def __init__(self, parameter, lonLat, gridLimit,
gridSpace, gridInc, minSample=100, angular=False,
missingValue=sys.maxsize, progressbar=None,
prgStartValue=0, prgEndValue=1, calculateLater=False):
self.logger = logging.getLogger()
self.logger.debug('Initialising GenerateStats')
self.gridLimit = gridLimit
self.gridSpace = gridSpace
self.gridInc = gridInc
self.maxCell = stats.maxCellNum(self.gridLimit, self.gridSpace)
self.minSample = minSample
self.coeffs = parameters(self.maxCell+1)
self.angular = angular
self.missingValue = missingValue
self.domain_warning_raised = False
self.progressbar = progressbar
self.prgStartValue = prgStartValue
self.prgEndValue = prgEndValue
if not calculateLater:
if type(lonLat) is str:
self.lonLat = np.array(flLoadFile(lonLat, delimiter=','))
else:
self.lonLat = lonLat
if type(parameter) is str:
self.param = np.array(flLoadFile(parameter))
else:
self.param = parameter
self.calculateStatistics()
def setKDEOrigins(self, kdeOriginX=None, kdeOriginY=None, kdeOriginZ=None,
outputPath=None):
"""set kde origin parameters
"""
if outputPath:
try:
self.x, self.y. self.z = grdRead(os.path.join(self.outputPath,
'originPDF.txt'))
except IOError:
self.logger.critical('Error! Files relating to KDE of cyclone origins does not exist. Execute KDE of cyclone origins first.')
raise
self._calculateCDF() #calculate CDF of (x,Px) and (y,Py)
elif type(kdeOriginZ) == str:
try:
self.x = flLoadFile(kdeOriginX)
self.y = flLoadFile(kdeOriginY)
self.z = flLoadFile(kdeOriginZ)
except IOError:
self.logger.critical('Error! Files relating to CDF of cyclone parameters do not exist. Generate KDE of cyclone parameters first.')
raise
self._calculateCDF() # calculate CDF of (x,Px) and (y,Py)
elif type(kdeOriginZ) == ndarray:
self.x, self.y, self.z = grdRead(kdeOriginZ)
self._calculateCDF() # calculate CDF of (x,Px) and (y,Py)
else:
self.logger.error("No input arguments")
raise
def __init__(self, parameter, lonLat, gridLimit,
gridSpace, gridInc, minSample=100, angular=False,
missingValue=sys.maxint, progressbar=None,
prgStartValue=0, prgEndValue=1, calculateLater=False):
self.logger = logging.getLogger()
self.logger.debug('Initialising GenerateStats')
self.gridLimit = gridLimit
self.gridSpace = gridSpace
self.gridInc = gridInc
self.maxCell = stats.maxCellNum(self.gridLimit, self.gridSpace)
self.minSample = minSample
self.coeffs = parameters(self.maxCell+1)
self.angular = angular
self.missingValue = missingValue
self.domain_warning_raised = False
self.progressbar = progressbar
self.prgStartValue = prgStartValue
self.prgEndValue = prgEndValue
if not calculateLater:
if type(lonLat) is str:
self.lonLat = np.array(flLoadFile(lonLat, delimiter=','))
else:
self.lonLat = lonLat
if type(parameter) is str:
self.param = np.array(flLoadFile(parameter))
else:
self.param = parameter
self.calculateStatistics()
def setKDEOrigins(self,
kdeOriginX=None,
kdeOriginY=None,
kdeOriginZ=None,
outputPath=None):
"""
Set kernel density estimation origin parameters.
:param kdeOriginX: x coordinates of kde result generated
from :class:`KDEOrigin`
:param kdeOriginY: y coordinates of kde result generated
from :class:`KDEOrigin`
:param kdeOriginZ: z coordinates of kde result generated
from :class:`KDEOrigin`
:param outputPath: Path to output folder to load PDF file.
:type kdeOriginX: str or :class:`numpy.ndarray`
:type kdeOriginY: str or :class:`numpy.ndarray`
:type kdeOriginZ: str or :class:`numpy.ndarray`
:type outputPath: str
"""
if outputPath:
try:
self.x, self.y, self.z = grdRead(
pjoin(self.outputPath, 'originPDF.txt'))
except IOError:
LOG.critical(('Error! Files relating to KDE of cyclone '
'origins does not exist. Execute KDE of '
'cyclone origins first.'))
raise
self._calculateCDF()
elif isinstance(kdeOriginZ, str):
try:
self.x = flLoadFile(kdeOriginX)
self.y = flLoadFile(kdeOriginY)
self.z = flLoadFile(kdeOriginZ)
except IOError:
LOG.critical(('Error! Files relating to CDF of cyclone '
'parameters do not exist. Generate KDE of '
'cyclone parameters first.'))
raise
self._calculateCDF()
elif isinstance(kdeOriginZ, np.ndarray):
self.x, self.y, self.z = grdRead(kdeOriginZ)
self._calculateCDF()
else:
LOG.error("No input arguments")
raise
def generateGenesisDateCDF(self, genDays, lonLat, bw=None, genesisKDE=None):
"""
Calculate the PDF of genesis day using KDEs.
Since the data is periodic, we use a simple method to include the
periodicity in estimating the PDF. We prepend and append the data
to itself, then use the central third of the PDF and multiply by three to
obtain the required PDF. Probably notquite exact, but it should be
sufficient for our purposes.
"""
data = flLoadFile( genDays )
days = np.arange( 1, 366 )
ndays = np.concatenate( [days - 365, days, days + 365] )
ndata = np.concatenate( [data - 365, data, data + 365] )
if bw is None:
bw = KPDF.UPDFOptimumBandwidth( ndata )
try:
kdeMethod = getattr(KPDF, "UPDF%s" %self.kdeType)
except AttributeError:
self.logger.exception("Invalid input on option: KDE method UPDF%s does not exist"%self.kdeType)
raise
pdf = kdeMethod( ndata, ndays, bw )
# Actual PDF to return
apdf = 3.0*pdf[365:730]
cy = stats.cdf(days, apdf)
if genesisKDE is None:
return np.transpose(np.array(np.concatenate( [days, apdf, cy] ) ))
else:
# Assume both kdeParameters and cdfParameters are defined as files:
self.logger.debug("Saving KDE and CDF data to files")
#flSaveFile(genesisKDE, transpose(numpy.concatenate([days, pdf])))
flSaveFile(genesisKDE, np.transpose(np.array([days, cy])))
def __init__(self, configFile, kdeType, gridLimit, kdeStep, lonLat=None, progressbar=None):
"""
"""
self.logger = logging.getLogger()
self.progressbar = progressbar
if self.progressbar:
KPDF.set_callback(self.updateProgressBar)
self.logger.info("Initialising KDEOrigins")
self.configFile = configFile
self.x = numpy.arange(gridLimit['xMin'], gridLimit['xMax'], kdeStep)
self.y = numpy.arange(gridLimit['yMax'], gridLimit['yMin'], -kdeStep)
self.kdeType = kdeType
self.kdeStep = kdeStep
config = ConfigParser()
config.read(configFile)
if lonLat is None:
self.outputPath = config.get('Output', 'Path')
self.processPath = os.path.join(self.outputPath, 'process')
self.logger.debug("Loading "+os.path.join(self.processPath,
'init_lon_lat'))
ll = flLoadFile(os.path.join(self.processPath, 'init_lon_lat'),
'%', ',')
self.lonLat = ll[:,0:2]
else:
self.lonLat = lonLat[:,0:2]
self.bw = KPDF.MPDFOptimumBandwidth(self.lonLat)
self.logger.debug("Optimal bandwidth: %f"%self.bw)
def generateGenesisDateCDF(self,
genDays,
lonLat,
bw=None,
genesisKDE=None):
"""
Calculate the PDF of genesis day using KDEs.
Since the data is periodic, we use a simple method to include
the periodicity in estimating the PDF. We prepend and append
the data to itself, then use the central third of the PDF and
multiply by three to obtain the required PDF. Probably not
quite exact, but it should be sufficient for our purposes.
:param str genDays: Name of file containing genesis days
(as day of year).
:param lonLat: Array of genesis longitudes and latitudes.
:param float bw: Optional. Bandwidth of the KDE to use.
:param str genesisKDE: Optional. File name to save resulting CDF to.
:type lonLat: :class:`numpy.ndarray`
:returns: :class:`numpy.ndarray` containing the days, the PDF and CDF
of the genesis days.
"""
data = flLoadFile(genDays)
days = np.arange(1, 366)
ndays = np.concatenate([days - 365, days, days + 365])
ndata = np.concatenate([data - 365, data, data + 365])
if bw is None:
bw = stats.bandwidth(self.parameters)
kde = sm.nonparametric.KDEUnivariate(self.parameters)
kde.fit(kernel=self.kdeType,
bw=bw,
fft=False,
gridsize=len(grid),
clip=(min(grid), max(grid)),
cut=0)
#try:
# kdeMethod = getattr(KPDF, "UPDF%s" % self.kdeType)
#except AttributeError:
# LOG.exception(("Invalid input on option: "
# "KDE method UPDF%s does not exist"),
# self.kdeType)
# raise
veceval = np.vectorize(kde.evaluate)
pdf = np.nan_to_num(veceval(grid))
# Actual PDF to return
apdf = 3.0 * pdf[365:730]
cy = stats.cdf(days, apdf)
if genesisKDE is None:
return np.transpose(np.array(np.concatenate([days, apdf, cy])))
else:
# Assume both kdeParameters and cdfParameters are defined as files:
LOG.debug("Saving KDE and CDF data to files")
flSaveFile(genesisKDE, np.transpose(np.array([days, cy])))
def __init__(self, lon_lat, bearing_list, speed_list, pressure_list,
bearing_rate_list, speed_rate_list, pressure_rate_list,
cellNum, gridLimit, gridSpace):
"""
initialize the data needed for the plots including
longitudes & latitudes of cyclone origins,
cyclone bearings,
cyclone speeds,
cyclone pressures,
as well as calculating and storing the
cyclone index counts for a specific inputted cell number
"""
self.gridLimit = gridLimit
self.gridSpace = gridSpace
self.lonlat = files.flLoadFile(lon_lat, '%', ',')
self.bearing_list = files.flLoadFile(bearing_list)
self.speed_list = files.flLoadFile(speed_list)
self.pressure_list = files.flLoadFile(pressure_list)
self.bearingRate_list = files.flLoadFile(bearing_rate_list)
self.speedRate_list = files.flLoadFile(speed_rate_list)
self.pressureRate_list = files.flLoadFile(pressure_rate_list)
self.cellNum = cellNum
self.extractParameters(cellNum)
def __init__(self, lon_lat, bearing_list, speed_list, pressure_list,
bearing_rate_list, speed_rate_list, pressure_rate_list,
cellNum, gridLimit, gridSpace):
"""
initialize the data needed for the plots including
longitudes & latitudes of cyclone origins,
cyclone bearings,
cyclone speeds,
cyclone pressures,
as well as calculating and storing the
cyclone index counts for a specific inputted cell number
"""
self.gridLimit = gridLimit
self.gridSpace = gridSpace
self.lonlat = files.flLoadFile(lon_lat, '%', ',')
self.bearing_list = files.flLoadFile(bearing_list)
self.speed_list = files.flLoadFile(speed_list)
self.pressure_list = files.flLoadFile(pressure_list)
self.bearingRate_list = files.flLoadFile(bearing_rate_list)
self.speedRate_list = files.flLoadFile(speed_rate_list)
self.pressureRate_list = files.flLoadFile(pressure_rate_list)
self.cellNum = cellNum
self.extractParameters(cellNum)
def calc(self):
"""
Calculate the frequency of TC events in a pre-defined domain, based
on the input dataset and the full range of years contained in the
:attr:`origin_year` file.
The :attr:`origin_year` file is created in
:class:`DataProcess.processData` and restricts the range to a
user-selected range of years.
"""
logger.info("Calculating annual frequency of TC events")
origin_year = np.array(flLoadFile(
pjoin(self.outputPath, 'process', 'origin_year'), '%', ','),
dtype='int')
origin_lon_lat = flLoadFile(
pjoin(self.outputPath, 'process', 'origin_lon_lat'), '%', ',')
origin_lon = origin_lon_lat[:, 0]
origin_lat = origin_lon_lat[:, 1]
min_year = origin_year.min()
# Skip last year from average since may contain only partial year record
max_year = origin_year.max() - 1
freq_count = np.zeros(3000)
for year in range(min_year, max_year + 1):
freq_count[year] = sum((origin_year == year) & \
(origin_lon > self.tg_domain['xMin']) & \
(origin_lon < self.tg_domain['xMax']) & \
(origin_lat > self.tg_domain['yMin']) & \
(origin_lat < self.tg_domain['yMax']))
freq = np.mean(freq_count[min_year:max_year + 1])
freq = np.round(freq * 100) / 100
fname = pjoin(self.outputPath, 'process', 'region_frequency')
data = np.array([
np.arange(min_year, max_year + 1),
freq_count[min_year:max_year + 1]
])
header = "Year,count"
np.savetxt(fname, data.T, fmt="%d", delimiter=",", header=header)
return freq
def calc(self):
"""
Calculate the frequency of TC events in a pre-defined domain, based
on the input dataset and the full range of years contained in the
:attr:`origin_year` file.
The :attr:`origin_year` file is created in
:class:`DataProcess.processData` and restricts the range to a
user-selected range of years.
"""
logger.info("Calculating annual frequency of TC events")
origin_year = np.array(flLoadFile(pjoin(self.outputPath,
'process', 'origin_year'),
'%', ','), dtype='int')
origin_lon_lat = flLoadFile(pjoin(self.outputPath,
'process', 'origin_lon_lat'),
'%', ',')
origin_lon = origin_lon_lat[:, 0]
origin_lat = origin_lon_lat[:, 1]
min_year = origin_year.min()
# Skip last year from average since may contain only partial year record
max_year = origin_year.max() - 1
freq_count = np.zeros(3000)
for year in range(min_year, max_year + 1):
freq_count[year] = sum((origin_year == year) & \
(origin_lon > self.tg_domain['xMin']) & \
(origin_lon < self.tg_domain['xMax']) & \
(origin_lat > self.tg_domain['yMin']) & \
(origin_lat < self.tg_domain['yMax']))
freq = np.mean(freq_count[min_year:max_year + 1])
freq = np.round(freq*100)/100
fname = pjoin(self.outputPath, 'process', 'region_frequency')
X = np.array([np.arange(min_year,max_year + 1),
freq_count[min_year:max_year + 1]])
header = "Year,count"
np.savetxt(fname, X.T, fmt="%d", delimiter=",", header=header)
return freq
def setKDEOrigins(self, kdeOriginX=None, kdeOriginY=None, kdeOriginZ=None,
outputPath=None):
"""
Set kernel density estimation origin parameters.
:param kdeOriginX: x coordinates of kde result generated
from :class:`KDEOrigin`
:param kdeOriginY: y coordinates of kde result generated
from :class:`KDEOrigin`
:param kdeOriginZ: z coordinates of kde result generated
from :class:`KDEOrigin`
:param outputPath: Path to output folder to load PDF file.
:type kdeOriginX: str or :class:`numpy.ndarray`
:type kdeOriginY: str or :class:`numpy.ndarray`
:type kdeOriginZ: str or :class:`numpy.ndarray`
:type outputPath: str
"""
if outputPath:
try:
self.x, self.y. self.z = grdRead(os.path.join(self.outputPath,
'originPDF.txt'))
except IOError:
self.logger.critical('Error! Files relating to KDE of cyclone origins does not exist. Execute KDE of cyclone origins first.')
raise
self._calculateCDF() #calculate CDF of (x,Px) and (y,Py)
elif type(kdeOriginZ) == str:
try:
self.x = flLoadFile(kdeOriginX)
self.y = flLoadFile(kdeOriginY)
self.z = flLoadFile(kdeOriginZ)
except IOError:
self.logger.critical('Error! Files relating to CDF of cyclone parameters do not exist. Generate KDE of cyclone parameters first.')
raise
self._calculateCDF() # calculate CDF of (x,Px) and (y,Py)
elif type(kdeOriginZ) == np.ndarray:
self.x, self.y, self.z = grdRead(kdeOriginZ)
self._calculateCDF() # calculate CDF of (x,Px) and (y,Py)
else:
self.logger.error("No input arguments")
raise
def __init__(self, configFile):
"""
Read configuration settings, load station data and set up
output recarrays.
:param str configFile: path to a configuration file.
"""
config = ConfigParser()
config.read(configFile)
self.meta = False
stnFile = config.get('Timeseries', 'LocationFile')
self.outputPath = pjoin(config.get('Output', 'Path'),
'process', 'timeseries')
self.maxfile = pjoin(config.get('Output', 'Path'),
'process', 'maxima.csv')
self.minfile = pjoin(config.get('Output', 'Path'),
'process', 'minima.csv')
log.info(f"Loading timeseries stations from {stnFile}")
log.debug(f"Timeseries data will be written into {self.outputPath}")
self.stations = []
if stnFile.endswith("shp"):
try:
key_name = config.get('Timeseries', 'StationID')
except NoOptionError:
key_name = None
vertices = shpGetVertices(stnFile, key_name=key_name)
for stn in list(vertices.keys()):
lat = vertices[stn][0][1]
lon = vertices[stn][0][0]
lon = np.where(lon < 0., lon + 360., lon)
self.stations.append(Station(stn, lon, lat))
else:
stndata = flLoadFile(stnFile, delimiter=',')
# If there are more than 3 columns, save the additional
# columns as 'metadata'
if stndata.shape[1] > 3:
self.metadata = stndata[:, 3:]
self.meta = True
stnid = stndata[:, 0]
stnlon = stndata[:, 1].astype(float)
stnlat = stndata[:, 2].astype(float)
for sid, lon, lat in zip(stnid, stnlon, stnlat):
self.stations.append(Station(sid, lon, lat))
log.info(f"There are {len(self.stations)} stations that will collect timeseries data")
def __init__(self, configFile):
"""
Read configuration settings, load station data and set up
output recarrays.
:param str configFile: path to a configuration file.
"""
config = ConfigParser()
config.read(configFile)
self.meta = False
stnFile = config.get('Timeseries', 'StationFile')
self.outputPath = pjoin(config.get('Output', 'Path'),
'process', 'timeseries')
self.maxfile = pjoin(config.get('Output', 'Path'),
'process', 'maxima.csv')
self.minfile = pjoin(config.get('Output', 'Path'),
'process', 'minima.csv')
log.debug("Loading stations from %s"%stnFile)
log.debug("Timeseries data will be written into %s"%self.outputPath)
self.stations = []
if stnFile.endswith("shp"):
try:
key_name = config.get('Timeseries', 'StationID')
except NoOptionError:
key_name = None
vertices = shpGetVertices(stnFile, key_name=key_name)
for stn in vertices.keys():
self.stations.append(Station(stn, vertices[stn][0][0],
vertices[stn][0][1]))
else:
stndata = flLoadFile(stnFile, delimiter=',')
# If there are more than 3 columns, save the additional
# columns as 'metadata'
if stndata.shape[1] > 3:
self.metadata = stndata[:, 3:]
self.meta = True
stnid = stndata[:, 0]
stnlon = stndata[:, 1].astype(float)
stnlat = stndata[:, 2].astype(float)
for sid, lon, lat in zip(stnid, stnlon, stnlat):
self.stations.append(Station(sid, lon, lat))
def setParameters(self, cdfParameters):
"""Set parameters
"""
if type(cdfParameters) == str:
try:
self.xacy = flLoadFile(cdfParameters)
except IOError:
self.logger.exception('Error! Files relating to cdf of cyclone parameters does not exist, please generate KDE of cyclone parameters first.')
raise
else:
self.xacy = cdfParameters
return self
def generateGenesisDateCDF(self,
genDays,
lonLat,
bw=None,
genesisKDE=None):
"""
Calculate the PDF of genesis day using KDEs.
Since the data is periodic, we use a simple method to include
the periodicity in estimating the PDF. We prepend and append
the data to itself, then use the central third of the PDF and
multiply by three to obtain the required PDF. Probably not
quite exact, but it should be sufficient for our purposes.
:param str genDays: Name of file containing genesis days
(as day of year).
:param lonLat: Array of genesis longitudes and latitudes.
:param float bw: Optional. Bandwidth of the KDE to use.
:param str genesisKDE: Optional. File name to save resulting CDF to.
:type lonLat: :class:`numpy.ndarray`
:returns: :class:`numpy.ndarray` containing the days, the PDF and CDF
of the genesis days.
"""
data = flLoadFile(genDays)
days = np.arange(1, 366)
ndays = np.concatenate([days - 365, days, days + 365])
ndata = np.concatenate([data - 365, data, data + 365])
if bw is None:
bw = KPDF.UPDFOptimumBandwidth(ndata)
try:
kdeMethod = getattr(KPDF, "UPDF%s" % self.kdeType)
except AttributeError:
LOG.exception(("Invalid input on option: "
"KDE method UPDF%s does not exist"), self.kdeType)
raise
pdf = kdeMethod(ndata, ndays, bw)
# Actual PDF to return
apdf = 3.0 * pdf[365:730]
cy = stats.cdf(days, apdf)
if genesisKDE is None:
return np.transpose(np.array(np.concatenate([days, apdf, cy])))
else:
# Assume both kdeParameters and cdfParameters are defined as files:
LOG.debug("Saving KDE and CDF data to files")
flSaveFile(genesisKDE, np.transpose(np.array([days, cy])))
def __init__(self, cdfParameters=None):
"""Initialize the data needed for the plots including CDF of
cyclone parameters
"""
self.logger = logging.getLogger()
if type(cdfParameters) == str:
try:
self.xacy = flLoadFile(cdfParameters)
except IOError:
self.logger.exception('Error! Files relating to cdf of cyclone parameters does not exist, please generate KDE of cyclone parameters first.')
raise
elif type(cdfParameters) == ndarray:
self.xacy = cdfParameters
else:
self.xacy = array([])
def __init__(self, cdfParameters=None):
"""Initialize the data needed for the plots including CDF of
cyclone parameters
"""
self.logger = logging.getLogger()
if type(cdfParameters) == str:
try:
self.xacy = flLoadFile(cdfParameters)
except IOError:
self.logger.exception('Error! Files relating to cdf of cyclone parameters does not exist, please generate KDE of cyclone parameters first.')
raise
elif type(cdfParameters) == np.ndarray:
self.xacy = cdfParameters
else:
self.xacy = np.array([])
def __init__(self,
configFile,
gridLimit,
kdeStep,
lonLat=None,
progressbar=None):
"""
"""
self.progressbar = progressbar
LOGGER.info("Initialising KDEOrigin")
self.x = np.arange(gridLimit['xMin'], gridLimit['xMax'], kdeStep)
self.y = np.arange(gridLimit['yMax'], gridLimit['yMin'], -kdeStep)
self.kdeStep = kdeStep
self.kde = None
self.pdf = None
self.cz = None
self.configFile = configFile
self.config = ConfigParser()
self.config.read(configFile)
if lonLat is None:
# Load the data from file:
self.outputPath = self.config.get('Output', 'Path')
self.processPath = pjoin(self.outputPath, 'process')
LOGGER.debug("Loading " + pjoin(self.processPath, 'init_lon_lat'))
ll = flLoadFile(pjoin(self.processPath, 'init_lon_lat'), '%', ',')
self.lonLat = ll[:, 0:2]
else:
self.lonLat = lonLat[:, 0:2]
ii = np.where((self.lonLat[:, 0] >= gridLimit['xMin'])
& (self.lonLat[:, 0] <= gridLimit['xMax'])
& (self.lonLat[:, 1] >= gridLimit['yMin'])
& (self.lonLat[:, 1] <= gridLimit['yMax']))
self.lonLat = self.lonLat[ii]
self.bw = getOriginBandwidth(self.lonLat)
LOGGER.info("Bandwidth: %s", repr(self.bw))
def calcDomainFromFile(self):
"""
Calculate track generation domain, using a file as the input source
:rtype: dict
:returns: the domain where the tracks will be generated.
The :class:`dict` should contain the keys :attr:`xMin`,
:attr:`xMax`, :attr:`yMin` and :attr:`yMax`. The *x*
variable bounds the longitude and the *y* variable
bounds the latitude.
"""
# Load tracks from file
cyclone_tracks = flLoadFile(
pjoin(self.outputPath, 'process', 'cyclone_tracks'), '%', ',')
tg_domain = self.calc(cyclone_tracks[:, 0], cyclone_tracks[:, 1],
cyclone_tracks[:, 2])
return tg_domain
def calcDomainFromFile(self):
"""
Calculate track generation domain, using a file as the input source
:rtype tg_domain: :class:`dict`
:return tg_domain: the domain where the tracks will be generated.
The :class:`dict` should contain the keys :attr:`xMin`,
:attr:`xMax`, :attr:`yMin` and :attr:`yMax`. The *x*
variable bounds the longitude and the *y* variable
bounds the latitude.
"""
# Load tracks from file
cyclone_tracks = flLoadFile(pjoin(self.outputPath, 'process',
'cyclone_tracks'),
'%', ',')
tg_domain = self._calc(cyclone_tracks[:, 0],
cyclone_tracks[:, 1],
cyclone_tracks[:, 2])
return tg_domain
def setParameters(self, cdfParameters):
"""
Set parameters.
:param cdfParameters: Name of a file containing the CDF of
a parameter, or the actual CDF values.
:type cdfParamters: str or :class:`numpy.ndarray`
:raises IOError: If the CDF files do not exist.
"""
if type(cdfParameters) == str:
try:
self.xacy = flLoadFile(cdfParameters)
except IOError:
self.logger.exception('Error! Files relating to cdf of cyclone parameters does not exist, please generate KDE of cyclone parameters first.')
raise
else:
self.xacy = cdfParameters
return self
def setParameters(self, cdfParameters):
"""
Set parameters.
:param cdfParameters: Name of a file containing the CDF of
a parameter, or the actual CDF values.
:type cdfParamters: str or :class:`numpy.ndarray`
:raises IOError: If the CDF files do not exist.
"""
if type(cdfParameters) == str:
try:
self.xacy = flLoadFile(cdfParameters)
except IOError:
self.logger.exception(
"Error! Files relating to cdf of cyclone parameters does not exist, please generate KDE of cyclone parameters first."
)
raise
else:
self.xacy = cdfParameters
return self
def main():
import Utilities.files as files
from os.path import join as pjoin, dirname, normpath
baseDir = normpath(pjoin(dirname(__file__), '..'))
inputPath = pjoin(baseDir, 'output', 'process')
saveWindProfilesFigure(-12., 130., 100700., 95000., 30., 1.6)
pressureRates = files.flLoadFile(pjoin(inputPath, 'pressure_rate'))
pressures = files.flLoadFile(pjoin(inputPath, 'all_pressure'))
savePressureFigure(pressures, pressureRates)
speedRates = files.flLoadFile(pjoin(inputPath, 'speed_rate'))
speeds = files.flLoadFile(pjoin(inputPath, 'all_speed'))
saveSpeedFigures(speeds, speedRates)
bearingRates = files.flLoadFile(pjoin(inputPath, 'bearing_rate'))
bearings = files.flLoadFile(pjoin(inputPath, 'all_bearing'))
saveBearingFigure(bearings, bearingRates)
freq = files.flLoadFile(pjoin(inputPath, 'frequency'))
saveFrequencyFigure(np.array(freq[:,0],int), freq[:,1])
def main():
import Utilities.files as files
from os.path import join as pjoin, dirname, normpath
baseDir = normpath(pjoin(dirname(__file__), '..'))
inputPath = pjoin(baseDir, 'output', 'process')
saveWindProfilesFigure(-12., 130., 100700., 95000., 30., 1.6)
pressureRates = files.flLoadFile(pjoin(inputPath, 'pressure_rate'))
pressures = files.flLoadFile(pjoin(inputPath, 'all_pressure'))
savePressureFigure(pressures, pressureRates)
speedRates = files.flLoadFile(pjoin(inputPath, 'speed_rate'))
speeds = files.flLoadFile(pjoin(inputPath, 'all_speed'))
saveSpeedFigures(speeds, speedRates)
bearingRates = files.flLoadFile(pjoin(inputPath, 'bearing_rate'))
bearings = files.flLoadFile(pjoin(inputPath, 'all_bearing'))
saveBearingFigure(bearings, bearingRates)
freq = files.flLoadFile(pjoin(inputPath, 'frequency'))
saveFrequencyFigure(np.array(freq[:, 0], int), freq[:, 1])
def allDistributions(self, lonLat, parameterList, parameterName=None,
kdeStep=0.1, angular=False, periodic=False,
plotParam=False):
"""
Calculate a distribution for each individual cell and store in a
file or return the distribution.
:param lonLat: The longitude/latitude of all observations in
the model domain. If a string is given, then
it is the path to a file containing the
longitude/latitude information. If an array
is given, then it should be a 2-d array
containing the data values.
:type lonLat: str or :class:`numpy.ndarray`
:param parameterList: Parameter values. If a string is given,
then it is the path to a file containing
the values. If an array is passed, then it
should hold the parameter values.
:type parameterList: str or :class:`numpy.ndarray`
:param str parameterName: Optional. If given, then the
cell distributions will be saved to a
file with this name. If absent,
the distribution values are returned.
:param kdeStep: Increment of the ordinate values at which
the distributions will be calculated.
:type kdeStep: float, default=`0.1`
:param angular: Does the data represent an angular measure
(e.g. bearing).
:type angular: boolean, default=``False``
:param periodic: Does the data represent some form of periodic
data (e.g. day of year). If given, it should
be the period of the data (e.g. for annual data,
``periodic=365``).
:type periodic: boolean or float, default=``False``
:param boolean plotParam: Plot the parameters. Default is ``False``.
:returns: If no ``parameterName`` is given returns ``None``
(data are saved to file), otherwise
:class:`numpy.ndarray`.
"""
if parameterName:
self.logger.debug("Running allDistributions for %s",
parameterName)
else:
self.logger.debug("Running allDistributions")
if isinstance(lonLat, str):
self.logger.debug("Loading lat/lon data from file")
self.lonLat = np.array(flLoadFile(lonLat, delimiter=','))
else:
self.lonLat = lonLat
if isinstance(parameterList, str):
self.logger.debug("Loading parameter data from file: %s",
parameterList)
self.pList = np.array(flLoadFile(parameterList))
else:
self.pList = parameterList
self.pName = parameterName
if len(self.pList) != len(self.lonLat):
errmsg = ("Parameter data and "
"Lon/Lat data are not the same length "
"for {}.".format(parameterName))
self.logger.critical(errmsg)
raise IndexError(errmsg)
maxCellNum = stats.maxCellNum(self.gridLimit, self.gridSpace)
# Writing CDF dataset for all individual cell number into files
self.logger.debug(("Writing CDF dataset for all individual "
"cells into files"))
for cellNum in range(0, maxCellNum + 1):
self.logger.debug("Processing cell number %i", cellNum)
# Generate cyclone parameter data for the cell number
self.extractParameter(cellNum)
# Estimate cyclone parameter data using KDE
# The returned array contains the grid, the PDF and the CDF
cdf = self.kdeParameter.generateKDE(self.parameter, kdeStep,
angular=angular,
periodic=periodic)
if plotParam:
self._plotParameter(cellNum, kdeStep)
self.logger.debug(('size of parameter array = %d: '
'size of cdf array = %d'),
self.parameter.size, cdf.size)
cellNumlist = []
for i in range(len(cdf)):
cellNumlist.append(cellNum)
if cellNum == 0:
results = np.transpose(np.array([cellNumlist,
cdf[:, 0], cdf[:, 2]]))
else:
self.logger.debug('size of results = %s', str(results.size))
results = np.concatenate((results,
np.transpose(np.array([cellNumlist,
cdf[:, 0],
cdf[:, 2]]))))
if parameterName == None:
self.logger.debug(("Returning CDF dataset for all "
"individual cell numbers"))
return results
else:
cdfHeader = "Cell_Number, CDF_" + self.pName + "_x, CDF_" + \
self.pName + "_y"
allCellCdfOutput = pjoin(self.outputPath, 'process',
'all_cell_cdf_' + self.pName)
args = {"filename":allCellCdfOutput, "data":results,
"header":cdfHeader, "delimiter":",", "fmt":"%f"}
self.logger.debug(("Writing CDF dataset for all individual "
"cell numbers into files"))
flSaveFile(**args)
# Save to netcdf too
filename = allCellCdfOutput + '.nc'
ncdf = Dataset(filename, 'w')
ncdf.createDimension('cell', len(results[:, 0]))
cell = ncdf.createVariable('cell', 'i', ('cell',))
cell[:] = results[:, 0]
x = ncdf.createVariable('x', 'f', ('cell',))
x[:] = results[:, 1]
y = ncdf.createVariable('CDF', 'f', ('cell',))
y[:] = results[:, 2]
ncdf.close()
def allDistributions(self, lonLat, parameterList, parameterName=None,
kdeStep=0.1, angular=False, periodic=False,
plotParam=False):
"""
Calculate a distribution for each individual cell and store in a
file or return
"""
if parameterName:
self.logger.debug("Running allDistributions for %s"%parameterName)
else:
self.logger.debug("Running allDistributions")
if type(lonLat) is str:
self.logger.debug("Loading lat/lon data from file")
self.lonLat = np.array(flLoadFile(lonLat, delimiter=','))
else:
self.lonLat = lonLat
if type(parameterList) is str:
self.logger.debug("Loading parameter data from file: %s" %
parameterList)
self.pList = np.array(flLoadFile(parameterList))
else:
self.pList = parameterList
self.pName = parameterName
maxCellNum = stats.maxCellNum(self.gridLimit, self.gridSpace)
# Writing CDF dataset for all individual cell number into files
self.logger.debug("Writing CDF dataset for all individual cells into files")
for cellNum in xrange(0, maxCellNum + 1):
self.logger.debug("Processing cell number %i"%cellNum)
# Generate cyclone parameter data for the cell number
self.extractParameter(cellNum)
# Estimate cyclone parameter data using KDE
# The returned array contains the grid, the PDF and the CDF
cdf = self.kdeParameter.generateKDE(self.parameter, kdeStep,
angular=angular,
periodic=periodic)
if plotParam:
self._plotParameter(cellNum, kdeStep)
self.logger.debug('size of parameter array = %d: size of cdf array = %d'
% (self.parameter.size,cdf.size))
cellNumlist = []
for i in range(len(cdf)):
cellNumlist.append(cellNum)
if cellNum == 0:
results = np.transpose(np.array([cellNumlist, cdf[:,0], cdf[:,2]]))
else:
self.logger.debug('size of results array = %s'%str(results.size))
results = np.concatenate((results, np.transpose(np.array([cellNumlist,
cdf[:,0],
cdf[:,2]]))))
if parameterName == None:
self.logger.debug("Returning CDF dataset for all individual cell numbers")
return results
else:
cdfHeader = "Cell_Number, CDF_" + self.pName + "_x, CDF_" + \
self.pName + "_y"
allCellCdfOutput = pjoin(self.outputPath, 'process',
'all_cell_cdf_' + self.pName)
args = {"filename":allCellCdfOutput, "data":results,
"header":cdfHeader, "delimiter":",", "fmt":"%f"}
self.logger.debug("Writing CDF dataset for all individual cell numbers into files")
flSaveFile(**args)
# Save to netcdf too
filename = allCellCdfOutput + '.nc'
ncdf = Dataset(filename, 'w')
ncdf.createDimension('cell', len(results[:,0]))
cell = ncdf.createVariable('cell', 'i', ('cell',))
cell[:] = results[:,0]
x = ncdf.createVariable('x', 'f', ('cell',))
x[:] = results[:,1]
y = ncdf.createVariable('CDF', 'f', ('cell',))
y[:] = results[:,2]
ncdf.close()
def generateKDE(self, parameters, kdeStep, kdeParameters=None,
cdfParameters=None, angular=False, periodic=False,
missingValue=sys.maxint):
"""
Generate a PDF and CDF for a given parameter set using the
method of kernel density estimators.
Optionally return the PDF and CDF as an array, or write both
to separate files.
"""
self.logger.debug("Running generateKDE")
if type(parameters) is str:
self.parameters = stats.statRemoveNum(flLoadFile(parameters, '%', ','), missingValue)
else:
if parameters.size <= 1:
self.logger.error("Insufficient members in parameter list")
raise IndexError, "Insufficient members in parameter list"
self.parameters = stats.statRemoveNum(parameters, missingValue)
if angular:
xmin = 0.0
xmax = 360.0
elif periodic:
xmin = 0.0
xmax = periodic
else:
xmin = self.parameters.min()
xmax = self.parameters.max()
self.logger.debug("xmin=%7.3f, xmax=%7.3f, kdeStep=%7.3f" %
(xmin, xmax, kdeStep))
if periodic:
x = np.arange(1, periodic + 1, kdeStep)
self.grid = np.concatenate( [x - periodic, x, x + periodic] )
self.parameters = np.concatenate([self.parameters - periodic,
self.parameters,
self.parameters + periodic])
else:
self.grid = np.arange(xmin, xmax, kdeStep)
if self.grid.size<2:
self.logger.critical("Grid for CDF generation is a single value")
self.logger.critical("xmin=%7.3f, xmax=%7.3f, kdeStep=%7.3f" %
(xmin, xmax,kdeStep))
raise ValueError
bw = KPDF.UPDFOptimumBandwidth(self.parameters)
self.pdf = self._generatePDF(self.grid, bw, self.parameters)
if periodic:
self.pdf = 3.0*self.pdf[(periodic/kdeStep):2*(periodic/kdeStep)]
self.grid = self.grid[(periodic/kdeStep):2*(periodic/kdeStep)]
self.cy = stats.cdf(self.grid, self.pdf)
if kdeParameters is None:
return np.transpose(np.array([self.grid, self.pdf, self.cy]))
else:
# Assume both kdeParameters and cdfParameters are defined as files:
self.logger.debug("Saving KDE and CDF data to files")
flSaveFile(kdeParameters, np.transpose(np.array([self.grid, self.pdf])))
flSaveFile(cdfParameters, np.transpose(np.array([self.grid, self.cy])))
def testLoadFile(self):
"""Test flLoadFile loads data correctly"""
data = files.flLoadFile(self.testfile, comments='%', delimiter=',')
assert_almost_equal(self.lon, data[:, 0])
assert_almost_equal(self.lat, data[:, 1])
def generateKDE(self,
parameters,
kdeStep,
kdeParameters=None,
cdfParameters=None,
angular=False,
periodic=False,
missingValue=sys.maxsize):
"""
Generate a PDF and CDF for a given parameter set using the
method of kernel density estimators. Optionally return the PDF
and CDF as an array, or write both to separate files.
:param parameters: Parameter values. If a string is given,
then it is the path to a file containing
the values. If an array is passed, then it
should hold the parameter values.
:param kdeStep: Increment of the ordinate values at which
the distributions will be calculated.
:type kdeStep: float, default=`0.1`
:param str kdeParameters: Optional. If given, then the
cell distributions will be saved to a
file with this name. If absent,
the distribution values are returned.
:param str cdfParameters: Optional. If given, then the
cell distributions will be saved to a
file with this name. If absent,
the distribution values are returned.
:param angular: Does the data represent an angular measure
(e.g. bearing).
:type angular: boolean, default=``False``
:param periodic: Does the data represent some form of periodic
data (e.g. day of year). If given, it should
be the period of the data (e.g. for annual data,
``periodic=365``).
:type periodic: boolean or int, default=``False``
:param missingValue: Missing values have this value (default
:attr:`sys.maxint`).
returns: If ``kdeParameters`` is given, returns ``None``
(data are saved to file), otherwise
:class:`numpy.ndarray` of the parameter grid, the PDF and CDF.
"""
LOG.debug("Running generateKDE")
if type(parameters) is str:
self.parameters = stats.statRemoveNum(
flLoadFile(parameters, '%', ','), missingValue)
else:
if parameters.size <= 1:
LOG.error("Insufficient members in parameter list")
raise IndexError("Insufficient members in parameter list")
self.parameters = stats.statRemoveNum(parameters, missingValue)
if angular:
xmin = 0.0
xmax = 360.0
elif periodic:
xmin = 0.0
xmax = periodic
else:
xmin = self.parameters.min()
xmax = self.parameters.max()
LOG.debug("xmin=%7.3f, xmax=%7.3f, kdeStep=%7.3f" %
(xmin, xmax, kdeStep))
if periodic:
x = np.arange(1, periodic + 1, kdeStep)
self.grid = np.concatenate([x - periodic, x, x + periodic])
self.parameters = np.concatenate([
self.parameters - periodic, self.parameters,
self.parameters + periodic
])
else:
self.grid = np.arange(xmin, xmax, kdeStep)
if self.grid.size < 2:
LOG.critical("Grid for CDF generation is a single value")
LOG.critical("xmin=%7.3f, xmax=%7.3f, kdeStep=%7.3f", xmin, xmax,
kdeStep)
raise ValueError
#bw = KPDF.UPDFOptimumBandwidth(self.parameters)
bw = stats.bandwidth(self.parameters)
self.pdf = self._generatePDF(self.grid, bw, self.parameters)
if periodic:
idx = int(periodic / kdeStep)
self.pdf = 3.0 * self.pdf[idx:2 * idx]
self.grid = self.grid[idx:2 * idx]
self.cy = stats.cdf(self.grid, self.pdf)
if kdeParameters is None:
return np.transpose(np.array([self.grid, self.pdf, self.cy]))
else:
# Assume both kdeParameters and cdfParameters are defined as files:
LOG.debug("Saving KDE and CDF data to files")
flSaveFile(kdeParameters,
np.transpose(np.array([self.grid, self.pdf])))
flSaveFile(cdfParameters,
np.transpose(np.array([self.grid, self.cy])))
def allDistributions(self, lonLat, parameterList, parameterName=None,
kdeStep=0.1, angular=False, periodic=False,
plotParam=False):
"""
Calculate a distribution for each individual cell and store in a
file or return the distribution.
:param lonLat: The longitude/latitude of all observations in
the model domain. If a string is given, then
it is the path to a file containing the
longitude/latitude information. If an array
is given, then it should be a 2-d array
containing the data values.
:type lonLat: str or :class:`numpy.ndarray`
:param parameterList: Parameter values. If a string is given,
then it is the path to a file containing
the values. If an array is passed, then it
should hold the parameter values.
:type parameterList: str or :class:`numpy.ndarray`
:param str parameterName: Optional. If given, then the
cell distributions will be saved to a
file with this name. If absent,
the distribution values are returned.
:param kdeStep: Increment of the ordinate values at which
the distributions will be calculated.
:type kdeStep: float, default=`0.1`
:param angular: Does the data represent an angular measure
(e.g. bearing).
:type angular: boolean, default=``False``
:param periodic: Does the data represent some form of periodic
data (e.g. day of year). If given, it should
be the period of the data (e.g. for annual data,
``periodic=365``).
:type periodic: boolean or float, default=``False``
:param boolean plotParam: Plot the parameters. Default is ``False``.
:returns: If no ``parameterName`` is given returns ``None``
(data are saved to file), otherwise
:class:`numpy.ndarray`.
"""
if parameterName:
self.logger.debug("Running allDistributions for %s"%parameterName)
else:
self.logger.debug("Running allDistributions")
if type(lonLat) is str:
self.logger.debug("Loading lat/lon data from file")
self.lonLat = np.array(flLoadFile(lonLat, delimiter=','))
else:
self.lonLat = lonLat
if type(parameterList) is str:
self.logger.debug("Loading parameter data from file: %s" %
parameterList)
self.pList = np.array(flLoadFile(parameterList))
else:
self.pList = parameterList
self.pName = parameterName
maxCellNum = stats.maxCellNum(self.gridLimit, self.gridSpace)
# Writing CDF dataset for all individual cell number into files
self.logger.debug("Writing CDF dataset for all individual cells into files")
for cellNum in xrange(0, maxCellNum + 1):
self.logger.debug("Processing cell number %i"%cellNum)
# Generate cyclone parameter data for the cell number
self.extractParameter(cellNum)
# Estimate cyclone parameter data using KDE
# The returned array contains the grid, the PDF and the CDF
cdf = self.kdeParameter.generateKDE(self.parameter, kdeStep,
angular=angular,
periodic=periodic)
if plotParam:
self._plotParameter(cellNum, kdeStep)
self.logger.debug('size of parameter array = %d: size of cdf array = %d'
% (self.parameter.size,cdf.size))
cellNumlist = []
for i in range(len(cdf)):
cellNumlist.append(cellNum)
if cellNum == 0:
results = np.transpose(np.array([cellNumlist, cdf[:,0], cdf[:,2]]))
else:
self.logger.debug('size of results array = %s'%str(results.size))
results = np.concatenate((results, np.transpose(np.array([cellNumlist,
cdf[:,0],
cdf[:,2]]))))
if parameterName == None:
self.logger.debug("Returning CDF dataset for all individual cell numbers")
return results
else:
cdfHeader = "Cell_Number, CDF_" + self.pName + "_x, CDF_" + \
self.pName + "_y"
allCellCdfOutput = pjoin(self.outputPath, 'process',
'all_cell_cdf_' + self.pName)
args = {"filename":allCellCdfOutput, "data":results,
"header":cdfHeader, "delimiter":",", "fmt":"%f"}
self.logger.debug("Writing CDF dataset for all individual cell numbers into files")
flSaveFile(**args)
# Save to netcdf too
filename = allCellCdfOutput + '.nc'
ncdf = Dataset(filename, 'w')
ncdf.createDimension('cell', len(results[:,0]))
cell = ncdf.createVariable('cell', 'i', ('cell',))
cell[:] = results[:,0]
x = ncdf.createVariable('x', 'f', ('cell',))
x[:] = results[:,1]
y = ncdf.createVariable('CDF', 'f', ('cell',))
y[:] = results[:,2]
ncdf.close()
def generateKDE(self, parameters, kdeStep, kdeParameters=None,
cdfParameters=None, angular=False, periodic=False,
missingValue=sys.maxint):
"""
Generate a PDF and CDF for a given parameter set using the
method of kernel density estimators. Optionally return the PDF
and CDF as an array, or write both to separate files.
:param parameters: Parameter values. If a string is given,
then it is the path to a file containing
the values. If an array is passed, then it
should hold the parameter values.
:param kdeStep: Increment of the ordinate values at which
the distributions will be calculated.
:type kdeStep: float, default=`0.1`
:param str kdeParameters: Optional. If given, then the
cell distributions will be saved to a
file with this name. If absent,
the distribution values are returned.
:param str cdfParameters: Optional. If given, then the
cell distributions will be saved to a
file with this name. If absent,
the distribution values are returned.
:param angular: Does the data represent an angular measure
(e.g. bearing).
:type angular: boolean, default=``False``
:param periodic: Does the data represent some form of periodic
data (e.g. day of year). If given, it should
be the period of the data (e.g. for annual data,
``periodic=365``).
:type periodic: boolean or float, default=``False``
:param missingValue: Missing values have this value (default
:attr:`sys.maxint`).
returns: If ``kdeParameters`` is given, returns ``None``
(data are saved to file), otherwise
:class:`numpy.ndarray` of the parameter grid, the PDF and CDF.
"""
self.logger.debug("Running generateKDE")
if type(parameters) is str:
self.parameters = stats.statRemoveNum(flLoadFile(parameters, '%', ','), missingValue)
else:
if parameters.size <= 1:
self.logger.error("Insufficient members in parameter list")
raise IndexError, "Insufficient members in parameter list"
self.parameters = stats.statRemoveNum(parameters, missingValue)
if angular:
xmin = 0.0
xmax = 360.0
elif periodic:
xmin = 0.0
xmax = periodic
else:
xmin = self.parameters.min()
xmax = self.parameters.max()
self.logger.debug("xmin=%7.3f, xmax=%7.3f, kdeStep=%7.3f" %
(xmin, xmax, kdeStep))
if periodic:
x = np.arange(1, periodic + 1, kdeStep)
self.grid = np.concatenate( [x - periodic, x, x + periodic] )
self.parameters = np.concatenate([self.parameters - periodic,
self.parameters,
self.parameters + periodic])
else:
self.grid = np.arange(xmin, xmax, kdeStep)
if self.grid.size<2:
self.logger.critical("Grid for CDF generation is a single value")
self.logger.critical("xmin=%7.3f, xmax=%7.3f, kdeStep=%7.3f" %
(xmin, xmax,kdeStep))
raise ValueError
bw = KPDF.UPDFOptimumBandwidth(self.parameters)
self.pdf = self._generatePDF(self.grid, bw, self.parameters)
if periodic:
self.pdf = 3.0*self.pdf[(periodic/kdeStep):2*(periodic/kdeStep)]
self.grid = self.grid[(periodic/kdeStep):2*(periodic/kdeStep)]
self.cy = stats.cdf(self.grid, self.pdf)
if kdeParameters is None:
return np.transpose(np.array([self.grid, self.pdf, self.cy]))
else:
# Assume both kdeParameters and cdfParameters are defined as files:
self.logger.debug("Saving KDE and CDF data to files")
flSaveFile(kdeParameters, np.transpose(np.array([self.grid, self.pdf])))
flSaveFile(cdfParameters, np.transpose(np.array([self.grid, self.cy])))
def doDataPlotting(configFile):
"""
Plot the pre-processed input data. Requires the Data Processing step to have
been executed first (``Actions -- DataProcess = True``)
:param str configFile: Name of configuration file.
"""
config = ConfigParser()
config.read(configFile)
showProgressBar = config.get('Logging', 'ProgressBar')
pbar = ProgressBar('Plotting results: ', showProgressBar)
outputPath = config.get('Output', 'Path')
statsPlotPath = pjoin(outputPath, 'plots', 'stats')
processPath = pjoin(outputPath, 'process')
pRateData = flLoadFile(pjoin(processPath, 'pressure_rate'))
pAllData = flLoadFile(pjoin(processPath, 'all_pressure'))
bRateData = flLoadFile(pjoin(processPath, 'bearing_rate'))
bAllData = flLoadFile(pjoin(processPath, 'all_bearing'))
sRateData = flLoadFile(pjoin(processPath, 'speed_rate'))
sAllData = flLoadFile(pjoin(processPath, 'all_speed'))
freq = flLoadFile(pjoin(processPath, 'frequency'))
indLonLat = flLoadFile(pjoin(processPath, 'cyclone_tracks'),
delimiter=',')
indicator = indLonLat[:, 0]
lonData = indLonLat[:, 1]
latData = indLonLat[:, 2]
jdayobs = flLoadFile(pjoin(processPath, 'jday_obs'), delimiter=',')
jdaygenesis = flLoadFile(pjoin(processPath, 'jday_genesis'), delimiter=',')
from PlotInterface.plotStats import PlotPressure, PlotBearing, \
PlotSpeed, PlotFrequency, PlotDays, PlotLonLat
log.info('Plotting pressure data')
pbar.update(0.05)
PrsPlot = PlotPressure(statsPlotPath, "png")
PrsPlot.plotPressure(pAllData)
PrsPlot.plotPressureRate(pRateData)
PrsPlot.plotMinPressure(indicator, pAllData)
#FIXME: To be moved into `PlotPressure` class.
#plotting.minPressureLat(pAllData, latData)
log.info('Plotting bearing data')
pbar.update(0.15)
BearPlot = PlotBearing(statsPlotPath, "png")
BearPlot.plotBearing(bAllData)
BearPlot.plotBearingRate(bRateData)
log.info('Plotting speed data')
pbar.update(0.25)
SpeedPlot = PlotSpeed(statsPlotPath, "png")
SpeedPlot.plotSpeed(sAllData)
SpeedPlot.plotSpeedRate(sRateData)
log.info('Plotting longitude and latitude data')
pbar.update(0.45)
# FIXME: To be moved to it's own class in PlotStats
LLPlot = PlotLonLat(statsPlotPath, "png")
LLPlot.plotLonLat(lonData, latData, indicator)
pbar.update(0.65)
log.info('Plotting frequency data')
pbar.update(0.85)
FreqPlot = PlotFrequency(statsPlotPath, "png")
FreqPlot.plotFrequency(freq[:, 0], freq[:, 1])
DayPlot = PlotDays(statsPlotPath, "png")
DayPlot.plotJulianDays(jdayobs, jdaygenesis)
pbar.update(1.0)
def doDataPlotting(configFile):
"""
Plot the data.
:param str configFile: Name of configuration file.
"""
import matplotlib
matplotlib.use('Agg') # Use matplotlib backend
config = ConfigParser()
config.read(configFile)
showProgressBar = config.get('Logging', 'ProgressBar')
pbar = ProgressBar('Plotting results: ', showProgressBar)
outputPath = config.get('Output', 'Path')
statsPlotPath = pjoin(outputPath, 'plots', 'stats')
processPath = pjoin(outputPath, 'process')
pRateData = flLoadFile(pjoin(processPath, 'pressure_rate'))
pAllData = flLoadFile(pjoin(processPath, 'all_pressure'))
bRateData = flLoadFile(pjoin(processPath, 'bearing_rate'))
bAllData = flLoadFile(pjoin(processPath, 'all_bearing'))
sRateData = flLoadFile(pjoin(processPath, 'speed_rate'))
sAllData = flLoadFile(pjoin(processPath, 'all_speed'))
indLonLat = flLoadFile(pjoin(processPath, 'cyclone_tracks'),
delimiter=',')
indicator = indLonLat[:, 0]
lonData = indLonLat[:, 1]
latData = indLonLat[:, 2]
from PlotInterface.plotStats import PlotData
plotting = PlotData(statsPlotPath, "png")
log.info('Plotting pressure data')
pbar.update(0.05)
plotting.plotPressure(pAllData, pRateData)
plotting.scatterHistogram(
pAllData[1:], pAllData[:-1], 'prs_scatterHist', allpos=True)
plotting.scatterHistogram(
pRateData[1:], pRateData[:-1], 'prsRate_scatterHist')
plotting.minPressureHist(indicator, pAllData)
plotting.minPressureLat(pAllData, latData)
log.info('Plotting bearing data')
pbar.update(0.15)
plotting.plotBearing(bAllData, bRateData)
log.info('Plotting speed data')
pbar.update(0.25)
plotting.plotSpeed(sAllData, sRateData)
log.info('Plotting longitude and lattitude data')
pbar.update(0.45)
plotting.plotLonLat(lonData, latData, indicator)
log.info('Plotting quantiles for pressure, bearing, and speed')
pbar.update(0.65)
plotting.quantile(pRateData, "Pressure", "logistic")
plotting.quantile(bRateData, "Bearing", "logistic")
plotting.quantile(sRateData, "Speed", "logistic")
log.info('Plotting frequency data')
pbar.update(0.85)
try:
freq = flLoadFile(pjoin(processPath, 'frequency'))
years = freq[:, 0]
frequency = freq[:, 1]
plotting.plotFrequency(years, frequency)
except IOError:
log.warning("No frequency file available - skipping this stage")
pbar.update(1.0)
def testLoadFile(self):
"""Test flLoadFile loads data correctly"""
data = files.flLoadFile(self.testfile, comments='%', delimiter=',')
assert_almost_equal(self.lon, data[:, 0])
assert_almost_equal(self.lat, data[:, 1])
pos = (2, -4.8)
pyplot.text(2, -4.9, r"$r^2=%1.4f$" % r, fontsize=12)
self.savefig('qqplot_%s' % parameterName)
#pyplot.rcdefaults()
if __name__=="__main__":
from os.path import join as pjoin
configFile = sys.argv[1]
dataPath = config.cnfGetIniValue(configFile, 'Output', 'Path', os.getcwd())
inputPath = pjoin(dataPath, 'process')
outputPath = pjoin(dataPath, 'plots')
pyplot.rcParams['figure.figsize'] = (7, 12)
pRateData = files.flLoadFile(pjoin(inputPath, 'pressure_rate'))
pAllData = files.flLoadFile(pjoin(inputPath, 'all_pressure'))
bRateData = files.flLoadFile(pjoin(inputPath, 'bearing_rate'))
bAllData = files.flLoadFile(pjoin(inputPath, 'all_bearing'))
sRateData = files.flLoadFile(pjoin(inputPath, 'speed_rate'))
sAllData = files.flLoadFile(pjoin(inputPath, 'all_speed'))
freq = files.flLoadFile(pjoin(inputPath, 'frequency'))
years = freq[:, 0]
frequency = freq[:, 1]
plotting = PlotData(outputPath, "png")
plotting.plotPressure(pAllData, pRateData)
plotting.plotBearing(bAllData, bRateData)
plotting.plotSpeed(sAllData, sRateData)
plotting.plotFrequency(years, frequency)
plotting.plotSpeedBear(sAllData, bAllData)