def scatter(r1, r2, statistic="roc", x1Label="", x2Label="", fileName=None, **args):
"""
a scatter plot for comparing the performance of two classifiers
:Parameters:
- `r1, r2` - both are either a list of Result classes, or a list of
success rates / ROC scores
- `statistic` - which measure of classifier success to plot
values : 'roc', 'successRate', 'balancedSuccessRate'
in order to specify parts of the roc curve you can use something like:
'roc50' or 'roc0.1'
:Keywords:
- `title` - the title of the plot
"""
if len(r1) != len(r2):
print "unequal lengths for r1 and r2"
if type(r1) != type({}):
raise ValueError, "Cannot handle unequal length when it is not a dict"
keys1 = r1.keys()
keys2 = r2.keys()
common = misc.intersect(keys1, keys2)
r1new = {}
r2new = {}
for key in common:
r1new[key] = r1[key]
r2new[key] = r2[key]
r1 = r1new
r2 = r2new
if type(r1) == type({}) and type(r2) == type({}):
I = r1.keys()
else:
I = range(len(r1))
if r1[I[0]].__class__.__name__ == "Results" or r1[I[0]].__class__.__name__ == "Container":
p1 = misc.extractAttribute(r1, statistic)
p2 = misc.extractAttribute(r2, statistic)
else:
p1 = r1
p2 = r2
if type(p1) == type({}):
p1 = p1.values()
p2 = p2.values()
from matplotlib import pylab
x = numpy.arange(0, 1, 0.01)
pylab.plot(p1, p2, "bo", x, x, "-k")
pylab.xlabel(x1Label, fontsize=18)
pylab.ylabel(x2Label, fontsize=18)
if "title" in args:
pylab.title(args["title"], fontsize=18)
pylab.show()
if fileName is not None:
pylab.savefig(fileName)
pylab.close()
def verifyData(self, data):
"""
verify that for a VectorDataSet the test examples refer to the same
features used in training.
"""
if data.__class__.__name__ != 'VectorDataSet':
return
if len(misc.intersect(self.featureID, data.featureID)) != len(
self.featureID):
raise ValueError, 'missing features in test data'
def commonKernel(kernelFile1, kernelFile2, kernelOutFileName1, kernelOutFileName2) :
delim = ' '
from datafunc import KernelData
import misc
kdata1 = KernelData(kernelFile1)
kdata2 = KernelData(kernelFile2)
print 'loaded data'
ids = misc.intersect(kdata1.labels.patternID, kdata2.labels.patternID)
ids.sort()
idDict1 = misc.list2dict(ids)
if len(ids) != len(kdata1) :
kernelOutFile1 = open(kernelOutFileName1, 'w')
idDict = {}
for i in range(len(kdata1)) :
if kdata1.labels.patternID[i] in idDict1 :
idDict[kdata1.labels.patternID[i]] = i
for id1 in ids :
print id1
kernelOutFile1.write(id1 + delim)
tokens = [str(kdata1.kernel.eval(kdata1, idDict[id1], idDict[id2]))
for id2 in ids]
kernelOutFile1.write(delim.join(tokens) + '\n')
if len(ids) != len(kdata2) :
kernelOutFile2 = open(kernelOutFileName2, 'w')
idDict = {}
for i in range(len(kdata2)) :
if kdata2.labels.patternID[i] in idDict1 :
idDict[kdata2.labels.patternID[i]] = i
for id1 in ids :
print id1
kernelOutFile2.write(id1 + delim)
tokens = [str(kdata2.kernel.eval(kdata2, idDict[id1], idDict[id2]))
for id2 in ids]
kernelOutFile2.write(delim.join(tokens) + '\n')
def significance(r1, r2, statistic = 'roc') :
"""
report the statistical significance of the difference in error rates
of a series of classification results of two classifiers
using the Wilcoxon signed rank test.
Returns: pvalue, (median1, median2)
where:
pvalue - the pvalue of the two sided Wilcoxon signed rank test; to get
the pvalue of a one sided test divide the pvalue by two.
(median1, median2) - the median of the statistics of the inputs r1 and r2.
:Parameters:
- `r1, r2` - both are either a list of Result classes, or a list of success
rates
- `statistic` - which measure of classifier success to plot
values : 'roc', 'successRate', 'balancedSuccessRate'
in order to specify parts of the roc curve you can use something like:
'roc50' or 'roc0.1'
"""
if type(r1) != type(r2) :
raise ValueError, 'r1 and r2 do not have the same type'
# if the two objects are dictionaries, then we can handle the case that
# the lengths are not equal:
if len(r1) != len(r2) :
print 'unequal lengths for r1 and r2'
if type(r1) != type({}) :
raise ValueError, 'Cannot handle unequal length when it is not a dict'
keys1 = r1.keys()
keys2 = r2.keys()
common = misc.intersect(keys1, keys2)
r1new = {}
r2new = {}
for key in common :
r1new[key] = r1[key]
r2new[key] = r2[key]
r1 = r1new
r2 = r2new
if type(r1) == type({}) :
if r1.keys() != r2.keys() :
raise ValueError, 'r1 and r2 do not have the same keys'
I = r1.keys()
else :
I = range(len(r1))
if r1[I[0]].__class__.__name__ == 'Results' or r1[I[0]].__class__.__name__ == 'Container' :
p1 = misc.extractAttribute(r1, statistic)
p2 = misc.extractAttribute(r2, statistic)
else :
p1 = r1
p2 = r2
if type(p1) == type({}) :
p1 = p1.values()
p2 = p2.values()
#import stats
import salstat_stats
test = salstat_stats.TwoSampleTests(p1, p2)
test.SignedRanks (p1, p2)
p = test.prob
median1 = numpy.median(numpy.array(p1))
median2 = numpy.median(numpy.array(p2))
return p, (median1,median2)
def scatter(r1, r2, statistic = 'roc', x1Label = '', x2Label= '',
fileName = None, **args) :
"""
a scatter plot for comparing the performance of two classifiers
:Parameters:
- `r1, r2` - both are either a list of Result classes, or a list of
success rates / ROC scores
- `statistic` - which measure of classifier success to plot
values : 'roc', 'successRate', 'balancedSuccessRate'
in order to specify parts of the roc curve you can use something like:
'roc50' or 'roc0.1'
:Keywords:
- `title` - the title of the plot
"""
if len(r1) != len(r2) :
print 'unequal lengths for r1 and r2'
if type(r1) != type({}) :
raise ValueError, 'Cannot handle unequal length when it is not a dict'
keys1 = r1.keys()
keys2 = r2.keys()
common = misc.intersect(keys1, keys2)
r1new = {}
r2new = {}
for key in common :
r1new[key] = r1[key]
r2new[key] = r2[key]
r1 = r1new
r2 = r2new
if type(r1) == type({}) and type(r2) == type({}) :
I = r1.keys()
else :
I = range(len(r1))
if (r1[I[0]].__class__.__name__ == 'Results' or
r1[I[0]].__class__.__name__ == 'Container') :
p1 = misc.extractAttribute(r1, statistic)
p2 = misc.extractAttribute(r2, statistic)
else :
p1 = r1
p2 = r2
if type(p1) == type({}) :
p1 = p1.values()
p2 = p2.values()
from matplotlib import pylab
x = numpy.arange(0,1,0.01)
pylab.plot(p1, p2, 'bo',x,x, '-k')
pylab.xlabel(x1Label, fontsize = 18)
pylab.ylabel(x2Label, fontsize = 18)
if 'title' in args :
pylab.title(args['title'], fontsize = 18)
pylab.show()
if fileName is not None :
pylab.savefig(fileName)
pylab.close()
def significance(r1, r2, statistic = 'roc') :
"""
report the statistical significance of the difference in error rates
of a series of classification results of two classifiers
using the Wilcoxon signed rank test.
Returns: pvalue, (median1, median2)
where:
pvalue - the pvalue of the two sided Wilcoxon signed rank test; to get
the pvalue of a one sided test divide the pvalue by two.
(median1, median2) - the median of the statistics of the inputs r1 and r2.
:Parameters:
- `r1, r2` - both are either a list of Result classes, or a list of success
rates
- `statistic` - which measure of classifier success to plot
values : 'roc', 'successRate', 'balancedSuccessRate'
in order to specify parts of the roc curve you can use something like:
'roc50' or 'roc0.1'
"""
if type(r1) != type(r2) :
raise ValueError, 'r1 and r2 do not have the same type'
# if the two objects are dictionaries, then we can handle the case that
# the lengths are not equal:
if len(r1) != len(r2) :
print 'unequal lengths for r1 and r2'
if type(r1) != type({}) :
raise ValueError, 'Cannot handle unequal length when it is not a dict'
keys1 = r1.keys()
keys2 = r2.keys()
common = misc.intersect(keys1, keys2)
r1new = {}
r2new = {}
for key in common :
r1new[key] = r1[key]
r2new[key] = r2[key]
r1 = r1new
r2 = r2new
if type(r1) == type({}) :
if r1.keys() != r2.keys() :
raise ValueError, 'r1 and r2 do not have the same keys'
I = r1.keys()
else :
I = range(len(r1))
if r1[I[0]].__class__.__name__ == 'Results' or r1[I[0]].__class__.__name__ == 'Container' :
p1 = misc.extractAttribute(r1, statistic)
p2 = misc.extractAttribute(r2, statistic)
else :
p1 = r1
p2 = r2
if type(p1) == type({}) :
p1 = p1.values()
p2 = p2.values()
#import stats
import salstat_stats
test = salstat_stats.TwoSampleTests(p1, p2)
test.SignedRanks (p1, p2)
p = test.prob
median1 = numpy.median(numpy.array(p1))
median2 = numpy.median(numpy.array(p2))
return p, (median1,median2)