def test_tree_to_word():
""" Test the transformation from a tree (root node) to a word """
root = Node("a", Node("b", Node("1"), Node("2")), Node("3"))
assert_equals(str(MPT(root)), "a b 1 2 3")
root = Node("a", Node("bef", Node("a", Node("6"), Node("8")), Node("2")),
Node("13"))
assert_equals(str(MPT(root)), "a bef a 6 8 2 13")
def test_equals():
""" Test the equality testing of MPTs """
mpt1 = MPT("a b c 1 2 a 4 e 4 5 d 6 7")
mpt2 = MPT("pq b c 1 2 pq 4 e 4 5 z 6 7")
mpt3 = MPT("a b c 1 2 a 4 e 4 5 6")
mpt4 = MPT("pq b c 1 2 pq 4 e 4 5 d 6 8")
assert_equals(mpt1, mpt2)
assert_false(mpt1 == mpt3)
assert_false(mpt1 != mpt2)
assert_false(mpt4 == mpt1)
def test_mpt_from_word():
""" Test if building from a word functions properly """
mpt_obj = context.MPTS["test1"]
mpt_obj2 = MPT("a bc c 0 1 a 2 e 2 3 d 4 5")
assert_equals(mpt_obj, mpt_obj2)
def build_mpt_from_subtrees(self, subtrees):
""" Build MPTs from the given subtrees
Parameters
----------
subtrees : [str]
List of subtrees
Returns
-------
"""
mpts = []
leaf_step = 0
for subtree in subtrees:
# transform each subtree to bmpt
bmpt = trans.easy_to_bmpt(subtree, leaf_step=leaf_step)
mpts.append(MPT(bmpt))
leaf_step += len(subtree)
joint = joint_tree.join(mpts)
joint.subtrees = subtrees # TODO to easy?
return joint
def test_to_tikz():
""" Test the conversion to tikz """
tikz_str = r"\Tree [.a 13 [.ce [.e 5 6 ] 0 ] ]"
mpt = MPT("a 13 ce e 5 6 0")
assert_equals(visualize_mpt.to_tikz(mpt), tikz_str)
def test_word_to_tree():
""" Test the transformation from a word to a tree (root node) """
root = Node("a", Node("bef", Node("a", Node("6"), Node("8")), Node("2")),
Node("13"))
root2 = transformations.word_to_nodes(MPTWord("a bef a 6 8 2 13"))
assert_equals(MPT(root), MPT(root2))
mpt = context.MPTS["2htms"]
word = MPTWord(
"y0 y5 y8 Do 0 G1 0 1 Dn 3 G1 2 3 y6 Do 4 G2 4 5 y7 Dn 7 G2 6 7 Do 8 G3 8 9 y1 y4 Dn 11 G3 10 11 Do 12 G4 12 13 y2 Dn 15 G4 14 15 y3 Do 16 G5 16 17 Dn 19 G5 18 19"
)
mpt2 = MPT(transformations.word_to_nodes(word))
print(type(mpt))
print(type(mpt2))
assert_equals(mpt, mpt2)
def test_get_levels():
str_ = "b c 2 1 a 2 d 1 0"
mpt = MPT(str_)
levels = mpt.get_levels(mpt.root)
levels = {
key: [node.content for node in value]
for key, value in levels.items()
}
print(levels)
assert_equals(
{
0: ["b"],
1: ["c", "a"],
2: ["2", "1", "2", "d"],
3: ["1", "0"]
}, levels)
def test_apply_rgs():
mpt = "a a 0 1 b 2 3"
param = "a"
rgs = [1, 0]
res = sub.apply_rgs(param, rgs, mpt.split(" "))
assert_equals(res, ["a1", "a", "0", "1", "b", "2", "3"])
p2 = "b"
rgs2 = [12]
subst = sub.Substitution({param: rgs, p2: rgs2})
mpt = MPT(mpt)
assert_equals(subst.apply(mpt), "a1 a 0 1 b12 2 3")
def test():
mpt1 = MPT("a bef a 6 8 2 13")
res = transformations.get_formulae(mpt1)
print(res)
assert_true({
'2': ['a * (1-bef)'],
'6': ['a * bef * a'],
'8': ['a * bef * (1-a)'],
'13': ['(1-a)']
} == res)
leaf = lambda x: all([ch in string.ascii_uppercase for ch in x])
mpt1 = MPT('p A B', leaf_test=leaf)
assert_equals(transformations.get_formulae(mpt1), {
'A': ['p'],
'B': ['(1-p)']
})
mpt2 = MPT('r N g N O', leaf_test=leaf)
assert_equals(transformations.get_formulae(mpt2), {
'N': ['r', '(1-r) * g'],
'O': ['(1-r) * (1-g)']
})
mpt3 = context.MPTS["test1"]
assert_equals(
transformations.get_formulae(mpt3), {
'0': ['a * bc * c'],
'1': ['a * bc * (1-c)'],
'2': ['a * (1-bc) * a', 'a * (1-bc) * (1-a) * e'],
'3': ['a * (1-bc) * (1-a) * (1-e)'],
'4': ['(1-a) * d'],
'5': ['(1-a) * (1-d)']
})
def eval_random_model(self, subtrees):
# deletion
del_tree = self.random_deletion_model()
# substitutions
param_rgs = self.random_substitution_configs(del_tree)
subst = substitution.Substitution(param_rgs)
model = MPT(subst.apply(del_tree))
model.subtrees = subtrees
if props.check(model, 'identifiable'):
evaluation = fitting.fit_mpt(model,
self.func,
self.data_path,
sep=self.sep)
print(str(model))
print(evaluation)
print()
sys.stdout.flush()
return str(model), evaluation
return None, None
def build_mpt_from_subtrees(self, subtrees):
""" Build MPTs from the given subtrees
Parameters
----------
subtrees : [str]
List of subtrees
Returns
-------
joint tree
"""
mpts = []
for subtree in subtrees:
bmpt = subtree[0]
mpts.append(MPT(bmpt, leaf_test=self.leaf_test))
joint = joint_tree.join(mpts)
joint.subtrees = subtrees # TODO to easy?
return joint
import os
from mptpy.tools.parsing import Parser
from mptpy.mpt import MPT
PARSER = Parser()
MPTS = {}
for entry in os.scandir('./tests/test_models/test_build'):
MPTS[entry.name.split(".")[0]] = PARSER.parse(entry.path)
MPTS["testdeletion"] = MPT("b c 2 1 a 2 d 1 0")
for mpt in MPTS:
print(mpt, MPTS[mpt])
def test_tree_length():
""" Test the tree length function """
mpt = MPT("pq b c 1 2 pq 4 e 4 5 z 6 7")
assert_equals(len(mpt.root), 13)
assert_equals(len(mpt.root.neg), 3)
assert_equals(len(mpt.root.pos), 9)