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from __future__ import division, print_function
import sys
print("\nexecuting test file", __file__, file=sys.stderr)
exec(compile(open('set_paths.py', "rb").read(), 'set_paths.py', 'exec'))
import numpy
import vigra
def _impl_test_labelMultiArray(dtype):
a = numpy.zeros( (10,10,10,10,2), dtype=dtype )
a[3:4, 5:8, 5:8, 5:8] = 100
a[4:5, 8:10, 5:8, 5:8] = 100 # touches above object on corners only.
a[3:4, 1:4, 5:8, 5:8] = 200
labeled = vigra.analysis.labelMultiArray(a)
assert labeled.dtype == numpy.uint32
assert labeled.max() == 4
labeled = vigra.analysis.labelMultiArrayWithBackground(a)
assert labeled.dtype == numpy.uint32
assert labeled.max() == 3
labeled = vigra.analysis.labelMultiArrayWithBackground(a, neighborhood='indirect')
assert labeled.dtype == numpy.uint32
assert labeled.max() == 2
labeled = vigra.analysis.labelMultiArrayWithBackground(a, background_value=100)
assert labeled.dtype == numpy.uint32
assert labeled.max() == 2
def test_labelMultiArray():
_impl_test_labelMultiArray(numpy.uint8)
_impl_test_labelMultiArray(numpy.uint32)
_impl_test_labelMultiArray(numpy.float32)
def _impl_test_applyMapping(dtype):
original = numpy.arange(100, dtype=dtype ).reshape(10,10)
mapping = dict( zip( original.flat[:], original.flat[:] + 100 ) )
# Not in-place
remapped = vigra.analysis.applyMapping(original, mapping)
assert remapped.dtype == original.dtype, "Default output dtype did not match input dtype!"
assert (remapped == original+100).all()
# in-place
original_copy = original.copy()
vigra.analysis.applyMapping(original_copy, mapping, out=original_copy)
assert (original_copy == original+100).all()
# Different dtypes
mapping = dict( zip( original.flat[:], (original.flat[:] + 100).astype(numpy.uint64) ) )
result = numpy.zeros_like( original, dtype=numpy.uint64 )
vigra.analysis.applyMapping(original, mapping, out=result)
assert (result == original+100).all()
mapping = dict( zip( original.flat[:], (original.flat[:] + 100).astype(numpy.uint8) ) )
result = numpy.zeros_like( original, dtype=numpy.uint8 )
vigra.analysis.applyMapping(original, mapping, out=result)
assert (result == original+100).all()
# Incomplete mapping
for i in range(10):
del mapping[i]
remapped = vigra.analysis.applyMapping(original, mapping, allow_incomplete_mapping=True)
assert (remapped[0] == original[0]).all()
assert (remapped[1:] == original[1:]+100).all()
try:
remapped = vigra.analysis.applyMapping(original, mapping, allow_incomplete_mapping=False)
except KeyError:
pass
else:
assert False, "Expected to get an exception due to the incomplete mapping!"
def test_applyMapping():
_impl_test_applyMapping(numpy.uint8)
_impl_test_applyMapping(numpy.uint32)
_impl_test_applyMapping(numpy.uint64)
def _impl_test_unique(dtype):
a = numpy.array([2,3,5,7,11,13,17,19,23,29] + [2,3,5,7,11,13,17,19,23,29], dtype=dtype)
u = vigra.analysis.unique(a, sort=True)
assert (u == [2,3,5,7,11,13,17,19,23,29]).all()
def test_unique():
_impl_test_unique(numpy.uint8)
_impl_test_unique(numpy.uint32)
_impl_test_unique(numpy.uint64)
def _impl_relabelConsecutive(dtype):
start = 17
a = numpy.random.randint(start,start+100, size=(100,100) ).astype(dtype)
a[-1] = numpy.arange(start,start+100, dtype=dtype) # Make sure every number is used
a[:] *= 3
consecutive, maxlabel, mapping = vigra.analysis.relabelConsecutive(a, start)
assert consecutive.dtype == a.dtype, "Default output dtype did not match input dtype!"
assert maxlabel == consecutive.max()
assert (vigra.analysis.applyMapping(a, mapping) == consecutive).all()
assert (numpy.unique(consecutive) == numpy.arange(start,start+100)).all(), \
"relabeled array does not have consecutive labels"
first_label_a = a[0,0]
first_label_c = consecutive[0,0]
assert ((a == first_label_a) == (consecutive == first_label_c)).all()
# Now in-place
orig = a.copy()
consecutive, maxlabel, mapping = vigra.analysis.relabelConsecutive(a, start, out=a)
assert consecutive is a
assert maxlabel == consecutive.max()
assert (vigra.analysis.applyMapping(orig, mapping) == consecutive).all()
assert (numpy.unique(a) == numpy.arange(start,start+100)).all(), \
"relabeled array does not have consecutive labels"
first_label_orig = orig[0,0]
first_label_a = a[0,0]
assert ((orig == first_label_orig) == (a == first_label_a)).all()
def test_relabelConsecutive():
_impl_relabelConsecutive(numpy.uint8)
_impl_relabelConsecutive(numpy.uint32)
_impl_relabelConsecutive(numpy.uint64)
def test_relabelConsecutive_keep_zeros():
a = numpy.arange(1,10, dtype=numpy.uint8)
a[1::2] = 0 # replace even numbers with zeros
# Check keep_zeros=True
consecutive, maxlabel, mapping = vigra.analysis.relabelConsecutive(a, start_label=100, keep_zeros=True)
assert (consecutive[1::2] == 0).all(), \
"Zeros were not left untouched!"
assert set(consecutive[0::2]) == set(range(100,100+len(consecutive[0::2]))), \
"Non-zero items were not correctly consecutivized!"
assert maxlabel == consecutive.max()
assert (vigra.analysis.applyMapping(a, mapping) == consecutive).all()
# Check keep_zeros=False
consecutive, maxlabel, mapping = vigra.analysis.relabelConsecutive(a, start_label=100, keep_zeros=False)
assert (numpy.unique(consecutive) == numpy.arange(100, 100+1+len(a[::2]))).all(), \
"relabeled array does not have consecutive labels: {}".format(consecutive)
assert maxlabel == consecutive.max()
assert (vigra.analysis.applyMapping(a, mapping) == consecutive).all()
def ok_():
print(".", file=sys.stderr)
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