def _dealWithRates(self, combinedRates, femaleRates, maleRates, **kwargs):
""" blah """
# Save code version info with instance. Here because I think
# it is screwing up based on # some weird scoping thing in MF
self.LcObjectINFO = LcObjectINFO
#raise(self.LcObjectINFO)
# Combined Rates
self.rates_textComb = combinedRates
self.nmxComb = LcUtil.parseRates(self.rates_textComb)
infs_or_nans = N.isinf(self.nmxComb) | N.isnan(self.nmxComb)
assert not infs_or_nans.any(), \
AssertionError("why are there infs or nans in combined_nmx???:\n %r" \
% N.round_(self.nmxComb, 2))
# F Rates
self.rates_textFem = femaleRates
self.nmxFem = LcUtil.parseRates(self.rates_textFem)
infs_or_nans = N.isinf(self.nmxFem) | N.isnan(self.nmxFem)
assert not infs_or_nans.any(), \
AssertionError("why are there infs or nans in female_nmx???:\n %r" \
% N.round_(self.nmxFem, 2))
# M Rates
self.rates_textMale = maleRates
self.nmxMale = LcUtil.parseRates(self.rates_textMale)
infs_or_nans = N.isinf(self.nmxMale) | N.isnan(self.nmxMale)
assert not infs_or_nans.any(), \
AssertionError("why are there infs or nans in nmxMale???:\n %r" \
% N.round_(self.nmxMale, 2))
def _dealWithRates(self, combinedRates, femaleRates, maleRates, **kwargs):
""" blah """
# Save code version info with instance. Here because I think
# it is screwing up based on # some weird scoping thing in MF
self.LcObjectINFO = LcObjectINFO
#raise(self.LcObjectINFO)
# Combined Rates
self.rates_textComb = combinedRates
self.nmxComb = LcUtil.parseRates(self.rates_textComb)
infs_or_nans = N.isinf(self.nmxComb) | N.isnan(self.nmxComb)
assert not infs_or_nans.any(), \
AssertionError("why are there infs or nans in combined_nmx???:\n %r" \
% N.round_(self.nmxComb, 2))
# F Rates
self.rates_textFem = femaleRates
self.nmxFem = LcUtil.parseRates(self.rates_textFem)
infs_or_nans = N.isinf(self.nmxFem) | N.isnan(self.nmxFem)
assert not infs_or_nans.any(), \
AssertionError("why are there infs or nans in female_nmx???:\n %r" \
% N.round_(self.nmxFem, 2))
# M Rates
self.rates_textMale = maleRates
self.nmxMale = LcUtil.parseRates(self.rates_textMale)
infs_or_nans = N.isinf(self.nmxMale) | N.isnan(self.nmxMale)
assert not infs_or_nans.any(), \
AssertionError("why are there infs or nans in nmxMale???:\n %r" \
% N.round_(self.nmxMale, 2))
def _dealWithRates(self, rates, **kwargs):
"""Parses the rates. Sets up datastructures for missing data."""
# Save code version info with instance. Here because I think
# it is screwing up based on # some weird scoping thing in MF
self.LcObjectINFO = LcObjectINFO
assert type(rates) == types.StringType, \
AssertionError("Rates should be as string for input. Instead: %s." % type(rates))
# Get rates from text, extend ...
self.rates_text = rates
self.nmx = LcUtil.parseRates(self.rates_text)
# ... handle missing data: if there are nans after parsing,
# determine which years (rows) they are in ...
self.nmxNans = N.isnan(self.nmx)
self.goodRowsBool = (~self.nmxNans).any(axis=1)
self.goodRowsNum = N.where(self.goodRowsBool)[0].tolist() # weird numpy.where() return
self.yearIndices = N.arange(1, self.nmx.shape[0]+1, dtype=N.int0) # XXX 1 indexed for missing data formulas
# ... extend everything ...
self.nmxExtended = LcUtil.emptyLikeWithNans(self.nmx)
tmp = LcExtension.extendMx(self.nmx[self.goodRowsNum,:], ageCutoff=self.ageCutoff)
assert self.nmxExtended[self.goodRowsNum,:].shape == tmp.shape, \
AssertionError("orig shape: %s. extended shape: %s" \
% (tmp.shape, self.nmxExtended[self.goodRowsNum,:].shape))
self.nmxExtended[self.goodRowsNum,:] = tmp
assert (self.nmxExtended[self.goodRowsNum,:] > 0.0).all() and (N.isfinite(self.nmxExtended[self.goodRowsNum,:])).all(), \
AssertionError("%s" % self.nmxExtended)
# ... asserts, and hopefully fall of the end (only update object state).
self.nmxInfs = N.isinf(self.nmx)
assert not self.nmxInfs.any(), \
AssertionError("why are there infs in nmx???:\n %r" % N.round_(self.nmx, 2))
return None
def _dealWithRates(self, populations, mortRates, labels='', **kwargs):
""" Store the population and rate data. Create the combined rates matrix. """
# Save code version info with instance. Here because I think
# it is screwing up based on # some weird scoping thing in MF
self.LcObjectINFO = LcObjectINFO
# Age cutoff
self.ageCutoffIndex = LCFIT_AGE_INDICES[self.ageCutoff] + 1
# Population data
self.populationText = re.sub('\n', '\n', populations)
self.populationText = re.sub('\r', '', self.populationText).strip()
self.populationText = re.sub('\n+$', '', self.populationText)
self.populationText = re.sub('^\n+', '', self.populationText)
if LCFIT_EMPTY_ALL_RE.search(self.populationText):
self.useWeightedMx = False
self.populationTextList = []
self.populationList = []
else:
self.useWeightedMx = True
self.populationTextList = re.split('\n\n+', self.populationText)
self.populationList = [LcUtil.parseRates(pops) for pops in self.populationTextList]
# Mortality data
self.mortRatesText = re.sub('\n', '\n', mortRates)
self.mortRatesText = re.sub('\r', '', mortRates)
self.mortRatesText = re.sub('\n+$', '', self.mortRatesText)
self.mortRatesText = re.sub('^\n+', '', self.mortRatesText)
if LCFIT_EMPTY_ALL_RE.search(self.mortRatesText):
raise LcException("empty rates data")
self.mortRatesTextList = re.split('\n\n+', self.mortRatesText) #
self.mortRatesList = [LcUtil.parseRates(rates) for rates in self.mortRatesTextList]
# Go over each data matrix, check input: no weird numbers, same size.
shapeList = []
shapeShape = self.mortRatesList[0].shape
for i, data in enumerate(self.populationList + self.mortRatesList):
if data.shape != shapeShape:
raise LcException("Inconsistent rate matrix shapes. First matrix shape: %r, current matrix [%r] shape: %r\nData: %r" % \
(shapeShape, i, data.shape, data[0,:].tolist()))
shapeList.append(data.shape)
pass
if self.useWeightedMx:
if len(self.populationList) != len(self.mortRatesList):
raise LcException("Must have pop and mx of same length. Pop = %i, Mort = %i." % \
(len(self.populationList), len(self.mortRatesList)))
# CG and takes logs of each of the rates
self.mortRatesListLog = []
for i, mxMatrix in enumerate(self.mortRatesList):
self.mortRatesList[i] = LcExtension.extendMx(mxData=mxMatrix, ageCutoff=LCFIT_DEFAULT_AGE_CUTOFF)
self.mortRatesListLog.append(N.log(self.mortRatesList[i]))
# Labels
if labels == '':
self.labels = map(str,range(1, len(self.mortRatesListLog)+1))
else:
self.labels = re.split('\s+', labels.strip())
if len(self.labels) < len(self.mortRatesListLog):
labelExtraNumbers = range(len(self.labels)+1, len(self.mortRatesListLog)+1)
labelExtra = map(str, labelExtraNumbers)
self.labels = self.labels + labelExtra
elif len(self.labels) > len(self.mortRatesListLog):
self.labels = self.labels[0:(len(self.mortRatesListLog))]
# Years
self.yearIndices = N.arange(1, self.mortRatesList[0].shape[0]+1, dtype=N.int0)
years_end = self.start_year + self.mortRatesList[-1].shape[0]
self.years = N.array(range(self.start_year, years_end))
assert len(self.years) >= 1, AssertionError("years: %s" % self.years)
self.years_fcst = N.array(range(years_end-1, years_end + self.stepsForward))
# Create an average mx matrix. If populations empty, no
# weights; if there is data for populations (1) check for
# reasonableness in size and number and (2) use population as
# weights and do the averaging.
if self.useWeightedMx:
self.totalWeightedMx = N.zeros_like(self.mortRatesList[0])
self.totalPop = N.zeros_like(self.populationList[0])
for (mx, pop) in zip(self.mortRatesList, self.populationList):
self.totalWeightedMx = self.totalWeightedMx + (mx*pop)
self.totalPop = self.totalPop + pop
pass
self.averagedMx = self.totalWeightedMx/self.totalPop
else:
temp_mx = N.zeros_like(self.mortRatesList[0])
for mx in self.mortRatesList:
temp_mx += mx
self.averagedMx = temp_mx / len(self.mortRatesList)
self.averagedMx = LcExtension.extendMx(mxData=self.averagedMx, ageCutoff=LCFIT_DEFAULT_AGE_CUTOFF)
self.averagedMxLog = N.log(self.averagedMx)
# Check data for ok-ness in mortality (not population, since
# that might be non-CG'ed and have nans).
for i, data in enumerate(self.mortRatesList + self.mortRatesListLog + [self.averagedMxLog, self.averagedMx]):
assert N.isfinite(data).all(), \
AssertionError("Bad data in mx[%r]:\n %r" % (N.round_(data, 2), i))
# Check for weird (ie > 1.0) numbers
for i, data in enumerate(self.mortRatesList + [self.averagedMx]):
if not (data<1.2).all():
raise LcException("Weird mx: \n%s\n%s" % (data[data<1.2], i))