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 __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 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 test_MaxCellNum(self):
"""Testing maxCellNum"""
maxCellNum = 175
self.assertEqual(maxCellNum,
statutils.maxCellNum(self.gridLimit, self.gridSpace))
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 test_MaxCellNum(self):
"""Testing maxCellNum"""
maxCellNum = 175
self.assertEqual(maxCellNum, statutils.maxCellNum(self.gridLimit, self.gridSpace))
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()