def __init__(self, template):
self.template = self.templateToList(template)
self.query = Query(self.template)
self.subject = Subject(self.template)
if len(self.query.pairedFeatures) != len(self.subject.pairedFeatures):
raise ValueError(
'The query and subject do not have the same number of paired '
'features (%d != %d)' % (len(self.query.pairedFeatures),
len(self.subject.pairedFeatures)))
# Union the landmark and trig point names from the query and subject.
self.landmarks = self.query.landmarks | self.subject.landmarks
self.trigPoints = self.query.trigPoints | self.subject.trigPoints
self.histogram = Histogram(1)
for queryPair, subjectPair in zip(self.query.pairedFeatures,
self.subject.pairedFeatures):
_, queryLandmark, _, queryTrigPoint = queryPair
_, subjectLandmark, _, subjectTrigPoint = subjectPair
self.histogram.add(0, {
'queryLandmark': queryLandmark,
'queryTrigPoint': queryTrigPoint,
'subjectLandmark': subjectLandmark,
'subjectTrigPoint': subjectTrigPoint,
})
self.histogram.finalize()
def testFinalizeWithNoData(self):
"""
If finalize is called and the histogram has no data, all
bins must have zero counts.
"""
h = Histogram(5)
h.finalize()
self.assertEqual([0, 0, 0, 0, 0], [len(bin_) for bin_ in h.bins])
def testNineElementsInThreeBins(self):
"""
If a histogram is created with 9 elements placed into 2 bins, the
bins must contain the expected values.
"""
h = Histogram(3)
list(map(h.add, range(9)))
h.finalize()
self.assertEqual([[0, 1, 2], [3, 4, 5], [6, 7, 8]], h.bins)
def testTenElementsInThreeBinsBinWidth(self):
"""
If a histogram is created with 10 elements (0-9) placed into 3 bins,
the bin width must be 3.0.
"""
h = Histogram(3)
list(map(h.add, range(10)))
h.finalize()
self.assertEqual(3.0, h.binWidth)
def testGetItem(self):
"""
The __getitem__ method must return the correct bin.
"""
h = Histogram(3)
list(map(h.add, range(9)))
h.finalize()
self.assertEqual([0, 1, 2], h[0])
self.assertEqual([3, 4, 5], h[1])
def testAlwaysMustBeTrue(self):
"""
The Always significance method must return True.
"""
histogram = Histogram(5)
list(map(histogram.add, [1, 1, 1, 1, 1, 6, 7, 8, 9]))
histogram.finalize()
significance = Always()
self.assertTrue(significance.isSignificant(0))
def testMaxBinHeightIsSignificantWhenNotSignificant(self):
"""
The isSignificant method must return False if asked about a bin
that is not significant.
"""
histogram = Histogram(5)
list(map(histogram.add, [1, 1, 1, 1, 1, 7, 8, 9]))
histogram.finalize()
significance = MaxBinHeight(histogram, SQUIRRELPOX, DB)
self.assertFalse(significance.isSignificant(1))
def testMeanBinHeightIsSignificantWhenSignificant(self):
"""
The isSignificant method must return True if asked about a bin
that is significant.
"""
histogram = Histogram(5)
list(map(histogram.add, [1, 1, 1, 1, 1, 6, 7, 8, 9]))
histogram.finalize()
significance = MeanBinHeight(histogram, COWPOX, DB)
self.assertTrue(significance.isSignificant(0))
def testHashFractionIsSignificantWhenSignificant(self):
"""
The isSignificant method must return True if asked about a bin
that is significant.
"""
histogram = Histogram(5)
list(map(histogram.add, [1, 1, 1, 1, 1, 6, 7, 8, 9]))
histogram.finalize()
significance = HashFraction(histogram, 10, 0.1)
self.assertTrue(significance.isSignificant(0))
def testGetItemInvalidIndex(self):
"""
The __getitem__ method must raise IndexError if passed the index
of a non-existent bin.
"""
h = Histogram(3)
list(map(h.add, range(9)))
h.finalize()
six.assertRaisesRegex(self, IndexError, '^list index out of range$',
h.__getitem__, 4)
def testAlwaysSignificanceAnalysis(self):
"""
The correct analysis must be provided.
"""
histogram = Histogram(5)
list(map(histogram.add, [1, 1, 1, 1, 1, 6, 7, 8, 9]))
histogram.finalize()
significance = Always()
self.assertEqual({'significanceMethod': 'Always'},
significance.analysis)
def testHashFractionSignificanceAnalysis(self):
"""
The correct analysis must be provided.
"""
histogram = Histogram(5)
list(map(histogram.add, [1, 1, 1, 1, 1, 6, 7, 8, 9]))
histogram.finalize()
significance = HashFraction(histogram, 10, 0.1)
self.assertEqual({'significanceCutoff': 1.0,
'significanceMethod': 'HashFraction'},
significance.analysis)
def testMaxBinHeightSignificanceAnalysis(self):
"""
The correct analysis must be provided.
"""
histogram = Histogram(5)
list(map(histogram.add, [1, 1, 1, 1, 1, 6, 7, 8, 9]))
histogram.finalize()
significance = MaxBinHeight(histogram, COWPOX, DB)
self.assertEqual({'significanceCutoff': 0.0,
'significanceMethod': 'MaxBinHeight'},
significance.analysis)
def testMeanBinHeightSignificanceAnalysis(self):
"""
The right analysis must be returned.
"""
histogram = Histogram(5)
list(map(histogram.add, [1, 1, 1, 1, 1, 6, 7, 8, 9]))
histogram.finalize()
significance = MeanBinHeight(histogram, COWPOX, DB)
self.assertEqual({'meanBinHeight': 0.0,
'significanceCutoff': 0.0,
'significanceMethod': 'MeanBinHeight',
'standardDeviation': 0.0},
significance.analysis)
def testNoData(self):
"""
If no data is given to the Histogram class, all bins must be empty.
"""
h = Histogram()
for bin_ in h.bins:
self.assertEqual(0, len(bin_))
def testActualNumberOfBins(self):
"""
If a bin count is given to the Histogram class, it must make the
expected number of bins.
"""
h = Histogram(5)
self.assertEqual(5, len(h.bins))
def testDefaultNumberOfBins(self):
"""
If no bin count is given to the Histogram class, it must make the
expected default number of bins.
"""
h = Histogram()
self.assertEqual(11, h.nBins)
def testNoDataMaxAndMin(self):
"""
If no data is given to the Histogram class, the max and min attributes
of the histogram must be None.
"""
h = Histogram()
self.assertIs(None, h.max)
self.assertIs(None, h.min)
def testThreeElementsMaxMin(self):
"""
If a histogram is created with three elements, the max and min
should be set to the correct values.
"""
h = Histogram()
h.add(3)
h.add(4)
h.add(5)
h.finalize()
self.assertEqual(5, h.max)
self.assertEqual(3, h.min)
def testFiveBinsMinusTwoPointFiveToPlusTwoPointFiveIntermediates(self):
"""
If a histogram is created with 5 bins and a data range of -2.5 to +2.5
items that are added between histogram boundaries must be placed in
the expected bins.
"""
for (value,
expectedCounts) in ((-2, [1, 0, 0, 0, 0]), (-1, [0, 1, 0, 0, 0]),
(+0, [0, 0, 1, 0,
0]), (+1, [0, 0, 0, 1,
0]), (+2, [0, 0, 0, 0, 1])):
h = Histogram(5)
h.add(-2.5) # Set min value.
h.add(2.5) # Set max value.
h.add(value)
h.finalize()
counts = [len(bin_) for bin_ in h.bins]
# Subract 1 from the first and last bin counts, to adjust for the
# -2.5 and 2.5 boundary values we added manually.
counts[0] -= 1
counts[-1] -= 1
self.assertEqual(expectedCounts, counts)
def testRepeatedFinalize(self):
"""
If finalize is called a second time, a RuntimeError must be raised.
"""
h = Histogram()
error = ('^Histogram already finalized$')
h.add(3)
h.finalize()
six.assertRaisesRegex(self, RuntimeError, error, h.finalize)
def testNoDataValue(self):
"""
If an element with no associated datum is added to a histogram,
the value that is passed must be stored in the bin.
"""
h = Histogram(1)
h.add(3)
h.finalize()
self.assertEqual([[3]], h.bins)
def testOneElementBinWidth(self):
"""
If a histogram is created with just one element, the bin width must be
zero.
"""
h = Histogram()
h.add(3)
h.finalize()
self.assertEqual(0.0, h.binWidth)
def testOneElementMaxMin(self):
"""
If a histogram is created with just one element, the max and min
should be set to that value.
"""
h = Histogram()
h.add(3)
h.finalize()
self.assertEqual(3, h.max)
self.assertEqual(3, h.min)
def testElementIsStoredInBin(self):
"""
If a histogram is created with just one element and one bin, the
exact element that was passed must be placed in the bin.
"""
element = object()
h = Histogram(1)
h.add(3, element)
h.finalize()
self.assertIs(element, h.bins[0][0])
def testTwoElementsBinWidth(self):
"""
If a histogram with 5 buckets is created with two elements that differ
by 1.0, the bin width should be set to the correct value of 0.2.
"""
h = Histogram(5)
h.add(3)
h.add(4)
h.finalize()
self.assertEqual(0.2, h.binWidth)
def testAddDataAfterFinalized(self):
"""
If an attempt is made to add to a histogram that has been finalized,
a RuntimeError must be raised.
"""
h = Histogram()
error = ('^Additional data cannot be added: histogram already '
'finalized$')
h.add(3)
h.finalize()
six.assertRaisesRegex(self, RuntimeError, error, h.add, 3)
def testAAFractionSignificanceAnalysis(self):
"""
The correct analysis must be provided.
"""
match = {
'subjectLandmark': Landmark('AlphaHelix', 'A', 0, 9),
'subjectTrigPoint': TrigPoint('Peaks', 'P', 21),
'queryLandmark': Landmark('AlphaHelix', 'A', 10, 9),
'queryTrigPoint': TrigPoint('Peaks', 'P', 25),
}
histogram = Histogram(3)
histogram.add(0, match)
histogram.add(1, match)
histogram.add(2, match)
histogram.finalize()
significance = AAFraction(histogram, 10, 0.75)
self.assertTrue(significance.isSignificant(0))
self.assertEqual({'significanceCutoff': 7.5,
'significanceMethod': 'AAFraction'},
significance.analysis)
def testAAFractionWhenSignificant(self):
"""
The isSignificant method must return True if asked about a bin that is
significant.
"""
match = {
'subjectLandmark': Landmark('AlphaHelix', 'A', 0, 9),
'subjectTrigPoint': TrigPoint('Peaks', 'P', 21),
'queryLandmark': Landmark('AlphaHelix', 'A', 10, 9),
'queryTrigPoint': TrigPoint('Peaks', 'P', 25),
}
histogram = Histogram(1)
histogram.add(0, match)
histogram.finalize()
significance = AAFraction(histogram, 10, 0.75)
self.assertTrue(significance.isSignificant(0))
def testNonDefaultNumberOfBins(self):
"""
The given number of bins must be stored on the histogram.
"""
h = Histogram(17)
self.assertEqual(17, h.nBins)