def __init__(self, **kwargs):
# initialize common configuration structure
TurfThreatGridFileFactory.__init__(self, **kwargs)
self.path_mode = 'default'
self.riskModels = {
'anthrac': anthracRiskModel,
'bpatch': bpatchRiskModel,
'dspot': dspotRiskModel,
'hstress': hstressRiskModel,
'pblight': pblightRiskModel,
}
self.weatherDataReaders = {
'anthrac': getAnthracWeatherData,
'bpatch': getBpatchWeatherData,
'dspot': getDspotWeatherData,
'hstress': getHstressWeatherData,
'pblight': getPblightWeatherData,
}
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
date_to_fix = options.date_to_fix
debug = options.debug
dev_mode = options.dev_mode
period = options.period
region_key = options.grid_region
verbose = options.verbose or debug
threat_key = args[0]
num_args = len(args)
if num_args == 2: target_year = int(args[1])
# create a factory for disease file access
factory = TurfThreatGridFileFactory(CONFIG)
if dev_mode: factory.useDirpathsForMode('dev')
region = factory.regionConfig(region_key)
threat = factory.threatConfig(threat_key)
# filter annoying numpy warnings
warnings.filterwarnings('ignore', "All-NaN axis encountered")
warnings.filterwarnings('ignore', "All-NaN slice encountered")
warnings.filterwarnings('ignore', "invalid value encountered in greater")
warnings.filterwarnings('ignore', "invalid value encountered in less")
warnings.filterwarnings('ignore', "Mean of empty slice")
# MUST ALSO TURN OFF WARNING FILTERS AT END OF SCRIPT !!!!!
# get grid file builder
manager = factory.threatFileManager(threat_key, period, target_year, region)
msg = '\nAttempting to repair first_valid date in %s threat/risk file :\n%s'
forecast = options.forecast
debug = options.debug
dev_mode = options.dev_mode
region_key = options.region
verbose = options.verbose or debug
threat_key = args[0]
period_key = args[1]
# assume forecast starts today
fcast_start = TODAY
# assume last obs was yesterday
previous_obs = TODAY - ONE_DAY
# factory for accessing threat data files
data_factory = TurfThreatGridFileFactory()
if dev_mode: data_factory.useDirpathsForMode('dev')
region = data_factory.regionConfig(region_key)
def findLastMap(map_factory, previous_obs, threat_key, period_key):
map_factory.turfMapFilename(threat_key, None, region)
if start_date is None:
reader = data_factory.threatFileReader(threat_key, period_key, TODAY.year)
else:
reader = data_factory.threatFileReader(threat_key, period_key,
start_date.year)
if verbose: print 'reading data from :\n', reader.filepath
else: # a single period was passed
periods = (args[1], )
# get reguired information from static file
factory = SeasonalStaticFileFactory()
if dev_mode: factory.useDirpathsForMode('dev')
region = factory.regionConfig(region_key)
source = factory.sourceConfig(source_key)
reader = factory.staticFileReader(source, region)
lats = reader.getData('lat')
lons = reader.getData('lon')
reader.close()
del reader, factory
# create a factory for disease file access
factory = TurfThreatGridFileFactory(CONFIG)
if dev_mode: factory.useDirpathsForMode('dev')
region = factory.regionConfig(region_key)
source = factory.sourceConfig(source_key)
threat = factory.threatConfig(threat_key)
# filter annoying numpy warnings
warnings.filterwarnings('ignore', "All-NaN axis encountered")
warnings.filterwarnings('ignore', "All-NaN slice encountered")
warnings.filterwarnings('ignore', "invalid value encountered in greater")
warnings.filterwarnings('ignore', "invalid value encountered in less")
warnings.filterwarnings('ignore', "Mean of empty slice")
# MUST ALSO TURN OFF WARNING FILTERS AT END OF SCRIPT !!!!!
for period_key in periods:
# get grid file builder
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
debug = options.debug
dev_mode = options.dev_mode
sub_region = options.sub_region
verbose = options.verbose or debug
threat = args[0]
path_key = 'threats.%s' % threat
include_avg = threat != 'hstress'
if num_args == 1: target_year = datetime.date.today().year
elif num_args == 2: target_year = int(args[1])
# create a factory for access to the threat file
factory = TurfThreatGridFileFactory()
if dev_mode: factory.useDirpathsForMode('dev')
region = factory.regionConfig(factory.project.region)
if include_avg:
# open average data file and extract lat, lon, data and it's dates
avg_reader = factory.threatFileReader(threat, 'average', target_year)
avg_dates = avg_reader.dateAttributes('risk', True)
avg_reader.close()
# open daily data file and extract lat, lon, data and it's dates
daily_reader = factory.threatFileReader(threat, 'daily', target_year)
daily_dates = daily_reader.dateAttributes('risk', True)
daily_reader.close()
# extract the dates needed for the json files and create the common json template
debug = options.debug
dev_mode = options.dev_mode
region_key = options.grid_region
verbose = options.verbose or debug
threat_key = args[0]
period = args[1]
new_date = datetime.date(*[int(arg) for arg in args[2:]])
if threat_key == 'hstess':
datasets = ('stress', 'risk')
else:
datasets = ('threat', 'risk')
# create a factory for disease file access
factory = TurfThreatGridFileFactory(CONFIG)
if dev_mode: factory.useDirpathsForMode('dev')
threat_name = factory.threatName(threat_key)
# get grid file builder
manager = factory.threatFileManager(threat_key, period, new_date.year)
manager.close()
msg = '\nAttempting to repair obs dates in %s %s threat/risk file :\n%s'
print msg % (threat_name, period.title(), manager.filepath)
for dataset in datasets:
manager.open('r')
fcast_start_date = manager.dateAttribute(dataset, 'fcast_start_date', None)
last_valid_date = manager.dateAttribute(dataset, 'last_valid_date', None)
last_obs_date = manager.dateAttribute(dataset, 'last_obs_date', None)
print '\nBefore repairs to %s dataset:' % dataset
month = int(args[2])
start_date = datetime.date(year,month,int(args[3]))
if num_date_args == 3: # single day
end_date = start_date
elif num_date_args == 4: # end on different day
end_date = datetime.date(year,month,int(args[4]))
elif num_date_args == 5: # end at different month and day
end_date = datetime.date(year,int(args[4]),int(args[5]))
else:
errmsg = 'Invalid number of date arguments (%d).' % num_date_args
raise ValueError, errmsg
target_year = start_date.year
# factory for accessing threat data files
grid_factory = TurfThreatGridFileFactory()
if dev_mode: grid_factory.useDirpathsForMode('dev')
region = grid_factory.regionConfig(region_key)
reader = grid_factory.gridFileReader(threat_key, 'daily', target_year, region)
if verbose: print 'reading data from :\n', reader.filepath
date_attrs = reader.dateAttributes('risk')
last_valid_date = date_attrs['last_valid_date']
data_start_date = date_attrs['start_date']
# factory for building and accessing map files
map_factory = TurfMapFileFactory()
if dev_mode: map_factory.useDirpathsForMode('dev')
map_options = map_factory.mapOptions(threat_key, region).attrs
threat = map_factory.configForThreat(threat_key)
def useDirpathsForMode(self, mode):
TurfThreatGridFileFactory.useDirpathsForMode(self, mode)
self.path_mode = mode
if arg_2 > 99:
month = int(args[3])
start_date = datetime.date(arg_2, month, int(args[4]))
end_date = datetime.date(arg_2, month, int(args[5]))
else:
year = today.year
start_date = datetime.date(year, arg_2, int(args[3]))
end_date = datetime.date(year, int(args[4]), int(args[5]))
elif num_date_args == 5:
start_date = datetime.date(arg_2, int(args[3]), int(args[4]))
end_date = datetime.date(arg_2, int(args[5]), int(args[6]))
target_year = end_date.year
threat_factory = TurfThreatGridFileFactory()
region = threat_factory.regionConfig(region_key)
period = threat_factory.threatConfig(threat).periods[period_key]
weather_reader = SmartThreatWeatherReader(region)
if dev_mode:
threat_factory.useDirpathsForMode('dev')
weather_reader.useDirpathsForMode('dev')
if start_date is None:
start_date = end_date
end_date += datetime.timedelta(days=period.num_days)
print '\nrequested :'
print ' today =', today