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# -*- coding: utf8 -*-
from __future__ import absolute_import, division, print_function
import pytest
import os.path
import numpy as np
from larray.tests.common import assert_array_equal, assert_nparray_equal
from larray import Axis, LGroup, IGroup, read_hdf
def test_init():
axis = Axis(3)
assert len(axis) == 3
assert list(axis.labels) == list(range(3))
axis = Axis(np.int32(3))
assert len(axis) == 3
assert list(axis.labels) == list(range(3))
axis = Axis([0, 1], name='test')
assert axis.name == 'test'
assert_nparray_equal(axis.labels, [0, 1])
axis = Axis([0, 1], name=np.str_('test'))
assert axis.name == 'test'
assert type(axis.name) is not np.str_
assert_nparray_equal(axis.labels, [0, 1])
sex_tuple = ('M', 'F')
sex_list = ['M', 'F']
sex_array = np.array(sex_list)
assert_array_equal(Axis(sex_tuple, 'sex').labels, sex_array)
assert_array_equal(Axis(sex_list, 'sex').labels, sex_array)
assert_array_equal(Axis(sex_array, 'sex').labels, sex_array)
assert_array_equal(Axis('sex=M,F').labels, sex_array)
assert_array_equal(Axis(range(116), 'age').labels, np.arange(116))
axis = Axis('0..115', 'age')
assert_array_equal(axis.labels, np.arange(116))
assert_array_equal(Axis('01..12', 'zero_padding').labels, [str(i).zfill(2) for i in range(1, 13)])
assert_array_equal(Axis('01,02,03,10,11,12', 'zero_padding').labels, ['01', '02', '03', '10', '11', '12'])
group = axis[:10]
group_axis = Axis(group)
assert_array_equal(group_axis.labels, np.arange(11))
assert_array_equal(group_axis.name, 'age')
other = Axis('other=0..10')
axis = Axis(other, 'age')
assert_array_equal(axis.labels, other.labels)
assert_array_equal(axis.name, 'age')
def test_equals():
assert Axis('sex=M,F').equals(Axis('sex=M,F'))
assert Axis('sex=M,F').equals(Axis(['M', 'F'], 'sex'))
assert not Axis('sex=M,W').equals(Axis('sex=M,F'))
assert not Axis('sex1=M,F').equals(Axis('sex2=M,F'))
assert not Axis('sex1=M,W').equals(Axis('sex2=M,F'))
def test_getitem():
age = Axis('age=0..10')
a159 = age[1, 5, 9]
assert a159.key == [1, 5, 9]
assert a159.name is None
assert a159.axis is age
a159 = age[[1, 5, 9]]
assert a159.key == [1, 5, 9]
assert a159.name is None
assert a159.axis is age
a159 = age['1,5,9']
assert a159.key == [1, 5, 9]
assert a159.name is None
assert a159.axis is age
a10to20 = age[5:9]
assert a10to20.key == slice(5, 9)
assert a10to20.axis is age
a10to20 = age['5:9']
assert a10to20.key == slice(5, 9)
assert a10to20.axis is age
group = age[[1, 5, 9]] >> 'test'
assert group.key == [1, 5, 9]
assert group.name == 'test'
assert group.axis is age
group = age[:] >> 'all'
assert group.key == slice(None)
assert group.axis is age
age2 = Axis('age=0..5')
group = age[age2]
assert list(group.key) == list(age2.labels)
def test_translate():
# an axis with labels having the object dtype
a = Axis(np.array(["a0", "a1"], dtype=object), 'a')
assert a.index('a1') == 1
assert a.index('a1 >> A1') == 1
def test_getitem_lgroup_keys():
def group_equal(g1, g2):
return (g1.key == g2.key and g1.name == g2.name and g1.axis is g2.axis)
age = Axis(range(100), 'age')
ages = [1, 5, 9]
val_only = LGroup(ages)
assert group_equal(age[val_only], LGroup(ages, axis=age))
assert group_equal(age[val_only] >> 'a_name', LGroup(ages, 'a_name', axis=age))
val_name = LGroup(ages, 'val_name')
assert group_equal(age[val_name], LGroup(ages, 'val_name', age))
assert group_equal(age[val_name] >> 'a_name', LGroup(ages, 'a_name', age))
val_axis = LGroup(ages, axis=age)
assert group_equal(age[val_axis], LGroup(ages, axis=age))
assert group_equal(age[val_axis] >> 'a_name', LGroup(ages, 'a_name', axis=age))
val_axis_name = LGroup(ages, 'val_axis_name', age)
assert group_equal(age[val_axis_name], LGroup(ages, 'val_axis_name', age))
assert group_equal(age[val_axis_name] >> 'a_name', LGroup(ages, 'a_name', age))
def test_getitem_group_keys():
a = Axis('a=a0..a2')
alt_a = Axis('a=a1..a3')
key = a['a1']
g = a[key]
assert g.key == 'a1'
assert g.axis is a
g = alt_a[key]
assert g.key == 'a1'
assert g.axis is alt_a
key = a['a1':'a2']
g = a[key]
assert g.key == slice('a1', 'a2')
assert g.axis is a
g = alt_a[key]
assert g.key == slice('a1', 'a2')
assert g.axis is alt_a
key = a[['a1', 'a2']]
g = a[key]
assert g.key == ['a1', 'a2']
assert g.axis is a
g = alt_a[key]
assert g.key == ['a1', 'a2']
assert g.axis is alt_a
key = a.i[1]
g = a[key]
assert isinstance(g, LGroup)
assert g.key == 'a1'
assert g.axis is a
g = alt_a[key]
assert isinstance(g, LGroup)
assert g.key == 'a1'
assert g.axis is alt_a
key = a.i[1:3]
g = a[key]
assert isinstance(g, LGroup)
assert g.key == slice('a1', 'a2')
assert g.axis is a
g = alt_a[key]
assert isinstance(g, LGroup)
assert g.key == slice('a1', 'a2')
assert g.axis is alt_a
key = a.i[[1, 2]]
g = a[key]
assert isinstance(g, LGroup)
assert list(g.key) == ['a1', 'a2']
assert g.axis is a
g = alt_a[key]
assert isinstance(g, LGroup)
assert list(g.key) == ['a1', 'a2']
assert g.axis is alt_a
lg_a1 = a['a1']
lg_a2 = a['a2']
g = a[lg_a1:lg_a2]
assert isinstance(g, LGroup)
assert g.key == slice('a1', 'a2')
assert g.axis is a
g = alt_a[lg_a1:lg_a2]
assert isinstance(g, LGroup)
assert g.key == slice('a1', 'a2')
assert g.axis is alt_a
pg_a1 = a.i[1]
pg_a2 = a.i[2]
g = a[pg_a1:pg_a2]
assert isinstance(g, LGroup)
assert g.key == slice('a1', 'a2')
assert g.axis is a
g = alt_a[pg_a1:pg_a2]
assert isinstance(g, LGroup)
assert g.key == slice('a1', 'a2')
assert g.axis is alt_a
key = [a['a1'], a['a2']]
g = a[key]
assert isinstance(g, LGroup)
assert g.key == ['a1', 'a2']
assert g.axis is a
g = alt_a[key]
assert isinstance(g, LGroup)
assert g.key == ['a1', 'a2']
assert g.axis is alt_a
key = [a.i[1], a.i[2]]
g = a[key]
assert isinstance(g, LGroup)
assert g.key == ['a1', 'a2']
assert g.axis is a
g = alt_a[key]
assert isinstance(g, LGroup)
assert g.key == ['a1', 'a2']
assert g.axis is alt_a
key = [a['a1', 'a2'], a['a2', 'a1']]
g = a[key]
assert isinstance(g, list)
assert isinstance(g[0], LGroup)
assert isinstance(g[1], LGroup)
assert g[0].key == ['a1', 'a2']
assert g[1].key == ['a2', 'a1']
assert g[0].axis is a
assert g[1].axis is a
g = alt_a[key]
assert isinstance(g, list)
assert isinstance(g[0], LGroup)
assert isinstance(g[1], LGroup)
assert g[0].key == ['a1', 'a2']
assert g[1].key == ['a2', 'a1']
assert g[0].axis is alt_a
assert g[1].axis is alt_a
key = (a.i[1, 2], a.i[2, 1])
g = a[key]
assert isinstance(g, tuple)
assert isinstance(g[0], LGroup)
assert isinstance(g[1], LGroup)
assert list(g[0].key) == ['a1', 'a2']
assert list(g[1].key) == ['a2', 'a1']
assert g[0].axis is a
assert g[1].axis is a
g = alt_a[key]
assert isinstance(g, tuple)
assert isinstance(g[0], LGroup)
assert isinstance(g[1], LGroup)
assert list(g[0].key) == ['a1', 'a2']
assert list(g[1].key) == ['a2', 'a1']
assert g[0].axis is alt_a
assert g[1].axis is alt_a
key = (a['a1'], a['a2'])
g = a[key]
assert isinstance(g, LGroup)
assert g.key == ['a1', 'a2']
assert g.axis is a
g = alt_a[key]
assert isinstance(g, LGroup)
assert g.key == ['a1', 'a2']
assert g.axis is alt_a
key = (a.i[1], a.i[2])
g = a[key]
assert isinstance(g, LGroup)
assert g.key == ['a1', 'a2']
assert g.axis is a
g = alt_a[key]
assert isinstance(g, LGroup)
assert g.key == ['a1', 'a2']
assert g.axis is alt_a
key = (a['a1', 'a2'], a['a2', 'a1'])
g = a[key]
assert isinstance(g, tuple)
assert isinstance(g[0], LGroup)
assert isinstance(g[1], LGroup)
assert g[0].key == ['a1', 'a2']
assert g[1].key == ['a2', 'a1']
assert g[0].axis is a
assert g[1].axis is a
g = alt_a[key]
assert isinstance(g, tuple)
assert isinstance(g[0], LGroup)
assert isinstance(g[1], LGroup)
assert g[0].key == ['a1', 'a2']
assert g[1].key == ['a2', 'a1']
assert g[0].axis is alt_a
assert g[1].axis is alt_a
key = (a.i[1, 2], a.i[2, 1])
g = a[key]
assert isinstance(g, tuple)
assert isinstance(g[0], LGroup)
assert isinstance(g[1], LGroup)
assert list(g[0].key) == ['a1', 'a2']
assert list(g[1].key) == ['a2', 'a1']
assert g[0].axis is a
assert g[1].axis is a
g = alt_a[key]
assert isinstance(g, tuple)
assert isinstance(g[0], LGroup)
assert isinstance(g[1], LGroup)
assert list(g[0].key) == ['a1', 'a2']
assert list(g[1].key) == ['a2', 'a1']
assert g[0].axis is alt_a
assert g[1].axis is alt_a
def test_init_from_group():
code = Axis('code=C01..C03')
code_group = code[:'C02']
subset_axis = Axis(code_group, 'code_subset')
assert_array_equal(subset_axis.labels, ['C01', 'C02'])
def test_matching():
sutcode = Axis(['A23', 'A2301', 'A25', 'A2501'], 'sutcode')
assert sutcode.matching(regex='^...$') == LGroup(['A23', 'A25'])
assert sutcode.startingwith('A23') == LGroup(['A23', 'A2301'])
assert sutcode.endingwith('01') == LGroup(['A2301', 'A2501'])
def test_iter():
sex = Axis('sex=M,F')
assert list(sex) == [IGroup(0, axis=sex), IGroup(1, axis=sex)]
def test_positional():
age = Axis('age=0..115')
key = age.i[:-1]
assert key.key == slice(None, -1)
assert key.axis is age
def test_contains():
# normal Axis
age = Axis('age=0..10')
age2 = age[2]
age2bis = age[(2,)]
age2ter = age[[2]]
age2qua = '2,'
age20 = LGroup('20')
age20bis = LGroup('20,')
age20ter = LGroup(['20'])
age20qua = '20,'
age247 = age['2,4,7']
age247bis = age[['2', '4', '7']]
age359 = age[['3', '5', '9']]
age468 = age['4,6,8'] >> 'even'
assert 5 in age
assert '5' not in age
assert age2 in age
assert age2bis not in age
assert age2ter not in age
assert age2qua not in age
assert age20 not in age
assert age20bis not in age
assert age20ter not in age
assert age20qua not in age
assert ['3', '5', '9'] not in age
assert '3,5,9' not in age
assert '3:9' not in age
assert age247 not in age
assert age247bis not in age
assert age359 not in age
assert age468 not in age
agg = Axis((age2, age247, age359, age468, '2,6', ['3', '5', '7'], ('6', '7', '9')), "agg")
assert age2bis not in agg
assert age2ter not in agg
assert age2qua not in age
assert age247 in agg
assert age247bis in agg
assert '2,4,7' in agg
assert ['2', '4', '7'] in agg
assert age359 in agg
assert '3,5,9' in agg
assert ['3', '5', '9'] in agg
assert age468 in agg
assert 'even' in agg
assert '2,6' in agg
assert ['2', '6'] in agg
assert age['2,6'] in agg
assert age[['2', '6']] in agg
assert '3,5,7' in agg
assert ['3', '5', '7'] in agg
assert age['3,5,7'] in agg
assert age[['3', '5', '7']] in agg
assert '6,7,9' in agg
assert ['6', '7', '9'] in agg
assert age['6,7,9'] in agg
assert age[['6', '7', '9']] in agg
assert 5 not in agg
assert '5' not in agg
assert age20 not in agg
assert age20bis not in agg
assert age20ter not in agg
assert age20qua not in agg
assert '2,7' not in agg
assert ['2', '7'] not in agg
assert age['2,7'] not in agg
assert age[['2', '7']] not in agg
def test_h5_io(tmpdir):
age = Axis('age=0..10')
lipro = Axis('lipro=P01..P05')
anonymous = Axis(range(3))
wildcard = Axis(3, 'wildcard')
string_axis = Axis(['@!àéè&%µ$~', '/*-+_§()><', 'another label'], 'string_axis')
fpath = os.path.join(str(tmpdir), 'axes.h5')
# ---- default behavior ----
# int axis
age.to_hdf(fpath)
age2 = read_hdf(fpath, key=age.name)
assert age.equals(age2)
# string axis
lipro.to_hdf(fpath)
lipro2 = read_hdf(fpath, key=lipro.name)
assert lipro.equals(lipro2)
# anonymous axis
with pytest.raises(ValueError, match="Argument key must be provided explicitly in case of anonymous axis"):
anonymous.to_hdf(fpath)
# wildcard axis
wildcard.to_hdf(fpath)
wildcard2 = read_hdf(fpath, key=wildcard.name)
assert wildcard2.iswildcard
assert wildcard.equals(wildcard2)
# string axis
string_axis.to_hdf(fpath)
string_axis2 = read_hdf(fpath, string_axis.name)
assert string_axis.equals(string_axis2)
# ---- specific key ----
# int axis
key = 'axis_age'
age.to_hdf(fpath, key)
age2 = read_hdf(fpath, key=key)
assert age.equals(age2)
# string axis
key = 'axis_lipro'
lipro.to_hdf(fpath, key)
lipro2 = read_hdf(fpath, key=key)
assert lipro.equals(lipro2)
# anonymous axis
key = 'axis_anonymous'
anonymous.to_hdf(fpath, key)
anonymous2 = read_hdf(fpath, key=key)
assert anonymous2.name is None
assert_array_equal(anonymous.labels, anonymous2.labels)
# wildcard axis
key = 'axis_wildcard'
wildcard.to_hdf(fpath, key)
wildcard2 = read_hdf(fpath, key=key)
assert wildcard2.iswildcard
assert wildcard.equals(wildcard2)
# ---- specific hdf group + key ----
hdf_group = 'my_axes'
# int axis
key = hdf_group + '/axis_age'
age.to_hdf(fpath, key)
age2 = read_hdf(fpath, key=key)
assert age.equals(age2)
# string axis
key = hdf_group + '/axis_lipro'
lipro.to_hdf(fpath, key)
lipro2 = read_hdf(fpath, key=key)
assert lipro.equals(lipro2)
# anonymous axis
key = hdf_group + '/axis_anonymous'
anonymous.to_hdf(fpath, key)
anonymous2 = read_hdf(fpath, key=key)
assert anonymous2.name is None
assert_array_equal(anonymous.labels, anonymous2.labels)
# wildcard axis
key = hdf_group + '/axis_wildcard'
wildcard.to_hdf(fpath, key)
wildcard2 = read_hdf(fpath, key=key)
assert wildcard2.iswildcard
assert wildcard.equals(wildcard2)
def test_split():
# test splitting an anonymous axis
a_b = Axis('a0_b0,a0_b1,a0_b2,a1_b0,a1_b1,a1_b2')
a, b = a_b.split()
assert a.equals(Axis(['a0', 'a1']))
assert b.equals(Axis(['b0', 'b1', 'b2']))
if __name__ == "__main__":
pytest.main()