def setUp(self):
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.log.logger.handlers.append(logging.StreamHandler())
self.log.logger.info(self.id())
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2014, 1, 2, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
output_dir = "/data/lm/tests/output"
test_dir = self.id().split('.')[-1]
self.output_path = os.path.join(output_dir, test_dir)
if not os.path.isdir(self.output_path):
os.makedirs(self.output_path)
self.output_formats = [ex.H5Trackline]
cache_dir = "/data/lm/tests/cache"
self.cache_path = os.path.join(cache_dir, test_dir, 'cache.nc')
self.bathy_file = "/data/lm/bathy/global/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def setUp(self):
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.log.logger.handlers.append(logging.StreamHandler())
self.log.logger.info(self.id())
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2014, 1, 2, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
output_dir = "/data/lm/tests/output"
test_dir = self.id().split('.')[-1]
self.output_path = os.path.join(output_dir, test_dir)
if not os.path.isdir(self.output_path):
os.makedirs(self.output_path)
self.output_formats = [ex.H5GDALShapefile, ex.H5Trackline]
cache_dir = "/data/lm/tests/cache"
self.cache_path = os.path.join(cache_dir, test_dir, 'cache.nc')
self.bathy_file = "/data/lm/bathy/global/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def setUp(self):
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2012, 8, 1, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.output_path = "/data/lm/output"
self.cache_path = "/data/lm/cache"
self.bathy_file = "/data/lm/bathy/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def setUp(self):
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2012, 8, 1, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.output_path = "/data/lm/output"
self.cache_path = "/data/lm/cache"
self.bathy_file = "/data/lm/bathy/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def setUp(self):
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.log.logger.info("**************************************")
self.log.logger.info(self.id())
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2014, 1, 2, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
output_dir = "/data/lm/tests/output"
self.output_path = os.path.join(output_dir, self.id())
cache_dir = "/data/lm/tests/cache"
self.cache_path = os.path.join(cache_dir, self.id())
self.bathy_file = "/data/lm/bathy/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
class LarvalBehaviourTest(unittest.TestCase):
def setUp(self):
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.log.logger.handlers.append(logging.StreamHandler())
self.log.logger.info(self.id())
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2014, 1, 2, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
output_dir = "/data/lm/tests/output"
test_dir = self.id().split('.')[-1]
self.output_path = os.path.join(output_dir, test_dir)
if not os.path.isdir(self.output_path):
os.makedirs(self.output_path)
self.output_formats = [ex.H5GDALShapefile, ex.H5Trackline]
cache_dir = "/data/lm/tests/cache"
self.cache_path = os.path.join(cache_dir, test_dir, 'cache.nc')
self.bathy_file = "/data/lm/bathy/global/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def tearDown(self):
self.log.close()
def draw_trackline(self, geojson_file):
with fiona.open(geojson_file) as src:
self.log.logger.info((gj2ascii.render(src, 100, fill='.', char='o', bbox=shape(src.next()['geometry']).buffer(0.1).envelope.bounds)))
def test_behavior_growth_and_settlement(self):
# 6 days
num_steps = 144
num_particles = 2
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__), "./resources/files/behavior_for_run_testing.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = CachingModelController(
latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=num_steps,
npart=num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=24,
horiz_chunk=4,
time_method='nearest',
bathy_path=self.bathy_file)
model.setup_run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=self.cache_path)
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
def test_quick_settlement(self):
num_steps = 24
num_particles = 4
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__), "./resources/files/behavior_quick_settle.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = CachingModelController(
latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=num_steps,
npart=num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=12,
horiz_chunk=2,
time_method='nearest',
bathy_path=self.bathy_file)
model.setup_run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_DAS.nc", cache=self.cache_path)
model.run(output_path=self.output_path, output_formats=self.output_formats)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
@unittest.skip("Lost behavior file")
def test_kayak_island(self):
# 6 days
num_steps = 1632
num_particles = 100
time_step = 3600
behavior_config = json.loads(urlopen("http://behaviors.larvamap.asascience.com/library/50ef1bb1cc7b61000700001d.json").read())
lb = LarvaBehavior(data=behavior_config[u'results'][0])
models = [Transport(horizDisp=0.01, vertDisp=0.001)]
models.append(lb)
start_time = datetime(2011, 5, 2, 00, tzinfo=pytz.utc)
start_lat = 59.93517413488866
start_lon = -144.496213677788
depth = -1
shoreline_path = os.path.join(self.shoreline_path, "westcoast", "New_Land_Clean.shp")
model = CachingModelController(
latitude=start_lat,
longitude=start_lon,
depth=depth,
start=start_time,
step=time_step,
nstep=num_steps,
npart=num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=24,
horiz_chunk=5,
time_method='interp',
shoreline_path=shoreline_path,
bathy_path=self.bathy_file)
model.setup_run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L1_FCST.nc", cache=self.cache_path)
model.run(output_path=self.output_path, output_formats=self.output_formats)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
@unittest.skip("Lost behavior file")
def test_sheep_bay(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: Sheep Bay")
# 6 days
num_steps = 1632
num_particles = 100
time_step = 3600
behavior_config = json.loads(urlopen("http://behaviors.larvamap.asascience.com/library/50ef1bb1cc7b61000700001d.json").read())
lb = LarvaBehavior(data=behavior_config[u'results'][0])
models = [Transport(horizDisp=0.01, vertDisp=0.001)]
models.append(lb)
start_time = datetime(2011, 5, 2, 00, tzinfo=pytz.utc)
start_lat = 60.60899655733162
start_lon = -145.97402533055956
depth = -1
shoreline_path = os.path.join(self.shoreline_path, "westcoast", "New_Land_Clean.shp")
model = CachingModelController(
latitude=start_lat,
longitude=start_lon,
depth=depth,
start=start_time,
step=time_step,
nstep=num_steps,
npart=num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=24,
horiz_chunk=5,
time_method='interp',
shoreline_path=shoreline_path,
bathy_path=self.bathy_file)
model.setup_run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=self.cache_path)
model.run(output_path=self.output_path, output_formats=self.output_formats)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
def test_diel_migration(self):
num_steps = 168
num_particles = 4
start_time = datetime(2013, 4, 1, 0, tzinfo=pytz.utc)
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__), "./resources/files/diel_suncycles.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = CachingModelController(
latitude=60.68,
longitude=-146.42,
depth=self.start_depth,
start=start_time,
step=self.time_step,
nstep=num_steps,
npart=num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=24,
horiz_chunk=2,
time_method='nearest',
bathy_path=self.bathy_file)
model.setup_run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_DAS.nc", cache=self.cache_path)
model.run(output_path=self.output_path, output_formats=self.output_formats)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
class CachingModelControllerTest(unittest.TestCase):
def setUp(self):
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.log.logger.info("**************************************")
self.log.logger.info(self.id())
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2014, 1, 2, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
output_dir = "/data/lm/tests/output"
self.output_path = os.path.join(output_dir, self.id())
cache_dir = "/data/lm/tests/cache"
self.cache_path = os.path.join(cache_dir, self.id())
self.bathy_file = "/data/lm/bathy/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def tearDown(self):
self.log.logger.info("**************************************")
self.log.close()
def test_run_from_multiple_files_with_cache(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = CachingModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
se_shoreline=False,
time_chunk=10,
horiz_chunk=4,
bathy_path=self.bathy_file)
particles = model.run("/data/lm/tests/pws_das_2014*.nc", output_formats = ['NetCDF'], output_path=self.output_path, cache_path=self.cache_path, remove_cache=False)
self.assertEquals(len(particles), self.num_particles)
self.assertTrue(os.path.exists(self.cache_path))
os.remove(self.cache_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "trajectories.nc")))
def test_run_from_multiple_files_without_cache_on_ipy_cluster(self):
try:
from IPython.parallel import Client
client = Client()
pool = client.load_balanced_view()
except:
raise unittest.SkipTest("Cluster connection failed")
self.test_run_from_multiple_files_without_cache(pool=pool)
def test_run_from_multiple_files_without_cache(self, pool=None):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
pool=pool)
particles = model.run("/data/lm/tests/pws_das_2014*.nc", output_formats = ['NetCDF', 'trackline'], output_path=self.output_path)
self.assertEquals(len(particles), self.num_particles)
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
self.assertTrue(os.path.exists(os.path.join(self.output_path, "trajectories.nc")))
def test_run_from_dap_with_cache(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = CachingModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=200,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=24,
horiz_chunk=4)
particles = model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", output_formats = ['NetCDF'], output_path=self.output_path, cache_path=self.cache_path, remove_cache=False)
self.assertEquals(len(particles), self.num_particles)
self.assertTrue(os.path.exists(self.cache_path))
os.remove(self.cache_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "trajectories.nc")))
def test_run_from_dap_without_cache(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = CachingModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
particles = model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", output_formats = ['NetCDF'], output_path=self.output_path)
self.assertEquals(len(particles), self.num_particles)
# We didn't pass remove_cache=False, so it should have been removed by the CachingModelController.
self.assertFalse(os.path.exists(self.cache_path))
self.assertTrue(os.path.exists(os.path.join(self.output_path, "trajectories.nc")))
def test_run_from_polygon(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat).buffer(0.001)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=datetime(2014, 1, 2, 0),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=10,
horiz_chunk=4)
particles = model.run("/data/lm/tests/pws_das_2014*.nc", output_formats=['NetCDF'], output_path=self.output_path)
self.assertEquals(len(particles), self.num_particles)
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
self.assertTrue(os.path.exists(os.path.join(self.output_path, "trajectories.nc")))
def test_run_from_point(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
particles = model.run("/data/lm/tests/pws_das_2014*.nc", output_formats = ['NetCDF'], output_path=self.output_path)
self.assertEquals(len(particles), self.num_particles)
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
self.assertTrue(os.path.exists(os.path.join(self.output_path, "trajectories.nc")))
def test_run_from_point_with_wfs_shoreline(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
shoreline_path='http://geo.asascience.com/geoserver/shorelines/ows',
shoreline_feature='shorelines:10m_land_polygons')
particles = model.run("/data/lm/tests/pws_das_2014*.nc", output_formats = ['NetCDF'], output_path=self.output_path)
self.assertEquals(len(particles), self.num_particles)
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
self.assertTrue(os.path.exists(os.path.join(self.output_path, "trajectories.nc")))
def test_time_method_interp(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_method="interp")
particles = model.run("/data/lm/tests/pws_das_2014*.nc", output_formats = ['NetCDF'], output_path=self.output_path)
self.assertEquals(len(particles), self.num_particles)
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
self.assertTrue(os.path.exists(os.path.join(self.output_path, "trajectories.nc")))
def test_time_method_nearest(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_method="nearest")
particles = model.run("/data/lm/tests/pws_das_2014*.nc", output_formats = ['NetCDF'], output_path=self.output_path)
self.assertEquals(len(particles), self.num_particles)
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
self.assertTrue(os.path.exists(os.path.join(self.output_path, "trajectories.nc")))
def test_time_method_bad(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
with self.assertRaises(TypeError):
BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_method="umm_what_am_i")
def test_start_on_land_from_lat_lon(self):
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
models = [self.transport]
model = BaseModelController(latitude=start_lat,
longitude=start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True)
with raises(ModelError):
model.run("/data/lm/tests/pws_das_2014*.nc")
def test_start_on_land_from_point_no_depth(self):
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
p = Point(start_lon, start_lat)
models = [self.transport]
model = BaseModelController(geometry=p,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True)
with raises(ModelError):
model.run("/data/lm/tests/pws_das_2014*.nc")
def test_start_on_land_from_point_with_depth(self):
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
depth = -10
p = Point(start_lon, start_lat)
models = [self.transport]
model = BaseModelController(geometry=p,
depth=depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True)
with raises(ModelError):
model.run("/data/lm/tests/pws_das_2014*.nc")
def test_bad_dataset(self):
models = [self.transport]
model = BaseModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with raises(BaseDataControllerError):
model.run("http://example.com/thisisnotadataset.nc")
def test_timechunk_greater_than_timestep(self):
models = [self.transport]
model = CachingModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=48,
horiz_chunk=2)
particles = model.run("/data/lm/tests/pws_das_2014*.nc", output_formats = ['NetCDF'], output_path=self.output_path, cache_path=self.cache_path, remove_cache=False)
self.assertEquals(len(particles), self.num_particles)
self.assertTrue(os.path.exists(self.cache_path))
os.remove(self.cache_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "trajectories.nc")))
def test_no_local_data_for_requested_run(self):
models = [self.transport]
# Start is after available time
model = BaseModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime.utcnow() + timedelta(days=30),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.run("/data/lm/tests/pws_das_2014*.nc", output_formats = ['NetCDF'], output_path=self.output_path, cache_path=self.cache_path, remove_cache=False)
# Start is OK but Ending is after available time
model = BaseModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime(2014, 1, 1, 0),
step=self.time_step,
nstep=500,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.run("/data/lm/tests/pws_das_2014*.nc", output_formats = ['NetCDF'], output_path=self.output_path, cache_path=self.cache_path, remove_cache=False)
def test_no_dap_data_for_requested_run(self):
models = [self.transport]
# Start is after available time
model = CachingModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime.utcnow() + timedelta(days=30),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", output_formats = ['NetCDF'], output_path=self.output_path, cache_path=self.cache_path, remove_cache=False)
# Start is OK but Ending is after available time
model = CachingModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime.utcnow() - timedelta(days=2),
step=self.time_step,
nstep=500,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", output_formats = ['NetCDF'], output_path=self.output_path, cache_path=self.cache_path, remove_cache=False)
def test_run_10m_shoreline(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=300,
npart=2,
models=models,
use_bathymetry=False,
use_shoreline=True,
shoreline_index_buffer=0.05)
particles = model.run("/data/lm/tests/pws_das_2014*.nc")
self.assertEquals(len(particles), 2)
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_run_west_coast_shoreline(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=300,
npart=2,
models=models,
use_bathymetry=False,
use_shoreline=True,
shoreline_path='/data/lm/shore/westcoast/New_Land_Clean.shp',
shoreline_index_buffer=0.05)
particles = model.run("/data/lm/tests/pws_das_2014*.nc")
self.assertEquals(len(particles), 2)
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
class ModelControllerTest(unittest.TestCase):
def setUp(self):
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.log.logger.handlers.append(logging.StreamHandler())
self.log.logger.info(self.id())
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2014, 1, 2, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
output_dir = "/data/lm/tests/output"
test_dir = self.id().split('.')[-1]
self.output_path = os.path.join(output_dir, test_dir)
if not os.path.isdir(self.output_path):
os.makedirs(self.output_path)
self.output_formats = [ex.H5Trackline]
cache_dir = "/data/lm/tests/cache"
self.cache_path = os.path.join(cache_dir, test_dir, 'cache.nc')
self.bathy_file = "/data/lm/bathy/global/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def tearDown(self):
self.log.close()
def draw_trackline(self, geojson_file):
with fiona.open(geojson_file) as src:
self.log.logger.info((gj2ascii.render(src, 100, fill='.', char='o', bbox=shape(src.next()['geometry']).buffer(0.1).envelope.bounds)))
def test_run_from_multiple_files_with_cache(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = CachingModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
se_shoreline=False,
time_chunk=10,
horiz_chunk=4)
model.setup_run("/data/lm/tests/pws_das_2014*.nc", cache_path=self.cache_path, remove_cache=False)
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
self.assertTrue(os.path.exists(self.cache_path))
os.remove(self.cache_path)
def test_run_from_multiple_files_without_cache_on_ipy_cluster(self):
try:
from IPython.parallel import Client
client = Client()
pool = client.load_balanced_view()
except:
raise unittest.SkipTest("Cluster connection failed")
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = IPythonClusterModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
pool=pool)
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_run_from_multiple_files_without_cache(self, pool=None):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
pool=pool)
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_run_from_dap_with_cache(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = CachingModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=200,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=24,
horiz_chunk=4)
model.setup_run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache_path=self.cache_path, remove_cache=False)
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
self.assertTrue(os.path.exists(self.cache_path))
os.remove(self.cache_path)
def test_run_from_dap_without_cache(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = CachingModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
model.setup_run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc")
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
# We didn't pass remove_cache=False, so it should have been removed by the CachingModelController.
self.assertFalse(os.path.exists(self.cache_path))
def test_run_from_polygon(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat).buffer(0.001)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=datetime(2014, 1, 2, 0),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=10,
horiz_chunk=4)
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_distributed_from_polygon(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat).buffer(0.001)
model = DistributedModelController(geometry=p,
depth=self.start_depth,
start=datetime(2014, 1, 2, 0),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=10,
horiz_chunk=4)
model.setup_run("/data/lm/tests/pws_das_2014*.nc", redis_url='redis://127.0.0.1:6379/150', redis_results_channel='test_distributed_from_polygon:results')
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
@unittest.skip("Need to find a new WFS server to test against")
def test_run_from_point_with_wfs_shoreline(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
shoreline_path='http://geo.asascience.com/geoserver/shorelines/ows',
shoreline_feature='shorelines:10m_land_polygons')
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_time_method_interp(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_method="interp")
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_time_method_nearest(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_method="nearest")
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_time_method_bad(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
with self.assertRaises(TypeError):
BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_method="umm_what_am_i")
def test_start_on_land_from_lat_lon(self):
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
models = [self.transport]
model = BaseModelController(latitude=start_lat,
longitude=start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True)
with raises(ModelError):
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run()
def test_start_on_land_from_point_no_depth(self):
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
p = Point(start_lon, start_lat)
models = [self.transport]
model = BaseModelController(geometry=p,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True)
with raises(ModelError):
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run()
def test_start_on_land_from_point_with_depth(self):
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
depth = -10
p = Point(start_lon, start_lat)
models = [self.transport]
model = BaseModelController(geometry=p,
depth=depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True)
with raises(ModelError):
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run()
def test_bad_dataset(self):
models = [self.transport]
model = BaseModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.setup_run("http://example.com/thisisnotadataset.nc")
def test_timechunk_greater_than_timestep(self):
models = [self.transport]
model = CachingModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=48,
horiz_chunk=2)
model.setup_run("/data/lm/tests/pws_das_2014*.nc", cache_path=self.cache_path, remove_cache=False)
model.run(output_formats=self.output_formats, output_path=self.output_path)
self.assertTrue(os.path.exists(os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(os.path.join(self.output_path, "simple_trackline.geojson"))
self.assertTrue(os.path.exists(self.cache_path))
os.remove(self.cache_path)
def test_no_local_data_for_requested_run(self):
models = [self.transport]
# Start is after available time
model = BaseModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime.utcnow() + timedelta(days=30),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
# Start is OK but Ending is after available time
model = BaseModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime(2014, 1, 1, 0),
step=self.time_step,
nstep=500,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
def test_no_dap_data_for_requested_run(self):
models = [self.transport]
# Start is after available time
model = CachingModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime.utcnow() + timedelta(days=30),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.setup_run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc")
# Start is OK but Ending is after available time
model = CachingModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime.utcnow() - timedelta(days=2),
step=self.time_step,
nstep=500,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.setup_run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc")
def test_run_10m_shoreline(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=300,
npart=2,
models=models,
use_bathymetry=False,
use_shoreline=True,
shoreline_index_buffer=0.05)
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run()
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_run_west_coast_shoreline(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=300,
npart=2,
models=models,
use_bathymetry=False,
use_shoreline=True,
shoreline_path='/data/lm/shore/westcoast/New_Land_Clean.shp',
shoreline_index_buffer=0.05)
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run()
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
class ModelControllerTest(unittest.TestCase):
def setUp(self):
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.log.logger.handlers.append(logging.StreamHandler())
self.log.logger.info(self.id())
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2014, 1, 2, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
output_dir = "/data/lm/tests/output"
test_dir = self.id().split('.')[-1]
self.output_path = os.path.join(output_dir, test_dir)
if not os.path.isdir(self.output_path):
os.makedirs(self.output_path)
self.output_formats = [ex.H5Trackline]
cache_dir = "/data/lm/tests/cache"
self.cache_path = os.path.join(cache_dir, test_dir, 'cache.nc')
self.bathy_file = "/data/lm/bathy/global/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def tearDown(self):
self.log.close()
def draw_trackline(self, geojson_file):
with fiona.open(geojson_file) as src:
self.log.logger.info((gj2ascii.render(
src,
100,
fill='.',
char='o',
bbox=shape(
src.next()['geometry']).buffer(0.1).envelope.bounds)))
def test_run_from_multiple_files_with_cache(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = CachingModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
se_shoreline=False,
time_chunk=10,
horiz_chunk=4)
model.setup_run("/data/lm/tests/pws_das_2014*.nc",
cache_path=self.cache_path,
remove_cache=False)
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
self.assertTrue(os.path.exists(self.cache_path))
os.remove(self.cache_path)
def test_run_from_multiple_files_without_cache_on_ipy_cluster(self):
try:
from IPython.parallel import Client
client = Client()
pool = client.load_balanced_view()
except:
raise unittest.SkipTest("Cluster connection failed")
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = IPythonClusterModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
pool=pool)
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_run_from_multiple_files_without_cache(self, pool=None):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
pool=pool)
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_run_from_dap_with_cache(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = CachingModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=200,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=24,
horiz_chunk=4)
model.setup_run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
cache_path=self.cache_path,
remove_cache=False)
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
self.assertTrue(os.path.exists(self.cache_path))
os.remove(self.cache_path)
def test_run_from_dap_without_cache(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = CachingModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
model.setup_run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc")
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
# We didn't pass remove_cache=False, so it should have been removed by the CachingModelController.
self.assertFalse(os.path.exists(self.cache_path))
def test_run_from_polygon(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat).buffer(0.001)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=datetime(2014, 1, 2, 0),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=10,
horiz_chunk=4)
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_distributed_from_polygon(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat).buffer(0.001)
model = DistributedModelController(geometry=p,
depth=self.start_depth,
start=datetime(2014, 1, 2, 0),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=10,
horiz_chunk=4)
model.setup_run(
"/data/lm/tests/pws_das_2014*.nc",
redis_url='redis://127.0.0.1:6379/150',
redis_results_channel='test_distributed_from_polygon:results')
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
@unittest.skip("Need to find a new WFS server to test against")
def test_run_from_point_with_wfs_shoreline(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(
geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
shoreline_path='http://geo.asascience.com/geoserver/shorelines/ows',
shoreline_feature='shorelines:10m_land_polygons')
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_time_method_interp(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_method="interp")
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_time_method_nearest(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_method="nearest")
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_time_method_bad(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
with self.assertRaises(TypeError):
BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_method="umm_what_am_i")
def test_start_on_land_from_lat_lon(self):
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
models = [self.transport]
model = BaseModelController(latitude=start_lat,
longitude=start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True)
with raises(ModelError):
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run()
def test_start_on_land_from_point_no_depth(self):
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
p = Point(start_lon, start_lat)
models = [self.transport]
model = BaseModelController(geometry=p,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True)
with raises(ModelError):
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run()
def test_start_on_land_from_point_with_depth(self):
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
depth = -10
p = Point(start_lon, start_lat)
models = [self.transport]
model = BaseModelController(geometry=p,
depth=depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True)
with raises(ModelError):
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run()
def test_bad_dataset(self):
models = [self.transport]
model = BaseModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.setup_run("http://example.com/thisisnotadataset.nc")
def test_timechunk_greater_than_timestep(self):
models = [self.transport]
model = CachingModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False,
time_chunk=48,
horiz_chunk=2)
model.setup_run("/data/lm/tests/pws_das_2014*.nc",
cache_path=self.cache_path,
remove_cache=False)
model.run(output_formats=self.output_formats,
output_path=self.output_path)
self.assertTrue(
os.path.exists(
os.path.join(self.output_path, "simple_trackline.geojson")))
self.draw_trackline(
os.path.join(self.output_path, "simple_trackline.geojson"))
self.assertTrue(os.path.exists(self.cache_path))
os.remove(self.cache_path)
def test_no_local_data_for_requested_run(self):
models = [self.transport]
# Start is after available time
model = BaseModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime.utcnow() +
timedelta(days=30),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
# Start is OK but Ending is after available time
model = BaseModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime(2014, 1, 1, 0),
step=self.time_step,
nstep=500,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
def test_no_dap_data_for_requested_run(self):
models = [self.transport]
# Start is after available time
model = CachingModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime.utcnow() +
timedelta(days=30),
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.setup_run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc")
# Start is OK but Ending is after available time
model = CachingModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=datetime.utcnow() -
timedelta(days=2),
step=self.time_step,
nstep=500,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=False)
with self.assertRaises(BaseDataControllerError):
model.setup_run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc")
def test_run_10m_shoreline(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=300,
npart=2,
models=models,
use_bathymetry=False,
use_shoreline=True,
shoreline_index_buffer=0.05)
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run()
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
def test_run_west_coast_shoreline(self):
models = [self.transport]
p = Point(self.start_lon, self.start_lat)
model = BaseModelController(
geometry=p,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=300,
npart=2,
models=models,
use_bathymetry=False,
use_shoreline=True,
shoreline_path='/data/lm/shore/westcoast/New_Land_Clean.shp',
shoreline_index_buffer=0.05)
model.setup_run("/data/lm/tests/pws_das_2014*.nc")
model.run()
# Not a caching controller, no cache path should exist
self.assertFalse(os.path.exists(self.cache_path))
class ModelControllerTest(unittest.TestCase):
def setUp(self):
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2012, 8, 1, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.output_path = "/data/lm/output"
self.cache_path = "/data/lm/cache"
self.bathy_file = "/data/lm/bathy/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def tearDown(self):
self.log.close()
def test_run_from_point(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_point")
models = [self.transport]
p = Point(self.start_lon, self.start_lat, self.start_depth)
model = ModelController(geometry=p, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4)
cache_path = os.path.join(self.cache_path, "test_run_from_point.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_run_from_point_with_wfs(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_point_with_wfs")
models = [self.transport]
p = Point(self.start_lon, self.start_lat, self.start_depth)
model = ModelController(geometry=p, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4, shoreline_path='http://geo.asascience.com/geoserver/shorelines/ows', shoreline_feature='shorelines:10m_land_polygons')
cache_path = os.path.join(self.cache_path, "test_run_from_point.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_run_from_polygon(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_polygon")
models = [self.transport]
poly = Point(self.start_lon, self.start_lat, self.start_depth).buffer(0.001)
model = ModelController(geometry=poly, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4)
cache_path = os.path.join(os.path.dirname(__file__), "..", "paegan/transport/_cache/test_run_from_polygon.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_interp(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_interp")
models = [self.transport]
num_steps = 100
output_path = os.path.join(self.output_path, "test_interp")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline']
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=self.num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=10, horiz_chunk=4)
cache_path = os.path.join(self.cache_path, "test_interp.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
def test_nearest(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_nearest")
models = [self.transport]
num_steps = 100
output_path = os.path.join(self.output_path, "test_nearest")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline']
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=10, horiz_chunk=4, time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_nearest.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
def test_start_on_land(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_start_on_land")
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
models = [self.transport]
model = ModelController(latitude=start_lat, longitude=start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4, time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_start_on_land.nc")
with raises(ModelError):
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_bad_dataset(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_bad_dataset")
models = [self.transport]
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4, time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_bad_dataset.nc")
with raises(DataControllerError):
model.run("http://asascience.com/thisisnotadataset.nc", cache=cache_path)
"""
def test_behavior_growth_and_settlement(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_behavior_growth_and_settlement")
# 6 days
num_steps = 144
num_particles = 2
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/behavior_for_run_testing.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=4, time_method='nearest')
output_path = os.path.join(self.output_path, "test_behavior_growth_and_settlement")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline','Pickle']
cache_path = os.path.join(self.cache_path, "test_behavior_growth_and_settlement.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
"""
def test_quick_settlement(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_quick_settlement")
num_steps = 24
num_particles = 4
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/behavior_quick_settle.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=12, horiz_chunk=2, time_method='nearest')
output_path = os.path.join(self.output_path, "test_quick_settlement")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline']
cache_path = os.path.join(self.cache_path, "test_quick_settlement.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_DAS.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
def test_timechunk_greater_than_timestep(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_timechunk_greater_than_timestep")
# 6 days
num_steps = 10
num_particles = 2
models = [self.transport]
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=2)
cache_path = os.path.join(self.cache_path, "test_timechunk_greater_than_timestep.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path)
"""
def test_kayak_island(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: Kayak Island")
# 6 days
num_steps = 1632
num_particles = 100
time_step = 3600
behavior_config = json.loads(urllib.urlopen("http://behaviors.larvamap.asascience.com/library/50ef1bb1cc7b61000700001d.json").read())
lb = LarvaBehavior(data=behavior_config[u'results'][0])
#behavior_config = json.loads(open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/nick.json"))).read())
#lb = LarvaBehavior(data=behavior_config[u'results'][0])
models = [Transport(horizDisp=0.01, vertDisp=0.001)]
models.append(lb)
start_time = datetime(2011, 5, 2, 00, tzinfo=pytz.utc)
start_lat = 59.93517413488866
start_lon = -144.496213677788
depth = -1
shoreline_path = os.path.join(self.shoreline_path, "westcoast", "New_Land_Clean.shp")
model = ModelController(latitude=start_lat, longitude=start_lon, depth=depth, start=start_time, step=time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=5, time_method='interp', shoreline_path=shoreline_path)
output_path = os.path.join(self.output_path, "kayak_island")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline']
cache_path = os.path.join(self.cache_path, "kayak_island.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L1_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
def test_sheep_bay(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: Sheep Bay")
# 6 days
num_steps = 1632
num_particles = 100
time_step = 3600
behavior_config = json.loads(urllib.urlopen("http://behaviors.larvamap.asascience.com/library/50ef1bb1cc7b61000700001d.json").read())
lb = LarvaBehavior(data=behavior_config[u'results'][0])
models = [Transport(horizDisp=0.01, vertDisp=0.001)]
models.append(lb)
start_time = datetime(2011, 5, 2, 00, tzinfo=pytz.utc)
start_lat = 60.60899655733162
start_lon = -145.97402533055956
depth = -1
shoreline_path = os.path.join(self.shoreline_path, "westcoast", "New_Land_Clean.shp")
model = ModelController(latitude=start_lat, longitude=start_lon, depth=depth, start=start_time, step=time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=5, time_method='interp', shoreline_path=shoreline_path)
output_path = os.path.join(self.output_path, "sheep_bay")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline']
cache_path = os.path.join(self.cache_path, "sheep_bay.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
"""
def test_diel_migration(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_diel_migration")
num_steps = 168
num_particles = 4
start_time = datetime(2013,4,1,0, tzinfo=pytz.utc)
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/diel_suncycles.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=60.68, longitude=-146.42, depth=self.start_depth, start=start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=2, time_method='nearest')
output_path = os.path.join(self.output_path, "test_diel_migration")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline']
cache_path = os.path.join(self.cache_path, "test_diel_migration.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_DAS.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
class ModelControllerTest(unittest.TestCase):
def setUp(self):
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2012, 8, 1, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.output_path = "/data/lm/output"
self.cache_path = "/data/lm/cache"
self.bathy_file = "/data/lm/bathy/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def tearDown(self):
self.log.close()
def test_run_from_point(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_point")
models = [self.transport]
p = Point(self.start_lon, self.start_lat, self.start_depth)
model = ModelController(geometry=p,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4)
cache_path = os.path.join(self.cache_path, "test_run_from_point.nc")
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
cache=cache_path)
def test_run_from_polygon(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_polygon")
models = [self.transport]
poly = Point(self.start_lon, self.start_lat,
self.start_depth).buffer(0.001)
model = ModelController(geometry=poly,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4)
cache_path = os.path.join(
os.path.dirname(__file__), "..",
"paegan/transport/_cache/test_run_from_polygon.nc")
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
cache=cache_path)
def test_interp(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_interp")
models = [self.transport]
num_steps = 100
output_path = os.path.join(self.output_path, "test_interp")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile', 'NetCDF', 'Trackline']
model = ModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4)
cache_path = os.path.join(self.cache_path, "test_interp.nc")
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
bathy=self.bathy_file,
cache=cache_path,
output_path=output_path,
output_formats=output_formats)
def test_nearest(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_nearest")
models = [self.transport]
num_steps = 100
output_path = os.path.join(self.output_path, "test_nearest")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile', 'NetCDF', 'Trackline']
model = ModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4,
time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_nearest.nc")
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
bathy=self.bathy_file,
cache=cache_path,
output_path=output_path,
output_formats=output_formats)
def test_start_on_land(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_start_on_land")
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
models = [self.transport]
model = ModelController(latitude=start_lat,
longitude=start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4,
time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_start_on_land.nc")
with raises(ModelError):
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
cache=cache_path)
def test_bad_dataset(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_bad_dataset")
models = [self.transport]
model = ModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=self.num_steps,
npart=self.num_particles,
models=models,
use_bathymetry=False,
use_shoreline=True,
time_chunk=10,
horiz_chunk=4,
time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_bad_dataset.nc")
with raises(DataControllerError):
model.run("http://asascience.com/thisisnotadataset.nc",
cache=cache_path)
"""
def test_behavior_growth_and_settlement(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_behavior_growth_and_settlement")
# 6 days
num_steps = 144
num_particles = 2
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/behavior_for_run_testing.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=4, time_method='nearest')
output_path = os.path.join(self.output_path, "test_behavior_growth_and_settlement")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline','Pickle']
cache_path = os.path.join(self.cache_path, "test_behavior_growth_and_settlement.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
"""
def test_quick_settlement(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_quick_settlement")
num_steps = 24
num_particles = 4
# Behavior
behavior_config = open(
os.path.normpath(
os.path.join(
os.path.dirname(__file__),
"./resources/files/behavior_quick_settle.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=num_steps,
npart=num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=12,
horiz_chunk=2,
time_method='nearest')
output_path = os.path.join(self.output_path, "test_quick_settlement")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile', 'NetCDF', 'Trackline']
cache_path = os.path.join(self.cache_path, "test_quick_settlement.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_DAS.nc",
bathy=self.bathy_file,
cache=cache_path,
output_path=output_path,
output_formats=output_formats)
def test_timechunk_greater_than_timestep(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_timechunk_greater_than_timestep")
# 6 days
num_steps = 10
num_particles = 2
models = [self.transport]
model = ModelController(latitude=self.start_lat,
longitude=self.start_lon,
depth=self.start_depth,
start=self.start_time,
step=self.time_step,
nstep=num_steps,
npart=num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=24,
horiz_chunk=2)
cache_path = os.path.join(self.cache_path,
"test_timechunk_greater_than_timestep.nc")
model.run(
"http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc",
bathy=self.bathy_file,
cache=cache_path)
"""
def test_kayak_island(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: Kayak Island")
# 6 days
num_steps = 1632
num_particles = 100
time_step = 3600
behavior_config = json.loads(urllib.urlopen("http://behaviors.larvamap.asascience.com/library/50ef1bb1cc7b61000700001d.json").read())
lb = LarvaBehavior(data=behavior_config[u'results'][0])
#behavior_config = json.loads(open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/nick.json"))).read())
#lb = LarvaBehavior(data=behavior_config[u'results'][0])
models = [Transport(horizDisp=0.01, vertDisp=0.001)]
models.append(lb)
start_time = datetime(2011, 5, 2, 00, tzinfo=pytz.utc)
start_lat = 59.93517413488866
start_lon = -144.496213677788
depth = -1
shoreline_path = os.path.join(self.shoreline_path, "westcoast", "New_Land_Clean.shp")
model = ModelController(latitude=start_lat, longitude=start_lon, depth=depth, start=start_time, step=time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=5, time_method='interp', shoreline_path=shoreline_path)
output_path = os.path.join(self.output_path, "kayak_island")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline']
cache_path = os.path.join(self.cache_path, "kayak_island.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L1_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
def test_sheep_bay(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: Sheep Bay")
# 6 days
num_steps = 1632
num_particles = 100
time_step = 3600
behavior_config = json.loads(urllib.urlopen("http://behaviors.larvamap.asascience.com/library/50ef1bb1cc7b61000700001d.json").read())
lb = LarvaBehavior(data=behavior_config[u'results'][0])
models = [Transport(horizDisp=0.01, vertDisp=0.001)]
models.append(lb)
start_time = datetime(2011, 5, 2, 00, tzinfo=pytz.utc)
start_lat = 60.60899655733162
start_lon = -145.97402533055956
depth = -1
shoreline_path = os.path.join(self.shoreline_path, "westcoast", "New_Land_Clean.shp")
model = ModelController(latitude=start_lat, longitude=start_lon, depth=depth, start=start_time, step=time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=5, time_method='interp', shoreline_path=shoreline_path)
output_path = os.path.join(self.output_path, "sheep_bay")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline']
cache_path = os.path.join(self.cache_path, "sheep_bay.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
"""
def test_diel_migration(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_diel_migration")
num_steps = 168
num_particles = 4
start_time = datetime(2013, 4, 1, 0, tzinfo=pytz.utc)
# Behavior
behavior_config = open(
os.path.normpath(
os.path.join(os.path.dirname(__file__),
"./resources/files/diel_suncycles.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=60.68,
longitude=-146.42,
depth=self.start_depth,
start=start_time,
step=self.time_step,
nstep=num_steps,
npart=num_particles,
models=models,
use_bathymetry=True,
use_shoreline=True,
time_chunk=24,
horiz_chunk=2,
time_method='nearest')
output_path = os.path.join(self.output_path, "test_diel_migration")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile', 'NetCDF', 'Trackline']
cache_path = os.path.join(self.cache_path, "test_diel_migration.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_DAS.nc",
bathy=self.bathy_file,
cache=cache_path,
output_path=output_path,
output_formats=output_formats)
class ModelControllerTest(unittest.TestCase):
def setUp(self):
self.start_lat = 60.75
self.start_lon = -147
self.start_depth = 0
self.num_particles = 4
self.time_step = 3600
self.num_steps = 10
self.start_time = datetime(2012, 8, 1, 00)
self.transport = Transport(horizDisp=0.05, vertDisp=0.0003)
self.log = EasyLogger('testlog.txt', level=logging.PROGRESS)
self.output_path = "/data/lm/output"
self.cache_path = "/data/lm/cache"
self.bathy_file = "/data/lm/bathy/ETOPO1_Bed_g_gmt4.grd"
self.shoreline_path = "/data/lm/shore"
def tearDown(self):
self.log.close()
def test_run_from_point(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_point")
models = [self.transport]
p = Point(self.start_lon, self.start_lat, self.start_depth)
model = ModelController(geometry=p, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4)
cache_path = os.path.join(self.cache_path, "test_run_from_point.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_run_from_polygon(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_run_from_polygon")
models = [self.transport]
poly = Point(self.start_lon, self.start_lat, self.start_depth).buffer(0.001)
model = ModelController(geometry=poly, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4)
cache_path = os.path.join(os.path.dirname(__file__), "..", "paegan/transport/_cache/test_run_from_polygon.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_interp(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_interp")
models = [self.transport]
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4)
cache_path = os.path.join(self.cache_path, "test_interp.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_nearest(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_nearest")
models = [self.transport]
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4, time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_nearest.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_start_on_land(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_start_on_land")
# Set the start position and time for the models
start_lat = 60.15551950079041
start_lon = -148.1999130249019
models = [self.transport]
model = ModelController(latitude=start_lat, longitude=start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4, time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_start_on_land.nc")
with raises(ModelError):
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", cache=cache_path)
def test_bad_dataset(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_bad_dataset")
models = [self.transport]
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=self.num_steps, npart=self.num_particles, models=models, use_bathymetry=False, use_shoreline=True,
time_chunk=10, horiz_chunk=4, time_method='nearest')
cache_path = os.path.join(self.cache_path, "test_bad_dataset.nc")
with raises(DataControllerError):
model.run("http://asascience.com/thisisnotadataset.nc", cache=cache_path)
"""
def test_behavior_growth_and_settlement(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_behavior_growth_and_settlement")
# 6 days
num_steps = 144
num_particles = 2
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/behavior_for_run_testing.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=4, time_method='nearest')
output_path = os.path.join(self.output_path, "test_behavior_growth_and_settlement")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline','Pickle']
cache_path = os.path.join(self.cache_path, "test_behavior_growth_and_settlement.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
"""
def test_quick_settlement(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_quick_settlement")
num_steps = 24
num_particles = 4
# Behavior
behavior_config = open(os.path.normpath(os.path.join(os.path.dirname(__file__),"./resources/files/behavior_quick_settle.json"))).read()
lb = LarvaBehavior(json=behavior_config)
models = [self.transport]
models.append(lb)
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=12, horiz_chunk=2, time_method='nearest')
output_path = os.path.join(self.output_path, "test_quick_settlement")
shutil.rmtree(output_path, ignore_errors=True)
os.makedirs(output_path)
output_formats = ['Shapefile','NetCDF','Trackline','Pickle']
cache_path = os.path.join(self.cache_path, "test_quick_settlement.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path, output_path=output_path, output_formats=output_formats)
def test_timechunk_greater_than_timestep(self):
self.log.logger.info("**************************************")
self.log.logger.info("Running: test_timechunk_greater_than_timestep")
# 6 days
num_steps = 10
num_particles = 2
models = [self.transport]
model = ModelController(latitude=self.start_lat, longitude=self.start_lon, depth=self.start_depth, start=self.start_time, step=self.time_step, nstep=num_steps, npart=num_particles, models=models, use_bathymetry=True, use_shoreline=True,
time_chunk=24, horiz_chunk=2)
cache_path = os.path.join(self.cache_path, "test_timechunk_greater_than_timestep.nc")
model.run("http://thredds.axiomalaska.com/thredds/dodsC/PWS_L2_FCST.nc", bathy=self.bathy_file, cache=cache_path)
"""