413 lines
13 KiB
Python
413 lines
13 KiB
Python
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import datetime
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import os
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import sys
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from os.path import join as pjoin
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from io import StringIO
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import numpy as np
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from numpy.testing import (assert_array_almost_equal,
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assert_array_equal, assert_equal, assert_)
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import pytest
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from pytest import raises as assert_raises
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from scipy.io.arff.arffread import loadarff
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from scipy.io.arff.arffread import read_header, ParseArffError
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data_path = pjoin(os.path.dirname(__file__), 'data')
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test1 = pjoin(data_path, 'test1.arff')
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test2 = pjoin(data_path, 'test2.arff')
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test3 = pjoin(data_path, 'test3.arff')
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test4 = pjoin(data_path, 'test4.arff')
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test5 = pjoin(data_path, 'test5.arff')
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test6 = pjoin(data_path, 'test6.arff')
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test7 = pjoin(data_path, 'test7.arff')
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test8 = pjoin(data_path, 'test8.arff')
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test9 = pjoin(data_path, 'test9.arff')
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test10 = pjoin(data_path, 'test10.arff')
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test11 = pjoin(data_path, 'test11.arff')
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test_quoted_nominal = pjoin(data_path, 'quoted_nominal.arff')
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test_quoted_nominal_spaces = pjoin(data_path, 'quoted_nominal_spaces.arff')
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expect4_data = [(0.1, 0.2, 0.3, 0.4, 'class1'),
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(-0.1, -0.2, -0.3, -0.4, 'class2'),
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(1, 2, 3, 4, 'class3')]
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expected_types = ['numeric', 'numeric', 'numeric', 'numeric', 'nominal']
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missing = pjoin(data_path, 'missing.arff')
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expect_missing_raw = np.array([[1, 5], [2, 4], [np.nan, np.nan]])
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expect_missing = np.empty(3, [('yop', float), ('yap', float)])
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expect_missing['yop'] = expect_missing_raw[:, 0]
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expect_missing['yap'] = expect_missing_raw[:, 1]
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class TestData(object):
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def test1(self):
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# Parsing trivial file with nothing.
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self._test(test4)
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def test2(self):
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# Parsing trivial file with some comments in the data section.
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self._test(test5)
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def test3(self):
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# Parsing trivial file with nominal attribute of 1 character.
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self._test(test6)
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def _test(self, test_file):
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data, meta = loadarff(test_file)
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for i in range(len(data)):
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for j in range(4):
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assert_array_almost_equal(expect4_data[i][j], data[i][j])
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assert_equal(meta.types(), expected_types)
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def test_filelike(self):
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# Test reading from file-like object (StringIO)
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with open(test1) as f1:
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data1, meta1 = loadarff(f1)
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with open(test1) as f2:
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data2, meta2 = loadarff(StringIO(f2.read()))
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assert_(data1 == data2)
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assert_(repr(meta1) == repr(meta2))
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@pytest.mark.skipif(sys.version_info < (3, 6),
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reason='Passing path-like objects to IO functions requires Python >= 3.6')
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def test_path(self):
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# Test reading from `pathlib.Path` object
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from pathlib import Path
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with open(test1) as f1:
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data1, meta1 = loadarff(f1)
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data2, meta2 = loadarff(Path(test1))
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assert_(data1 == data2)
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assert_(repr(meta1) == repr(meta2))
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class TestMissingData(object):
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def test_missing(self):
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data, meta = loadarff(missing)
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for i in ['yop', 'yap']:
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assert_array_almost_equal(data[i], expect_missing[i])
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class TestNoData(object):
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def test_nodata(self):
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# The file nodata.arff has no data in the @DATA section.
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# Reading it should result in an array with length 0.
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nodata_filename = os.path.join(data_path, 'nodata.arff')
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data, meta = loadarff(nodata_filename)
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expected_dtype = np.dtype([('sepallength', '<f8'),
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('sepalwidth', '<f8'),
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('petallength', '<f8'),
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('petalwidth', '<f8'),
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('class', 'S15')])
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assert_equal(data.dtype, expected_dtype)
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assert_equal(data.size, 0)
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class TestHeader(object):
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def test_type_parsing(self):
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# Test parsing type of attribute from their value.
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with open(test2) as ofile:
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rel, attrs = read_header(ofile)
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expected = ['numeric', 'numeric', 'numeric', 'numeric', 'numeric',
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'numeric', 'string', 'string', 'nominal', 'nominal']
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for i in range(len(attrs)):
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assert_(attrs[i].type_name == expected[i])
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def test_badtype_parsing(self):
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# Test parsing wrong type of attribute from their value.
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def badtype_read():
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with open(test3) as ofile:
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_, _ = read_header(ofile)
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assert_raises(ParseArffError, badtype_read)
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def test_fullheader1(self):
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# Parsing trivial header with nothing.
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with open(test1) as ofile:
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rel, attrs = read_header(ofile)
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# Test relation
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assert_(rel == 'test1')
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# Test numerical attributes
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assert_(len(attrs) == 5)
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for i in range(4):
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assert_(attrs[i].name == 'attr%d' % i)
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assert_(attrs[i].type_name == 'numeric')
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# Test nominal attribute
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assert_(attrs[4].name == 'class')
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assert_(attrs[4].values == ('class0', 'class1', 'class2', 'class3'))
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def test_dateheader(self):
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with open(test7) as ofile:
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rel, attrs = read_header(ofile)
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assert_(rel == 'test7')
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assert_(len(attrs) == 5)
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assert_(attrs[0].name == 'attr_year')
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assert_(attrs[0].date_format == '%Y')
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assert_(attrs[1].name == 'attr_month')
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assert_(attrs[1].date_format == '%Y-%m')
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assert_(attrs[2].name == 'attr_date')
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assert_(attrs[2].date_format == '%Y-%m-%d')
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assert_(attrs[3].name == 'attr_datetime_local')
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assert_(attrs[3].date_format == '%Y-%m-%d %H:%M')
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assert_(attrs[4].name == 'attr_datetime_missing')
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assert_(attrs[4].date_format == '%Y-%m-%d %H:%M')
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def test_dateheader_unsupported(self):
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def read_dateheader_unsupported():
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with open(test8) as ofile:
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_, _ = read_header(ofile)
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assert_raises(ValueError, read_dateheader_unsupported)
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class TestDateAttribute(object):
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def setup_method(self):
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self.data, self.meta = loadarff(test7)
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def test_year_attribute(self):
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expected = np.array([
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'1999',
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'2004',
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'1817',
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'2100',
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'2013',
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'1631'
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], dtype='datetime64[Y]')
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assert_array_equal(self.data["attr_year"], expected)
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def test_month_attribute(self):
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expected = np.array([
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'1999-01',
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'2004-12',
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'1817-04',
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'2100-09',
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'2013-11',
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'1631-10'
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], dtype='datetime64[M]')
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assert_array_equal(self.data["attr_month"], expected)
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def test_date_attribute(self):
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expected = np.array([
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'1999-01-31',
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'2004-12-01',
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'1817-04-28',
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'2100-09-10',
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'2013-11-30',
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'1631-10-15'
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], dtype='datetime64[D]')
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assert_array_equal(self.data["attr_date"], expected)
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def test_datetime_local_attribute(self):
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expected = np.array([
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datetime.datetime(year=1999, month=1, day=31, hour=0, minute=1),
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datetime.datetime(year=2004, month=12, day=1, hour=23, minute=59),
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datetime.datetime(year=1817, month=4, day=28, hour=13, minute=0),
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datetime.datetime(year=2100, month=9, day=10, hour=12, minute=0),
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datetime.datetime(year=2013, month=11, day=30, hour=4, minute=55),
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datetime.datetime(year=1631, month=10, day=15, hour=20, minute=4)
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], dtype='datetime64[m]')
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assert_array_equal(self.data["attr_datetime_local"], expected)
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def test_datetime_missing(self):
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expected = np.array([
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'nat',
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'2004-12-01T23:59',
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'nat',
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'nat',
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'2013-11-30T04:55',
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'1631-10-15T20:04'
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], dtype='datetime64[m]')
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assert_array_equal(self.data["attr_datetime_missing"], expected)
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def test_datetime_timezone(self):
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assert_raises(ParseArffError, loadarff, test8)
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class TestRelationalAttribute(object):
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def setup_method(self):
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self.data, self.meta = loadarff(test9)
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def test_attributes(self):
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assert_equal(len(self.meta._attributes), 1)
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relational = list(self.meta._attributes.values())[0]
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assert_equal(relational.name, 'attr_date_number')
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assert_equal(relational.type_name, 'relational')
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assert_equal(len(relational.attributes), 2)
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assert_equal(relational.attributes[0].name,
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'attr_date')
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assert_equal(relational.attributes[0].type_name,
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'date')
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assert_equal(relational.attributes[1].name,
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'attr_number')
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assert_equal(relational.attributes[1].type_name,
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'numeric')
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def test_data(self):
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dtype_instance = [('attr_date', 'datetime64[D]'),
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('attr_number', np.float_)]
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expected = [
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np.array([('1999-01-31', 1), ('1935-11-27', 10)],
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dtype=dtype_instance),
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np.array([('2004-12-01', 2), ('1942-08-13', 20)],
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dtype=dtype_instance),
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np.array([('1817-04-28', 3)],
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dtype=dtype_instance),
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np.array([('2100-09-10', 4), ('1957-04-17', 40),
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('1721-01-14', 400)],
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dtype=dtype_instance),
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np.array([('2013-11-30', 5)],
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dtype=dtype_instance),
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np.array([('1631-10-15', 6)],
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dtype=dtype_instance)
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]
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for i in range(len(self.data["attr_date_number"])):
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assert_array_equal(self.data["attr_date_number"][i],
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expected[i])
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class TestRelationalAttributeLong(object):
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def setup_method(self):
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self.data, self.meta = loadarff(test10)
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def test_attributes(self):
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assert_equal(len(self.meta._attributes), 1)
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relational = list(self.meta._attributes.values())[0]
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assert_equal(relational.name, 'attr_relational')
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assert_equal(relational.type_name, 'relational')
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assert_equal(len(relational.attributes), 1)
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assert_equal(relational.attributes[0].name,
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'attr_number')
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assert_equal(relational.attributes[0].type_name, 'numeric')
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def test_data(self):
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dtype_instance = [('attr_number', np.float_)]
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expected = np.array([(n,) for n in range(30000)],
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dtype=dtype_instance)
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assert_array_equal(self.data["attr_relational"][0],
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expected)
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class TestQuotedNominal(object):
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"""
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Regression test for issue #10232 : Exception in loadarff with quoted nominal attributes.
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"""
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def setup_method(self):
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self.data, self.meta = loadarff(test_quoted_nominal)
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def test_attributes(self):
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assert_equal(len(self.meta._attributes), 2)
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age, smoker = self.meta._attributes.values()
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assert_equal(age.name, 'age')
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assert_equal(age.type_name, 'numeric')
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assert_equal(smoker.name, 'smoker')
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assert_equal(smoker.type_name, 'nominal')
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assert_equal(smoker.values, ['yes', 'no'])
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def test_data(self):
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age_dtype_instance = np.float_
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smoker_dtype_instance = '<S3'
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age_expected = np.array([
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18,
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24,
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44,
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56,
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89,
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11,
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], dtype=age_dtype_instance)
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smoker_expected = np.array([
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'no',
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'yes',
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'no',
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'no',
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'yes',
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'no',
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], dtype=smoker_dtype_instance)
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assert_array_equal(self.data["age"], age_expected)
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assert_array_equal(self.data["smoker"], smoker_expected)
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class TestQuotedNominalSpaces(object):
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"""
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Regression test for issue #10232 : Exception in loadarff with quoted nominal attributes.
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"""
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def setup_method(self):
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self.data, self.meta = loadarff(test_quoted_nominal_spaces)
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def test_attributes(self):
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assert_equal(len(self.meta._attributes), 2)
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age, smoker = self.meta._attributes.values()
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assert_equal(age.name, 'age')
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assert_equal(age.type_name, 'numeric')
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assert_equal(smoker.name, 'smoker')
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assert_equal(smoker.type_name, 'nominal')
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assert_equal(smoker.values, [' yes', 'no '])
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def test_data(self):
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age_dtype_instance = np.float_
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smoker_dtype_instance = '<S5'
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age_expected = np.array([
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18,
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24,
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44,
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56,
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89,
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11,
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], dtype=age_dtype_instance)
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smoker_expected = np.array([
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'no ',
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' yes',
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'no ',
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'no ',
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' yes',
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'no ',
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], dtype=smoker_dtype_instance)
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assert_array_equal(self.data["age"], age_expected)
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assert_array_equal(self.data["smoker"], smoker_expected)
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