid.node_lon[:]-360 # ice_aware_curr.grid.build_celltree() model.movers += i_c_mover model.movers += i_w_mover print 'adding an IceAwareRandomMover:' model.movers += IceAwareRandomMover( ice_conc_var=ice_aware_curr.ice_conc_var, diffusion_coef=1000) # renderer.add_grid(ice_aware_curr.grid) # renderer.add_vec_prop(ice_aware_curr) # renderer.set_viewport(((-190.9, 60), (-72, 89))) # curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc')) # c_mover = GridCurrentMover(curr_file) # model.movers += c_mover return model