419 lines
13 KiB
Python
419 lines
13 KiB
Python
import datetime
|
|
import os
|
|
import sys
|
|
from os.path import join as pjoin
|
|
|
|
from io import StringIO
|
|
|
|
import numpy as np
|
|
|
|
from numpy.testing import (assert_array_almost_equal,
|
|
assert_array_equal, assert_equal, assert_)
|
|
import pytest
|
|
from pytest import raises as assert_raises
|
|
|
|
from scipy.io.arff import loadarff
|
|
from scipy.io.arff._arffread import read_header, ParseArffError
|
|
|
|
|
|
data_path = pjoin(os.path.dirname(__file__), 'data')
|
|
|
|
test1 = pjoin(data_path, 'test1.arff')
|
|
test2 = pjoin(data_path, 'test2.arff')
|
|
test3 = pjoin(data_path, 'test3.arff')
|
|
|
|
test4 = pjoin(data_path, 'test4.arff')
|
|
test5 = pjoin(data_path, 'test5.arff')
|
|
test6 = pjoin(data_path, 'test6.arff')
|
|
test7 = pjoin(data_path, 'test7.arff')
|
|
test8 = pjoin(data_path, 'test8.arff')
|
|
test9 = pjoin(data_path, 'test9.arff')
|
|
test10 = pjoin(data_path, 'test10.arff')
|
|
test11 = pjoin(data_path, 'test11.arff')
|
|
test_quoted_nominal = pjoin(data_path, 'quoted_nominal.arff')
|
|
test_quoted_nominal_spaces = pjoin(data_path, 'quoted_nominal_spaces.arff')
|
|
|
|
expect4_data = [(0.1, 0.2, 0.3, 0.4, 'class1'),
|
|
(-0.1, -0.2, -0.3, -0.4, 'class2'),
|
|
(1, 2, 3, 4, 'class3')]
|
|
expected_types = ['numeric', 'numeric', 'numeric', 'numeric', 'nominal']
|
|
|
|
missing = pjoin(data_path, 'missing.arff')
|
|
expect_missing_raw = np.array([[1, 5], [2, 4], [np.nan, np.nan]])
|
|
expect_missing = np.empty(3, [('yop', float), ('yap', float)])
|
|
expect_missing['yop'] = expect_missing_raw[:, 0]
|
|
expect_missing['yap'] = expect_missing_raw[:, 1]
|
|
|
|
|
|
class TestData:
|
|
def test1(self):
|
|
# Parsing trivial file with nothing.
|
|
self._test(test4)
|
|
|
|
def test2(self):
|
|
# Parsing trivial file with some comments in the data section.
|
|
self._test(test5)
|
|
|
|
def test3(self):
|
|
# Parsing trivial file with nominal attribute of 1 character.
|
|
self._test(test6)
|
|
|
|
def test4(self):
|
|
# Parsing trivial file with trailing spaces in attribute declaration.
|
|
self._test(test11)
|
|
|
|
def _test(self, test_file):
|
|
data, meta = loadarff(test_file)
|
|
for i in range(len(data)):
|
|
for j in range(4):
|
|
assert_array_almost_equal(expect4_data[i][j], data[i][j])
|
|
assert_equal(meta.types(), expected_types)
|
|
|
|
def test_filelike(self):
|
|
# Test reading from file-like object (StringIO)
|
|
with open(test1) as f1:
|
|
data1, meta1 = loadarff(f1)
|
|
with open(test1) as f2:
|
|
data2, meta2 = loadarff(StringIO(f2.read()))
|
|
assert_(data1 == data2)
|
|
assert_(repr(meta1) == repr(meta2))
|
|
|
|
def test_path(self):
|
|
# Test reading from `pathlib.Path` object
|
|
from pathlib import Path
|
|
|
|
with open(test1) as f1:
|
|
data1, meta1 = loadarff(f1)
|
|
|
|
data2, meta2 = loadarff(Path(test1))
|
|
|
|
assert_(data1 == data2)
|
|
assert_(repr(meta1) == repr(meta2))
|
|
|
|
|
|
class TestMissingData:
|
|
def test_missing(self):
|
|
data, meta = loadarff(missing)
|
|
for i in ['yop', 'yap']:
|
|
assert_array_almost_equal(data[i], expect_missing[i])
|
|
|
|
|
|
class TestNoData:
|
|
def test_nodata(self):
|
|
# The file nodata.arff has no data in the @DATA section.
|
|
# Reading it should result in an array with length 0.
|
|
nodata_filename = os.path.join(data_path, 'nodata.arff')
|
|
data, meta = loadarff(nodata_filename)
|
|
if sys.byteorder == 'big':
|
|
end = '>'
|
|
else:
|
|
end = '<'
|
|
expected_dtype = np.dtype([('sepallength', f'{end}f8'),
|
|
('sepalwidth', f'{end}f8'),
|
|
('petallength', f'{end}f8'),
|
|
('petalwidth', f'{end}f8'),
|
|
('class', 'S15')])
|
|
assert_equal(data.dtype, expected_dtype)
|
|
assert_equal(data.size, 0)
|
|
|
|
|
|
class TestHeader:
|
|
def test_type_parsing(self):
|
|
# Test parsing type of attribute from their value.
|
|
with open(test2) as ofile:
|
|
rel, attrs = read_header(ofile)
|
|
|
|
expected = ['numeric', 'numeric', 'numeric', 'numeric', 'numeric',
|
|
'numeric', 'string', 'string', 'nominal', 'nominal']
|
|
|
|
for i in range(len(attrs)):
|
|
assert_(attrs[i].type_name == expected[i])
|
|
|
|
def test_badtype_parsing(self):
|
|
# Test parsing wrong type of attribute from their value.
|
|
def badtype_read():
|
|
with open(test3) as ofile:
|
|
_, _ = read_header(ofile)
|
|
|
|
assert_raises(ParseArffError, badtype_read)
|
|
|
|
def test_fullheader1(self):
|
|
# Parsing trivial header with nothing.
|
|
with open(test1) as ofile:
|
|
rel, attrs = read_header(ofile)
|
|
|
|
# Test relation
|
|
assert_(rel == 'test1')
|
|
|
|
# Test numerical attributes
|
|
assert_(len(attrs) == 5)
|
|
for i in range(4):
|
|
assert_(attrs[i].name == 'attr%d' % i)
|
|
assert_(attrs[i].type_name == 'numeric')
|
|
|
|
# Test nominal attribute
|
|
assert_(attrs[4].name == 'class')
|
|
assert_(attrs[4].values == ('class0', 'class1', 'class2', 'class3'))
|
|
|
|
def test_dateheader(self):
|
|
with open(test7) as ofile:
|
|
rel, attrs = read_header(ofile)
|
|
|
|
assert_(rel == 'test7')
|
|
|
|
assert_(len(attrs) == 5)
|
|
|
|
assert_(attrs[0].name == 'attr_year')
|
|
assert_(attrs[0].date_format == '%Y')
|
|
|
|
assert_(attrs[1].name == 'attr_month')
|
|
assert_(attrs[1].date_format == '%Y-%m')
|
|
|
|
assert_(attrs[2].name == 'attr_date')
|
|
assert_(attrs[2].date_format == '%Y-%m-%d')
|
|
|
|
assert_(attrs[3].name == 'attr_datetime_local')
|
|
assert_(attrs[3].date_format == '%Y-%m-%d %H:%M')
|
|
|
|
assert_(attrs[4].name == 'attr_datetime_missing')
|
|
assert_(attrs[4].date_format == '%Y-%m-%d %H:%M')
|
|
|
|
def test_dateheader_unsupported(self):
|
|
def read_dateheader_unsupported():
|
|
with open(test8) as ofile:
|
|
_, _ = read_header(ofile)
|
|
|
|
assert_raises(ValueError, read_dateheader_unsupported)
|
|
|
|
|
|
class TestDateAttribute:
|
|
def setup_method(self):
|
|
self.data, self.meta = loadarff(test7)
|
|
|
|
def test_year_attribute(self):
|
|
expected = np.array([
|
|
'1999',
|
|
'2004',
|
|
'1817',
|
|
'2100',
|
|
'2013',
|
|
'1631'
|
|
], dtype='datetime64[Y]')
|
|
|
|
assert_array_equal(self.data["attr_year"], expected)
|
|
|
|
def test_month_attribute(self):
|
|
expected = np.array([
|
|
'1999-01',
|
|
'2004-12',
|
|
'1817-04',
|
|
'2100-09',
|
|
'2013-11',
|
|
'1631-10'
|
|
], dtype='datetime64[M]')
|
|
|
|
assert_array_equal(self.data["attr_month"], expected)
|
|
|
|
def test_date_attribute(self):
|
|
expected = np.array([
|
|
'1999-01-31',
|
|
'2004-12-01',
|
|
'1817-04-28',
|
|
'2100-09-10',
|
|
'2013-11-30',
|
|
'1631-10-15'
|
|
], dtype='datetime64[D]')
|
|
|
|
assert_array_equal(self.data["attr_date"], expected)
|
|
|
|
def test_datetime_local_attribute(self):
|
|
expected = np.array([
|
|
datetime.datetime(year=1999, month=1, day=31, hour=0, minute=1),
|
|
datetime.datetime(year=2004, month=12, day=1, hour=23, minute=59),
|
|
datetime.datetime(year=1817, month=4, day=28, hour=13, minute=0),
|
|
datetime.datetime(year=2100, month=9, day=10, hour=12, minute=0),
|
|
datetime.datetime(year=2013, month=11, day=30, hour=4, minute=55),
|
|
datetime.datetime(year=1631, month=10, day=15, hour=20, minute=4)
|
|
], dtype='datetime64[m]')
|
|
|
|
assert_array_equal(self.data["attr_datetime_local"], expected)
|
|
|
|
def test_datetime_missing(self):
|
|
expected = np.array([
|
|
'nat',
|
|
'2004-12-01T23:59',
|
|
'nat',
|
|
'nat',
|
|
'2013-11-30T04:55',
|
|
'1631-10-15T20:04'
|
|
], dtype='datetime64[m]')
|
|
|
|
assert_array_equal(self.data["attr_datetime_missing"], expected)
|
|
|
|
def test_datetime_timezone(self):
|
|
assert_raises(ParseArffError, loadarff, test8)
|
|
|
|
|
|
class TestRelationalAttribute:
|
|
def setup_method(self):
|
|
self.data, self.meta = loadarff(test9)
|
|
|
|
def test_attributes(self):
|
|
assert_equal(len(self.meta._attributes), 1)
|
|
|
|
relational = list(self.meta._attributes.values())[0]
|
|
|
|
assert_equal(relational.name, 'attr_date_number')
|
|
assert_equal(relational.type_name, 'relational')
|
|
assert_equal(len(relational.attributes), 2)
|
|
assert_equal(relational.attributes[0].name,
|
|
'attr_date')
|
|
assert_equal(relational.attributes[0].type_name,
|
|
'date')
|
|
assert_equal(relational.attributes[1].name,
|
|
'attr_number')
|
|
assert_equal(relational.attributes[1].type_name,
|
|
'numeric')
|
|
|
|
def test_data(self):
|
|
dtype_instance = [('attr_date', 'datetime64[D]'),
|
|
('attr_number', np.float_)]
|
|
|
|
expected = [
|
|
np.array([('1999-01-31', 1), ('1935-11-27', 10)],
|
|
dtype=dtype_instance),
|
|
np.array([('2004-12-01', 2), ('1942-08-13', 20)],
|
|
dtype=dtype_instance),
|
|
np.array([('1817-04-28', 3)],
|
|
dtype=dtype_instance),
|
|
np.array([('2100-09-10', 4), ('1957-04-17', 40),
|
|
('1721-01-14', 400)],
|
|
dtype=dtype_instance),
|
|
np.array([('2013-11-30', 5)],
|
|
dtype=dtype_instance),
|
|
np.array([('1631-10-15', 6)],
|
|
dtype=dtype_instance)
|
|
]
|
|
|
|
for i in range(len(self.data["attr_date_number"])):
|
|
assert_array_equal(self.data["attr_date_number"][i],
|
|
expected[i])
|
|
|
|
|
|
class TestRelationalAttributeLong:
|
|
def setup_method(self):
|
|
self.data, self.meta = loadarff(test10)
|
|
|
|
def test_attributes(self):
|
|
assert_equal(len(self.meta._attributes), 1)
|
|
|
|
relational = list(self.meta._attributes.values())[0]
|
|
|
|
assert_equal(relational.name, 'attr_relational')
|
|
assert_equal(relational.type_name, 'relational')
|
|
assert_equal(len(relational.attributes), 1)
|
|
assert_equal(relational.attributes[0].name,
|
|
'attr_number')
|
|
assert_equal(relational.attributes[0].type_name, 'numeric')
|
|
|
|
def test_data(self):
|
|
dtype_instance = [('attr_number', np.float_)]
|
|
|
|
expected = np.array([(n,) for n in range(30000)],
|
|
dtype=dtype_instance)
|
|
|
|
assert_array_equal(self.data["attr_relational"][0],
|
|
expected)
|
|
|
|
|
|
class TestQuotedNominal:
|
|
"""
|
|
Regression test for issue #10232 : Exception in loadarff with quoted nominal attributes.
|
|
"""
|
|
|
|
def setup_method(self):
|
|
self.data, self.meta = loadarff(test_quoted_nominal)
|
|
|
|
def test_attributes(self):
|
|
assert_equal(len(self.meta._attributes), 2)
|
|
|
|
age, smoker = self.meta._attributes.values()
|
|
|
|
assert_equal(age.name, 'age')
|
|
assert_equal(age.type_name, 'numeric')
|
|
assert_equal(smoker.name, 'smoker')
|
|
assert_equal(smoker.type_name, 'nominal')
|
|
assert_equal(smoker.values, ['yes', 'no'])
|
|
|
|
def test_data(self):
|
|
|
|
age_dtype_instance = np.float_
|
|
smoker_dtype_instance = '<S3'
|
|
|
|
age_expected = np.array([
|
|
18,
|
|
24,
|
|
44,
|
|
56,
|
|
89,
|
|
11,
|
|
], dtype=age_dtype_instance)
|
|
|
|
smoker_expected = np.array([
|
|
'no',
|
|
'yes',
|
|
'no',
|
|
'no',
|
|
'yes',
|
|
'no',
|
|
], dtype=smoker_dtype_instance)
|
|
|
|
assert_array_equal(self.data["age"], age_expected)
|
|
assert_array_equal(self.data["smoker"], smoker_expected)
|
|
|
|
|
|
class TestQuotedNominalSpaces:
|
|
"""
|
|
Regression test for issue #10232 : Exception in loadarff with quoted nominal attributes.
|
|
"""
|
|
|
|
def setup_method(self):
|
|
self.data, self.meta = loadarff(test_quoted_nominal_spaces)
|
|
|
|
def test_attributes(self):
|
|
assert_equal(len(self.meta._attributes), 2)
|
|
|
|
age, smoker = self.meta._attributes.values()
|
|
|
|
assert_equal(age.name, 'age')
|
|
assert_equal(age.type_name, 'numeric')
|
|
assert_equal(smoker.name, 'smoker')
|
|
assert_equal(smoker.type_name, 'nominal')
|
|
assert_equal(smoker.values, [' yes', 'no '])
|
|
|
|
def test_data(self):
|
|
|
|
age_dtype_instance = np.float_
|
|
smoker_dtype_instance = '<S5'
|
|
|
|
age_expected = np.array([
|
|
18,
|
|
24,
|
|
44,
|
|
56,
|
|
89,
|
|
11,
|
|
], dtype=age_dtype_instance)
|
|
|
|
smoker_expected = np.array([
|
|
'no ',
|
|
' yes',
|
|
'no ',
|
|
'no ',
|
|
' yes',
|
|
'no ',
|
|
], dtype=smoker_dtype_instance)
|
|
|
|
assert_array_equal(self.data["age"], age_expected)
|
|
assert_array_equal(self.data["smoker"], smoker_expected)
|