def shuffle(self, brknumber, offset=0, span=6):
loxs=self.__xsegs[brknumber-1]
loys=self.__ysegs[brknumber-1]
loyrs=self.__yearsegs[brknumber-1]
hixs=self.__xsegs[brknumber]
hiys=self.__ysegs[brknumber]
hiyrs=self.__yearsegs[brknumber]
if span!=0:
xs=list(loxs[-span:])
xs.extend(hixs[:span])
ys=list(loys[-span:])
ys.extend(hiys[:span])
yrs=list(loyrs[-span:])
yrs.extend(hiyrs[:span])
stat=shuffle.shuffle_stat(xs, ys, yrs, span+offset)
else:
xs=list(loxs[:])
xs.extend(hixs[:])
ys=list(loys[:])
ys.extend(hiys[:])
yrs=list(loyrs[:])
yrs.extend(hiyrs[:])
stat=shuffle.shuffle_stat(xs, ys, yrs, len(loxs) + offset)
bins=np.bincount(stat[0])
mode=bins.argmax()
bv=bivariate.bivariate(ys, xs, anomalise=False, pr=0.01)
return stat, bins[yrs[0]:], yrs, mode, stats.norm.fit(stat[0]),stats.norm.fit(stat[1]),stats.norm.fit(stat[2]), bv.maxTi(), bv.stepChange()
def resample_break(testdata, datayears, N=30):
brks=[]
tis=[]
for i in range(N):
controldata = np.array([random.random() for y in datayears])
bv=bivariate.bivariate(testdata,controldata, anomalise=False, pr=0.01)
tis.append(bv.maxTi())
brks.append(datayears[bv.maxIndexTi()])
return stats.norm.fit(brks), stats.norm.fit(tis)
def resample_break(testdata, datayears, N=30, withmode=False):
brks=[]
tis=[]
shifts=[]
try:
for i in range(N):
step=0
controldata = np.array([random.random() for y in datayears])
step=1
bv=bivariate.bivariate(testdata,controldata, anomalise=False, pr=0.01)
step=2
tis.append(bv.maxTi())
step=3
brks.append(datayears[bv.maxIndexTi()])
step=4
shifts.append(bv.stepChange())
step=5
except Exception as e:
print str(e), step
raise e
if withmode:
yearfreqs=np.bincount(brks)
#print brks,len(yearfreqs),yearfreqs,range(int(datayears[0])-1,int(datayears[-1])-1)
first=second=firstval=secondval=0
for i in range(int(min(brks))-1,int(max(brks))+1):
# print i
if yearfreqs[i] >firstval:
second=first
first=i
firstval=yearfreqs[first]
secondval=yearfreqs[second]
elif yearfreqs[i] >secondval:
second=i
secondval=yearfreqs[second]
#now we also will need the mean of the Tis and shifts for each of the modal values
brks=np.array(brks)
mask1=np.where(brks==first)
timean1=np.mean(np.array(tis)[mask1])
shmean1=np.mean(np.array(shifts)[mask1])
if second == 0:
return stats.norm.fit(brks[mask1]), stats.norm.fit(np.array(tis)[mask1]),stats.norm.fit(np.array(shifts)[mask1]), [(first, float(firstval)/N), None, None,(timean1, shmean1), None]
else:
mask2=np.where(brks==second)
timean2=np.mean(np.array(tis)[mask2])
shmean2=np.mean(np.array(shifts)[mask2])
return stats.norm.fit(brks[mask1]), stats.norm.fit(np.array(tis)[mask1]),stats.norm.fit(np.array(shifts)[mask1]), [(first, float(firstval)/float(N)), (second, float(secondval)/float(N)), yearfreqs[-len(datayears):],(timean1, shmean1), (timean2, shmean2)]
# if second == 0:
# return stats.norm.fit(brks), stats.norm.fit(tis),stats.norm.fit(shifts), [(first, float(firstval)/N), None, None,(timean1, shmean1), None]
# else:
# mask2=np.where(brks==second)
# timean2=np.mean(np.array(tis)[mask2])
# shmean2=np.mean(np.array(shifts)[mask2])
# return stats.norm.fit(brks), stats.norm.fit(tis),stats.norm.fit(shifts), [(first, float(firstval)/float(N)), (second, float(secondval)/float(N)), yearfreqs[-len(datayears):],(timean1, shmean1), (timean2, shmean2)]
else:
return stats.norm.fit(brks), stats.norm.fit(tis),stats.norm.fit(shifts)
def classify(ys, years, Year, window=10, span=2):
spins=range(-span, span+1)
counts=np.zeros(np.shape(ys))
pos=list(years).index(Year)
# if #need to think about what if window - span < 0
for i in spins:
lo=max(0, pos-window+i)
hi=min(len(ys)+1, pos+window+i)
yslice=ys[lo:hi]
# yrslice=years[lo:hi]
# slpos=list(yrslice).index(Year)
for j in range(int(100/(2*span+1))):
bv=bivariate.bivariate(yslice, np.array([random.random() for y in yslice]), anomalise=False, pr=0.01) #(testdata,controldata, anomalise=False, pr=0.01)
bvpos=bv.maxIndexTi()
counts[lo+bvpos]+=1
return np.max(counts)/np.sum(counts)
def shuffle_stat(xs1, ys1, Years, pos, iterations=100):
'''
recompute Ti0 and breakpoint locations by reanalysing the values on each side of the breaks point
xs are control
ys are test
pos is the location being tested
iterations is the number of times to test
'''
#MUST take copies of input because the shuffles have side effects. JHR 13/10/2014
if len(xs1) == 0:
print "oops"
xs=copy.copy(xs1)
ys=copy.copy(ys1)
index=range(len(xs))
TiList = []
TiPosIndex=[]
ShiftList=[]
pos = min(pos, len(index))
for i in range(iterations):
lowx=xs[:pos+1]
lowy=ys[:pos+1]
hix=xs[pos+1:]
hiy=ys[pos+1:]
np.random.shuffle(lowx)
np.random.shuffle(lowy)
np.random.shuffle(hix)
np.random.shuffle(hiy)
lowx = np.append(lowx, hix)
lowy = np.append(lowy, hiy)
bv=bivariate.bivariate(lowy, lowx, anomalise=False, constantsxy=True)
try:
TiList.append(bv.maxTi())
TiPosIndex.append(Years[bv.maxIndexTi()])
ShiftList.append(bv.stepChange())
except Exception as e:
print str(e)
raise
return TiPosIndex, TiList,ShiftList
Created on Tue Feb 24 15:27:36 2015 @author: s4493222 """ import numpy as np import bivariate_multi as bivariate import random SVNRevision="$Revision: 308 $" #self, rawdata, xs, anomalise=True, step=1, averagesteps=False, critical=None, pr= None, window = 5, constantsxy=True): ys=np.array([random.random() + i/100. for i in range(100)]) xs=np.array([random.random() for i in range(100)]) bv=bivariate.bivariate(ys, xs, pr=0.05, anomalise=False, window=1) print "Trended",bv.maxIndexTi(), bv.maxTi() ys2=ys #ys2=np.array([random.random() + 0.1 + int(i >49) * 0.1 for i in range(100)]) #ys2=np.array([random.random() + 0.1 + int(i >49) * 0.1 + i/100. for i in range(100)]) #ys2=np.array([random.random() + 0.1 + int(i >49) * 0.1 + i/10. for i in range(100)]) ys2=np.array([random.random() + 0.1 + int(i >49) * 0.1 + (i/100.) * int(abs(i-49) <3) for i in range(100)]) #ys2=ys bv=bivariate.bivariate(ys2, xs, pr=0.05, anomalise=False, window=1) print bv.maxIndexTi(), bv.maxTi() loc=bv.maxIndexTi()
timestring="%d-%d-%d-%d-%d" % datetime.datetime.timetuple(datetime.datetime.utcnow())[0:5]
prewhiten=False
fn=os.environ["HOMEPATH"]+"\\Documents\\ReferenceData\\Rogers_Analysis_17Jul2014\\Data 4 Jim\\GISSTEMPto6-2013\\GISSTEMPto6-2013b.csv"
fn=os.environ["HOMEPATH"]+"\\Documents\\abrupt\\SpatialBPs\\Qld_191001-201312.csv"
fn=os.environ["HOMEPATH"]+"\\Documents\\ReferenceData\\Rogers_Analysis_17Jul2014\\Data 4 Jim\\GISSTEMPto6-2013\\GISSTEMPto6-2013b.csv"
fn="C:\Users\s4493222\Documents\CourseWork(ROP8001&2)\Confirmation\IllustrativeData.csv"
fn=os.environ["HOMEPATH"]+"\\Documents\\ReferenceData\\GISS\\gisstemp\\tabledata_v3\\GLB.Ts+dSST.csv"
TraceFile=fn+".trace"
trace=True
#fn=os.environ["HOMEPATH"]+"\\Documents\\ReferenceData\\BOM\\rutherglen_82039.csv"
#fn = tests17Aug.fn
data=np.genfromtxt(fn,delimiter=",",names=True,filling_values =np.NaN, skiprows=0) #fill with NaNs so must use their bounds
ys=data["JD"]
#ys=data["DeWobble"]
# ys=data["24SEQU"]
#ys=data["Mint"]
Years=data["Year"]
#xs=data["Maxt"]
xs = np.array([random.random() for i in range(len(ys))])
if prewhiten:
import STARS
import whitening
ys=whitening.prewhiten(ys,STARS.AlphaEst(ys, 15, option="optIPN4", returnmsgs=False))
print xs, ys
print convergentBreaks(ys, xs, Years, "64N90N", mode="control", guide="AIC",trace=trace)
bv=bivariate.bivariate(ys, xs, anomalise=False)
print bv.maxTi(), bv.maxIndexTi()
print bv.allPoints(0.05)
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))
@author: James
"""
#classify_breaks
import numpy as np;
import bivariate_multi as bivariate
import random
def classify(ys, years, Year, window=10, span=2):
spins=range(-span, span+1)
counts=np.zeros(np.shape(ys))
pos=list(years).index(Year)
# if #need to think about what if window - span < 0
for i in spins:
lo=max(0, pos-window+i)
hi=min(len(ys)+1, pos+window+i)
yslice=ys[lo:hi]
# yrslice=years[lo:hi]
# slpos=list(yrslice).index(Year)
for j in range(int(100/(2*span+1))):
bv=bivariate.bivariate(yslice, np.array([random.random() for y in yslice]), anomalise=False, pr=0.01) #(testdata,controldata, anomalise=False, pr=0.01)
bvpos=bv.maxIndexTi()
counts[lo+bvpos]+=1
return np.max(counts)/np.sum(counts)
if __name__ == "__main__":
ys=np.array([0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1])
ys=ys+np.array([0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,0.99,1,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9])
years=np.array([1900+i for i in range(len(ys))])
bv1=bivariate.bivariate(ys, np.array([random.random() for y in ys]), anomalise=False, pr=0.01)
print classify(ys, years, years[bv1.maxIndexTi()])