def __init__(self, ys, xs, years, model, pr=0.01, smooth=False, anom=False, onethreshold=True, trim=1, debug=False, ConstSxy=True, withshifts=False):
try:
#print "Pr size", pr, size
self.__size=len(xs)
#print self.__size, type(self.__size)
self.__threshold=bivariate.critTi(pr, self.__size)
self.__breakpoints=np.zeros((self.__size,))
self.__breakyears = {}
except Exception as e:
print bivariate.ExceptionInfo()
print "__init__",str(e)
raise recurseTestException("__init__:"+str(e))
if smooth:
if anom:
#print "window smooth anom"
txs, tys, td1, td2 = lowess.R().lowess(np.array(xs),np.array(ys), f=1./4., iter=1)
self.__ys = np.array(ys)-np.array(tys)
self.__xs=np.copy(xs)
else:
#print "window smooth not anom"
txs, tys, td1, td2 = lowess.R().lowess(np.array(xs),np.array(ys), f=1./4., iter=1)
self.__ys = np.array(ys)
self.__xs=np.array(tys)+np.array(xs)
else:
#print "window not smooth"
self.__ys=np.array(ys)
self.__xs=np.copy(xs)
#print "window call bivariate"
try:
#self.__bv=bivariate.bivariate(self.__ys, self.__xs, critical=self.__threshold, anomalise=False,constantsxy=ConstSxy)
self.__bv=bivariate.bivariate(self.__ys, self.__xs, critical=None, pr=pr, anomalise=False,constantsxy=ConstSxy)
if withshifts:
ap_MaxTis, ap_MaxIndexes, (ap_lows, ap_highs), ap_shifts = self.__bv.allPoints(pr, withshifts=True)
else:
ap_MaxTis, ap_MaxIndexes, (ap_lows, ap_highs)= self.__bv.allPoints(pr, withshifts=False)
#print "BV.BIVARIATE -> ", len(ap_MaxTis), len(ap_MaxIndexes), len(ap_lows), len(ap_highs)
except Exception as e:
print bivariate.ExceptionInfo()
raise recurseTestException("recurse.__init__ call to bivariate:"+str(e))
#print ap_MaxTis, ap_MaxIndexes, (ap_lows, ap_highs)
if trim == 1:
#==============================================================================
## This mode implements a trimming mode whereby breakpoints tested by
## bracketing them and accepting them if there ids a breakpoint in the interval
## The alternative (mode 2) is to replace them with the new breakpoint
#==============================================================================
try:
stepn = 0
if debug: print "trimming"
trimmed = True
while trimmed:
trimmed = False
for mi in range(len(ap_MaxIndexes)):
if debug: print "considering mi"
if not trimmed:
stepn = 1
self.__bv.reinit(ap_lows[int(mi)], ap_highs[int(mi)]+1, pr)
stepn=2
#print self.__bv.maxnTi() , ap_lows[int(mi)], ap_MaxIndexes[int(mi)], ap_highs[int(mi)], bivariate.critTi(pr, 1 + ap_highs[int(mi)]-ap_lows[int(mi)])
stepn = 3
if self.__bv.maxnTi() < bivariate.critTi(pr, 1 + ap_highs[int(mi)]-ap_lows[int(mi)]):
stepn = 4
trimmed = True
if debug: print "trimmer removed ", mi, ap_MaxIndexes[int(mi)], " between ", ap_lows[int(mi)], ap_highs[int(mi)]
stepn = 5
#print mi, len(ap_MaxTis), len(ap_MaxIndexes), len(ap_lows), len(ap_highs)
#print ap_MaxTis, " becomes ",
pop1 = ap_MaxTis.pop(int(mi))
#print ap_MaxTis
pop2 = ap_MaxIndexes.pop(int(mi))
pop3 = ap_lows.pop(int(mi))
pop4 = ap_highs.pop(int(mi))
with open("removals.txt","a") as rmf:
rmf.write("from %s trimmer removed element %s (Ti:%s ) %s between %s and %s crit=%s \n" % (str(model), str(mi), str(pop1), str(pop2), str(pop3), str(pop4), str( bivariate.critTi(pr, 1 + ap_highs[min(len(ap_highs)-1,mi)]-ap_lows[min(len(ap_lows)-1,mi)]))))
except Exception as e:
raise recurseTestException("at trim state "+str(stepn)+" in __init__:"+str(e))
if trim == 2:
#==============================================================================
## This mode implements a trimming mode whereby breakpoints tested by
## bracketing them and accepting them if there ids a breakpoint in the interval
## The alternative (mode 2) is to replace them with the new breakpoint
#==============================================================================
try:
stepn = 0
if debug: print "trimming mode 2"
trimmed = True
while trimmed:
trimmed = False
for mi in range(len(ap_MaxIndexes)):
if debug: print "considering mi"
if not trimmed:
stepn = 1
self.__bv.reinit(ap_lows[int(mi)], ap_highs[int(mi)]+1, pr)
stepn=2
print self.__bv.maxnTi() , ap_lows[int(mi)], ap_MaxIndexes[int(mi)], ap_highs[int(mi)], bivariate.critTi(pr, 1 + ap_highs[int(mi)]-ap_lows[int(mi)])
if self.__bv.maxnTi() < bivariate.critTi(pr, 1 + ap_highs[int(mi)]-ap_lows[int(mi)]):
trimmed = True
if debug: print "trimmer (mode 2) removed ", mi, ap_MaxIndexes[int(mi)], " between ", ap_lows[int(mi)], ap_highs[int(mi)]
pop1 = ap_MaxTis.pop(int(mi))
pop2 = ap_MaxIndexes.pop(int(mi))
pop3 = ap_lows.pop(int(mi))
pop4 = ap_highs.pop(int(mi))
with open("removals.txt","a") as rmf:
rmf.write("from %s trimmer (mode 2) removed element %s (Ti:%s ) %s between %s and %s crit=%s \n" % (str(model), str(mi), str(pop1), str(pop2), str(pop3), str(pop4), str( bivariate.critTi(pr, 1 + ap_highs[min(len(ap_highs)-1,mi)]-ap_lows[min(len(ap_lows)-1,mi)]))))
elif self.__bv.maxIndexnTi() != ap_MaxIndexes[int(mi)]:
trimmed = True
pop1 = ap_MaxTis[int(mi)]
pop2 = ap_MaxIndexes[int(mi)]
pop3 = ap_lows[int(mi)]
pop4 = ap_highs[int(mi)]
ap_MaxTis[int(mi)] = self.__bv.maxnTi()
ap_MaxIndexes[int(mi)] = self.__bv.maxIndexnTi()
with open("removals.txt","a") as rmf:
rmf.write("from %s trimmer (mode 2) substituted element %s (Ti:%s ) %s with %s between %s and %s crit=%s \n" % (str(model), str(mi), str(ap_MaxIndexes[int(mi)]), str(pop1), str(pop2), str(pop3), str(pop4), str( bivariate.critTi(pr, 1 + ap_highs[int(mi)]-ap_lows[int(mi)]))))
except Exception as e:
raise recurseTestException("at mode 2 trim state "+str(stepn)+" in __init__:"+str(e))
try:
stepn = 0
for mi in range(len(ap_MaxIndexes)):
#print mi
stepn = 1
if ((onethreshold and (ap_MaxTis[int(mi)] >= self.__threshold)) or
(not onethreshold and (ap_MaxTis[int(mi)] >=
bivariate.critTi(pr, 1 + ap_highs[int(mi)]-ap_lows[int(mi)])))):
self.__breakpoints[int(ap_MaxIndexes[int(mi)])] += 1
stepn = 2
self.__breakyears[years[int(ap_MaxIndexes[int(mi)])]] = None
stepn = 3
if withshifts:
self.__breakyears[years[int(ap_MaxIndexes[mi])]] = (ap_MaxTis[mi], years[int(ap_lows[mi])], years[int(ap_highs[mi])-1], ap_shifts[mi])
else:
self.__breakyears[years[int(ap_MaxIndexes[mi])]] = (ap_MaxTis[mi], years[int(ap_lows[mi])], years[int(ap_highs[mi])-1])
except Exception as e:
print "Exception -----------------------------------------------------------"
try:
print "mi",mi
#print "years",years
print "ap_MaxIndexes",ap_MaxIndexes
print "ap_MaxTis",ap_MaxTis
print "ap_lows",ap_lows
print "ap_highs",ap_highs
print "self.__breakyears",self.__breakyears
print "years[int(ap_MaxIndexes[int(mi)])]",years[int(ap_MaxIndexes[int(mi)])]
except:
pass
print bivariate.ExceptionInfo()
raise recurseTestException("Reporting loop of __init__: "+str(stepn)+" "+str(e))
def merge_pass(currentbreaks, testdata, controldata, datayears):
prevbreaks=copy.copy(currentbreaks)
newlist=[prevbreaks.pop(0)]
lo=takeClosestIndex(datayears, newlist[0])
print >>tf, "considering",str(prevbreaks)
#JHR 13/2/15 Here we consider a prolog and an epilog since it ius necessary to test within the
#first and last spans, just to see if something is shielded.
PrologDone=False
try:
if len(currentbreaks) < 2:
print "merge_pass.currentbreaks=",currentbreaks
if len(prevbreaks) > 1:
hi = takeClosestIndex(datayears, prevbreaks[1])+1
else: #JHR SVN 262 15/1/2015 If called with only the end data s bounds this will crash
hi = takeClosestIndex(datayears, prevbreaks[0])+1
PrologDone = True #so just prevent doing the same interval twice should we examine a provionally empty span
except:
print "merge_pass.prevbreaks=",prevbreaks,"merge_pass.currentbreaks=",currentbreaks
raise
#SVN 280 JHR 13/2/15 Consider
firsthi = takeClosestIndex(datayears, prevbreaks[0])+1
statlist = []
state=0
safetystep = 0
Terminating = False #Flag to say we are on last pass
while state >= 0: #state < 0 indicates termination
#state evaluation loop is always get new list, then depending on state process
if state==0: #ythen we have commenced
#It should not happen, but was getting exceptions causing hi to be wrongin termination case
#JHR 2/3/2015
if Terminating:
hi = takeClosestIndex(datayears, currentbreaks[-1])+1
rt1=recursetest.recurse(testdata[lo:hi], controldata[lo:hi], datayears[lo:hi], model, smooth=False, trim = 0, pr=screenpr, anom=False, withshifts=True)
candidates= np.sort(rt1.breakyears().keys()).tolist()
if Terminating and candidates != [] and trace:
print >>tf, "Final pass found ",candidates, " between ", datayears[[lo,hi-1]], "state[0] -> state[1]"
if not PrologDone:
PrologDone = True #so revert to previous code and commence testing spans
rtprolog=recursetest.recurse(testdata[lo:firsthi], controldata[lo:firsthi], datayears[lo:firsthi], model, smooth=False, trim = 0, pr=screenpr, anom=False, withshifts=True)
firstcandidates= np.sort(rtprolog.breakyears().keys()).tolist()
if firstcandidates != []:
if trace:
print >>tf, "B4 found ",firstcandidates, " between ", datayears[[lo,firsthi-1]], "state[0] -> state[0]"
prevbreaks.insert(0,firstcandidates[0])
hi = firsthi
state = 0
#The following can cause deletion of a year, better to just start over
#firstcandidates.extend(candidates)
#candidates=np.sort(list(set(firstcandidates))).tolist()
else:
state = 1
else:
state = 1
elif state == 1: #the state after we have a new list, candidates needs to be evaluated, firstly how many?
if len(candidates) == 0:
state = 2 #the state of do a drop
elif len(candidates) == 1:
state = 3 # the state of process just one
else:
state = 4 # the state of process multiples
elif state == 2: #then our test segment yielded no acceptable break and we will just drop it
if trace:
if len(prevbreaks) > 1:
print >>tf, "** Break ",prevbreaks[1],"no longer between ",datayears[lo], datayears[hi-1], statelabel(state,5)
else:
print >>tf, "** Break ",prevbreaks,"no longer between ",datayears[lo], datayears[hi-1], statelabel(state,5)
state = 5 #the state of a break was dropped by itself (therefore we don't move lo)
elif state == 3:# the state of process just one
#so now we set up an evaluation of one element.
#we rely on candidates, lo, and hi
modes=[None,None]
ystats, tstats, shiftstats,modes = resample_break(testdata[lo:hi], datayears[lo:hi],N=100,withmode=True)
#ystats, tstats, shiftstats = resample_break(testdata[lo:hi], datayears[lo:hi],withmode=False)
#now the tstats may mean it is no longer significant
#or the ystats may indicate it's too close to the previous
#or there may be another issue unthought about
#how about the Ti0?
crit30=bivariate.critTi(pr, max(minInterval,min(30, 1+datayears[hi-1]-datayears[lo])))
#now the retested point may have moved
if modes[-2][0] < crit30: #then it is not significant (was tstats[0])
if trace:
print >>tf, "-- Candidate ", candidates[0], "(",modes[0][0],")(",modes[-2][0],") did not exceed ", crit30, "between ",datayears[lo], datayears[hi-1], "state[",state,"]" ,
state= 6 #the state of a break was dropped because it was a problem
if trace:
print >>tf, "-> state[",state,"]"
elif modes[0][0] - (datayears[lo] -1) < minInterval:#JHR This was one year out, last break is datayears[0] -1 #was ystat[0] then it probably moved and in any case is too close to last break
if trace:
print >>tf, "<< Candidate ", candidates[0], "(",modes[0][0],")(",modes[-2][0],") too close to ", datayears[lo], "between ",datayears[lo], datayears[hi-1] , "state[",state,"]",
state= 5.5 #the state of two peaks close togeter - choose 1
if trace:
print >>tf, "-> state[",state,"]"
# hold this thought
#elif (ystats[0] - 2 * ystats[1] < min(testyr, datayears[lo]) or ystats[0] + 2 * ystats[1] > max(testyr, datayears[hi-1])):
#now we consider a bunch of rules about the modality if we have done this
elif modes[1] != None: #so there's more than one choice
#if the first mode is more than 90% (Roger's verbal rule) the all is OK
if modes[0][1] >= 0.9:
state = 7 #the state of save the stats and then move on
elif modes[0][1]+modes[1][1] < 0.7: #if less than 70% of the values are between two modes then it must be blurry
if trace:
print >>tf, "~~ Candidate no strong modes ", candidates[0], "(",modes,") less than 70% ", datayears[lo], "between ",datayears[lo], datayears[hi-1] , "state[",state,"]",
state = 6 #the state of a break was dropped because it was a problem
if trace:
print >>tf, "-> state[",state,"]"
elif modes[1][1] <= 0.2: #so at half the time the mode is one value
state = 7 #the state of save the stats and then move on
elif abs(modes[0][0] - modes[1][0]) <= minInterval /2.0:
if trace:
print >>tf, "~+ Candidate accepted with two modes ", candidates[0], "(",modes,") < minInterval /2.0 ", datayears[lo], "between ",datayears[lo], datayears[hi-1] , "state[",state,"]",
state = 7
if trace:
print >>tf, "-> state[",state,"]"
elif abs(modes[0][0] - modes[1][0]) > minInterval:
#so for now we will override the candidate list and treat as two candidates _NOT ANY MORE
if trace:
print >>tf, "~~ Candidate two strong modes - treat as both possible ", candidates[0], "(",modes,") > ", datayears[lo], "between ",datayears[lo], datayears[hi-1] , "state[",state,"]",
#candidates = [min(modes[0][0], modes[1][0])]#, max(modes[0][0], modes[1][0])]
state = 9.5
if trace:
print >>tf, "-> state[",state,"]"
else:
if trace:
print >>tf, "~~ Candidate two strong but close modes ", candidates[0], "(",modes,") > minInterval /2.0 ", datayears[lo], "between ",datayears[lo], datayears[hi-1] , "state[",state,"]",
state = 7 #This was a definite error - had been dropping these. setting to state 6
if trace:
print >>tf, "-> state[",state,"]"
#that's basically it for mode processing
#however one more thing to check
if state == 3: #final pass through
if abs(candidates[0] - ystats[0]) > 2.0 * ystats[1]:#resampling shows bad point JHR: 20150107 BAD TEST FIXME!
if trace:
print >>tf, "<<! Candidate ", candidates[0], "(",ystats,")(",tstats,") too far from ", candidates[0], "between ",datayears[lo], datayears[hi-1] , ". Will replace, state[",state,"]",
state= 9 #the state of a break was changed due to resampleing
if trace:
print >>tf, "-> state[",state,"]"
else:
state = 7 #the state of save the stats and then move on
if state == 7 and trace:
if candidates[0] != ystats[0]:
print >>tf, "Candidate has moved : modes are " ,modes
print >>tf, "=3! Candidate ", candidates[0], "(",ystats,")(",tstats,") OK between ",datayears[lo], datayears[hi-1] , " state[3] - state[7]"
elif state == 4:
#test the second candidate to see is it's going to be stable.
#But we first need to know what the first candidate is.
modes1=[None,None]
lo1 = takeClosestIndex(datayears, candidates[0])+1
hi1 = takeClosestIndex(datayears, candidates[1])+1
#SO WHAT IS the new lo bound?
#If this one is above critical use it, otherwise don't. Use the second candidate which by virtue of how is was generated is likely to persist
ystats0, tstats0, shiftstats0,modes0 = resample_break(testdata[lo:hi1], datayears[lo:hi1],N=100,withmode=True)
lo0 = takeClosestIndex(datayears, modes0[0][0])+1
#so now we use the new low bound against the proposed upper bound
ystats1, tstats1, shiftstats1,modes1 = resample_break(testdata[lo0:hi], datayears[lo0:hi],N=100,withmode=True)
crit30a=bivariate.critTi(pr, max(minInterval,min(30, 1+datayears[hi-1]-datayears[lo0])))
lowcandidate = candidates[0]
if modes1[-2][0] >= crit30a: #then we save that one to use
if trace:
print >>tf, "!-- Candidate ", candidates[0], " reset to ",modes0[0][0], " after resample gave ",modes0
lowcandidate = modes0[0][0]
lo1 = lo0
else: #otherwise need to make a decision with the unchnaged candidate
ystats1, tstats1, shiftstats1,modes1 = resample_break(testdata[lo1:hi], datayears[lo1:hi],N=100,withmode=True)
crit30a=bivariate.critTi(pr, max(minInterval,min(30, 1+datayears[hi-1]-datayears[lo1])))
if modes1[-2][0] < crit30a: #then it is not significant (was tstats[0])
if trace:
print >>tf, "!-- Candidate ", candidates[1], "(",modes1[0][0],")(",modes1[-2][0],") did not exceed ", crit30a, "between ",datayears[lo1], datayears[hi-1], " will not use: state[",state,"]" ,
else:
#insert
if trace and candidates[1] in prevbreaks:
print >>tf, "KNOWN DUPLICATE GOING INTO LIST", candidates[1], prevbreaks, "THIS IS OK"
if trace:
print >>tf, "++ (new) Candidate ", candidates[0], "will be tested and ", candidates[1],"inserted", prevbreaks, "becomes",
prevbreaks.insert(1, candidates[1]) #avoid relooping
if trace:
print >>tf, prevbreaks, "between ",datayears[lo], datayears[hi-1], "state[",state,"]",
#lo=takeClosestIndex(datayears, newlist[-1])+1
if not Terminating: hi = takeClosestIndex(datayears, prevbreaks[1])+1
candidates=[lowcandidate]
state = 3
if trace:
print >>tf, "-> state[",state,"]"
# elif state == 4.1: #Old code
# if trace:
# print >>tf, "++ (new) Candidate ", candidates[0], "will be tested and ", candidates[1],"inserted", prevbreaks, "becomes",
# prevbreaks.insert(1, candidates[1]) #avoid relooping
# if trace:
# print >>tf, prevbreaks, "between ",datayears[lo], datayears[hi-1], "state[",state,"]",
# #lo=takeClosestIndex(datayears, newlist[-1])+1
# hi = takeClosestIndex(datayears, prevbreaks[1])+1
# candidates=[candidates[0]]
# state = 3
# if trace:
# print >>tf, "-> state[",state,"]"
#
# elif state == 4.2: #working on
# if trace:
# print >>tf, "++ (new) Candidate ", candidates[0], "will be tested and ", candidates[1],"inserted", prevbreaks, "becomes",
# prevbreaks[0]= candidates[0]
# prevbreaks[1]= candidates[1] #avoid relooping
# if trace:
# print >>tf, prevbreaks, "between ",datayears[lo], datayears[hi-1], "state[",state,"]",
# #lo=takeClosestIndex(datayears, newlist[-1])+1
# hi = takeClosestIndex(datayears, prevbreaks[1])+1
# state = 0
# if trace:
# print >>tf, "-> state[",state,"]"
#
elif state == 5:
#the state of a break was dropped by itself (therefore we don't move lo)
#actually we have to move it a bit to stop a loop if we then get it back -
#lo=takeClosestIndex(datayears, newlist[0])
#do the dropping
if Terminating:
state = 10 # so avoid this processing
else:
prb=prevbreaks.pop(0)
if len(prevbreaks) >1:
hi = takeClosestIndex(datayears, prevbreaks[1])+1
lo += minInterval/2
if trace:
old = hi-1
print >>tf, "!! Hi bound, ",datayears[old], " to give ",datayears[lo], datayears[hi-1], "state[",state,"]",
state = 0
else:
if trace:
print >>tf, "!! Hi bound, ",datayears[hi-1], " last between",datayears[lo], datayears[hi-1], "state[",state,"]",
state = 8 #nothing to do after dropping an upper bound
if trace:
print >>tf, "-> state[",state,"]"
elif state == 5.5:
#the state of two peaks close togeter - choose 1 - if we choose the older one just drop this one
#if we choose the later 1 delete reference to the prior one
#similar code to state 3
#but to prevent a loop we must prevent setting up the same interval again
if len(statlist) == 0:
state = 7 #accept it
if trace: print >>tf, "--!! Candidate ", candidates[0], "must be too close to start, but accept it, state[5.5] -> state[7]"
else:
if trace: print >>tf, "In state[5.5]"
lo1=takeClosestIndex(datayears, newlist[-2])+1 #go back one step
ystats, tstats, shiftstats,nmodes = resample_break(testdata[lo1:hi], datayears[lo1:hi], withmode=True)
crit30=bivariate.critTi(pr, max(minInterval,min(30, 1+datayears[hi-1]-datayears[lo1])))
#now the retested point may have moved
if tstats[0] < crit30: #then it is not significant and this sia serious issue since one of these points previously was
if trace:
print >>tf, "--!! Candidate ", candidates[0], "(",ystats,")(",tstats,") did not exceed ", crit30, "between ",datayears[lo], datayears[hi-1], "state[",state,"]" ,
state= 5 #the state of a break was dropped because it was a problem
if trace:
print >>tf, "->!! state[",state,"]"
else:
if trace:
print >>tf, "--!! go back to old break ",newlist[-2], "from ", datayears[lo], " candidate ",candidates[0], "new ", ystats[0], "between ",datayears[lo1], datayears[hi-1],"state[5.5]->",
candidates=[round(ystats[0])]
if ystats[0] - datayears[lo] < minInterval:
#we haven't moved very far, so set up a safety step
safetystep = int(abs(ystats[0] - datayears[lo]))
if len(statlist) > 0: #if we have already got
try:
newlist.pop(-1)
statlist.pop(-1)
#remove old dates
state = 7 #the state of save the stats and then move on
except: #we must not be able to pop, just delete it
print >>tf, "no pop state [5.5] -> "
state = 5
pass
else:
state = 8 #nothing to do after dropping a candiate
if trace: print >>tf, "state[",state,"]"
#do the dropping
#alternative strategy when the new point is too close to the previous, go back and choose the
# highest Ti) of the two
elif state == 6: #the state of a break was dropped because it was a problem so currently just update the indices past the identified candidate break
#relies on candidate[0]
if Terminating:
state = 10
else:
oldlo = lo
lo = takeClosestIndex(datayears, candidates[0])+1
if len(prevbreaks) <2: #then cannot go further, we are done. JHR 15/1/2014 SVN262
if trace:
print >>tf, "$$ Lo bound ONLY updated to give ",datayears[lo], datayears[hi-1], "state[",state,"]",
state = 0 #nothing to do after dropping an upper bound
else:
#need to see if we can move the upper bound safely retaining the low
if len(prevbreaks)>2:
hi3 = takeClosestIndex(datayears, prevbreaks[2])+1
else:
hi3 = takeClosestIndex(datayears, prevbreaks[1])+1
ystats3, tstats3, shiftstats3,modes3 = resample_break(testdata[oldlo:hi3], datayears[oldlo:hi3],N=100,withmode=True)
if modes3[1] == None or modes3[0][1]+modes3[1][1] >= 0.7:
hi = hi3
lo = oldlo
state = 0 #no more to do but collect another point
prb=prevbreaks.pop(0)
if len(prevbreaks) >1 and prb == prevbreaks[0]: #JHR 17mar2015 was looping here.
prb=prevbreaks.pop(0) #remove the second instance if present to prevent a loop
if trace:
print >>tf, "$$ Moved high bound, NOW ",datayears[oldlo] , datayears[hi-1], "dropped ", prb, "to give", prevbreaks, "state[",state,"]",
#if this now violates the length rule update hi as well
elif datayears[hi-1] - datayears[lo] < minInterval:
if trace:
print >>tf, "$$ Lo bound, ",datayears[oldlo],"too close to Hi to use, cannot apply ",datayears[lo], datayears[hi-1], "state[",state,"]",
state = 5#the state of a break was dropped by itself (therefore we don't move lo)
else:
if trace:
print >>tf, "$$ Lo bound, updated to give ",datayears[lo], datayears[hi-1], "state[",state,"]",
state = 8 #nothing to do after dropping an upper bound
if trace:
print >>tf, "-> state[",state,"]"
elif state == 7:#the state of save the stats and then move on
#we rely on candidates, lo, and hi, ystats, tstats, shiftstats
if ystats == None:
print "Trouble - this is a debug line "
if not (Terminating and abs(currentbreaks[-1] -ystats[0]) < minInterval):
statlist.append((ystats, tstats, shiftstats))
newlist.append(int(round(ystats[0])))
#newlist.append(candidates[0]) #Save the actual candidate
if not Terminating:
lo = takeClosestIndex(datayears, newlist[-1])+1+safetystep
if lo > len(datayears): lo -= safetystep
safetystep =0
prb=prevbreaks.pop(0)
if len(prevbreaks) >1 and prb == prevbreaks[0]:
if trace:
print >>tf, "Investigate : just popped", prb, prevbreaks, "state[7]"
prb=prevbreaks.pop(0) #JHR remove the duplicate as well. 10/2/2015
if len(prevbreaks) >1:
hi = takeClosestIndex(datayears, prevbreaks[1])+1
state = 0 #round again
else:
state = 10 #nothing more to do
else:
state = 10
if trace:
print >>tf, "\\\\", "Saved ",newlist[-1],statlist[-1], "state[7] -> state[",state,"]"
elif state == 8: #nothing to do after dropping an upper bound
if trace:
print >>tf, "-- Update upper bound", datayears[hi-1], "to ",
try:
prb=prevbreaks.pop(0)
except:
if trace:
print >>tf, "empty list",
pass
if not Terminating and len(prevbreaks) >1:
hi = takeClosestIndex(datayears, prevbreaks[1])+1
if trace:
print >>tf,datayears[hi-1], "state[",state,"]",
state = 0 #round again
else:
state = 10 #nothing more to do
if trace:
print >>tf, "->","state[",state,"]"
elif state== 9: #the state of a break was changed due to resampleing
if trace:
print >>tf, "&& candidate, ",candidates[0], " no longer updated to give ",
#candidates[0] = round(ystats[0])
if trace:
print >>tf,round(ystats[0]),"state[",state,"]",
state = 7
if trace:
print >>tf, "-> state[",state,"]"
elif state== 9.5: #the state of two strong modes record and exit
if trace:
print >>tf, "&&-> candidate, ",candidates[0], "updated to give ",
if modes[3][0] >= crit30:
ystats=(modes[0][0],0.0)
tstats=(modes[3][0], 0.0)
shiftstats=(modes[3][1],0.0)
candidates = [modes[0][0]]
if trace:
print >>tf, " FIRST MODE ",
else:
ystats=(modes[1][0],0.0)
tstats=(modes[4][0], 0.0)
shiftstats=(modes[4][1],0.0)
candidates = [modes[1][0]]
if trace:
print >>tf, " SECOND MODE ",
if trace:
print >>tf,candidates[0],"state[",state,"]",
state = 7
if trace:
print >>tf, "-> state[",state,"]"
elif state == 10:
if Terminating:
newlist.append(currentbreaks[-1])
state = -1
else:
Terminating = True
#lo = takeClosestIndex(datayears, newlist[-1])+1+safetystep
#print "State 10 ",lo, hi
state = 0 #for last time
elif state < 0:
print state, newlist
return newlist, statlist
def convergentBreaks_Inner(testdata, controldata, datayears, aicControl, model, trace=True, shallow=False, keepFirst=False):
'''
This code attempst to iteratively test all
'''
#The issue with convergence is that whether a breakpoint is admitted to the yearly breaks is determined
#initial analysis over full data
if trace:
tf=open(TraceFile,"a")
rt0=recursetest.recurse(testdata, controldata, datayears, model, smooth=False, trim = 0, pr=0.01, anom=False)
oyears = rt0.breakyears() #initial set of breakpoints
byears = [datayears[0]]
byears.extend([k for k in np.sort(oyears.keys())])
#print "BYEARS", byears
#byears=np.insert(byears, 0, datayears[0])
if trace:
print >>tf,model, "trace=",trace, "shallow=",shallow
for i in range(len(testdata)):
print >>tf,i, testdata[i], controldata[i], datayears[i], aicControl[i]
byears.append(datayears[-1])
if trace: print >>tf,"BYEARS", byears
initialBreaks= copy.copy(byears)
low=0
crit30 = bivariate.critTi(0.01, 30)
print "initially", np.sort(oyears.keys()), crit30
testedlist = []
statlist = []
newbreaks=[datayears[0]] #the first list start is preserved
fails = 0
while len(byears) > 2:
popped=byears.pop(0)
testedlist.append(popped)
lo=np.argwhere(datayears==newbreaks[-1])[0][0]
hi=np.argwhere(datayears==byears[1])[0][0]+1
testyr = byears[0]
print "try", datayears[lo], datayears[hi-1],
rt1=recursetest.recurse(testdata[lo:hi], controldata[lo:hi], datayears[lo:hi], model, smooth=False, trim = 0, pr=0.01, anom=False)
print rt1.breakyears().keys()
nlist=rt1.breakyears().keys()
nlist.sort()
if fails > 0:
print nlist, "shortened to ",nlist[fails:]
nlist = nlist[fails:]
lennlist=len(nlist)
nlist.extend(byears[1:])
byears=nlist[:]
if lennlist == 0:
print popped, " gone, revised list empty"
else:
if lennlist > 1: #then lo and hi need to be computed
hi=np.argwhere(datayears==byears[1])[0][0]+1
testyr =byears[0]
ystats, tstats = resample_break(testdata[lo:hi], datayears[lo:hi])
print popped, datayears[hi-1],ystats, tstats, byears[0],
if tstats[0] + 2 * tstats[1] < crit30:
print " **"
if lennlist > 0:
fails += 1
else:
if crit30 > tstats[0]:
print " * "
else:
print " ",
if abs(testyr - ystats[0] ) -0.5 <= 2 * ystats[1]:
print "YOK",
#KeepOldDropNew
newbreaks.append(round(ystats[0],0))
statlist.append((ystats, tstats))
fails = 0
else:
print " Y* ",
#So does the spread of possible break years actually exceed the possible bounds - this is a sign of instability or trend, or badness, or we may already have this point eqarlier
if ystats[0] - 2 * ystats[1] < min(testyr, datayears[lo]) or ystats[0] + 2 * ystats[1] > max(testyr, datayears[hi-1]):
print" drop", testyr,"likehotpotato"
if lennlist > 0: fails += 1
else:
byears[0] = round(ystats[0],0)
newbreaks.append(byears[0])
statlist.append((ystats, tstats))
print "revised",testyr,"to",byears[0]
fails = 0
newbreaks.append(datayears[-1])
print "\nReturning",initialBreaks, "->", newbreaks, statlist
return initialBreaks, newbreaks, statlist
