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))