#!/usr/bin/env python __author__ = "Bert Palm" __email__ = "bert.palm@ufz.de" __copyright__ = "Copyright 2018, Helmholtz-Zentrum für Umweltforschung GmbH - UFZ" import pytest import numpy as np import pandas as pd from pandas.api.types import is_bool_dtype from saqc.flagger.baseflagger import BaseFlagger from saqc.flagger.dmpflagger import DmpFlagger from saqc.flagger.simpleflagger import SimpleFlagger from pandas.core.indexing import IndexingError from saqc.funcs.functions import flagRange, flagSesonalRange, forceFlags, clearFlags def get_dataset(rows, cols): index = pd.date_range(start='2011-01-01', end='2011-01-10', periods=rows) df = pd.DataFrame(index=index) for c in range(cols): df[f'var{c}'] = np.linspace(0 + 100 * c, index.size, index.size) return df field = 'var0' DATASETS = [ # get_dataset(0, 1), # get_dataset(1, 1), get_dataset(100, 1), # get_dataset(1000, 1), # get_dataset(0, 4), # get_dataset(1, 4), get_dataset(100, 4), # get_dataset(1000, 4), # get_dataset(10000, 40), ] TESTFLAGGERS = [ BaseFlagger(['NIL', 'GOOD', 'BAD']), DmpFlagger(), SimpleFlagger() ] @pytest.mark.parametrize('data', DATASETS) @pytest.mark.parametrize('flagger', TESTFLAGGERS) def test_initFlags(data, flagger): flags = flagger.initFlags(data).getFlags() assert isinstance(flags, pd.DataFrame) assert len(flags.index) == len(data.index) assert len(flags.columns) >= len(data.columns) @pytest.mark.parametrize('data', DATASETS) @pytest.mark.parametrize('flagger', TESTFLAGGERS) def test_getFlags(data, flagger): flagger.initFlags(data) # df flags0 = flagger.getFlags() assert isinstance(flags0, pd.DataFrame) assert flags0.shape == data.shape assert (flags0.columns == data.columns).all() for dt in flags0.dtypes: assert isinstance(dt, pd.CategoricalDtype) # series flags1 = flagger.getFlags(field) assert isinstance(flags1, pd.Series) assert isinstance(flags1.dtype, pd.CategoricalDtype) assert flags1.shape[0] == data.shape[0] assert flags1.name in data.columns @pytest.mark.parametrize('data', DATASETS) @pytest.mark.parametrize('flagger', TESTFLAGGERS) def test_isFlagged(data, flagger): # todo: add testcase with comparator flagger.initFlags(data) # df flagged0 = flagger.isFlagged() assert isinstance(flagged0, pd.DataFrame) assert flagged0.shape == data.shape assert (flagged0.columns == data.columns).all() for dt in flagged0.dtypes: assert is_bool_dtype(dt) # series flagged1 = flagger.isFlagged(field) assert isinstance(flagged1, pd.Series) assert is_bool_dtype(flagged1.dtype) assert flagged1.shape[0] == data.shape[0] assert flagged1.name in data.columns # both the same assert (flagged0[field] == flagged1).all() # # flag cannot be series # # NOTE: doesn't make sense here # flag = pd.Series(index=data.index, data=flagger.BAD).astype(flagger.categories) # try: # flagger.isFlagged(flags, field=field, flag=flag) # except TypeError: # pass # else: # raise AssertionError('this should not work') @pytest.mark.parametrize('data', DATASETS) @pytest.mark.parametrize('flagger', TESTFLAGGERS) def test_setFlags(data, flagger): base = flagger.initFlags(data).getFlags() sl = slice('2011-01-02', '2011-01-05') flags0 = flagger.setFlags(field, flag=flagger.GOOD, loc=sl).getFlags() assert flags0.shape == base.shape assert (flags0.columns == base.columns).all() assert (flags0.loc[sl, field] == flagger.GOOD).all() # overflag works BAD > GOOD flags1 = flagger.setFlags(field, flag=flagger.BAD).getFlags(field) assert (flags1 == flagger.BAD).all() # overflag doesn't work GOOD < BAD flags2 = flagger.setFlags(field, flag=flagger.GOOD).getFlags(field) assert (flags2 == flagger.BAD).all() # still BAD # overflag does work with force flags3 = flagger.setFlags(field, flag=flagger.GOOD, force=True).getFlags(field) assert (flags3 == flagger.GOOD).all() @pytest.mark.parametrize('data', DATASETS) @pytest.mark.parametrize('flagger', TESTFLAGGERS) def test_clearFlags(data, flagger): flagger.initFlags(data) origin = flagger.getFlags() sl = slice('2011-01-02', '2011-01-05') flagger.setFlags(field=field, flag=flagger.BAD) assert np.sum(flagger.isFlagged(field)) == len(origin) flagger.clearFlags(field) assert np.sum(flagger.isFlagged(field)) == 0 flagger.setFlags(field=field, flag=flagger.BAD) assert np.sum(flagger.isFlagged(field)) == len(origin) flagger.clearFlags(field, loc=sl) unflagged = flagger.isFlagged(field, loc=sl) assert np.sum(unflagged) == 0 assert np.sum(flagger.isFlagged(field)) == len(data) - len(unflagged) @pytest.mark.parametrize('data', DATASETS) @pytest.mark.parametrize('flagger', TESTFLAGGERS) def test_returnCopy(data, flagger): flagger.initFlags(data) origin = flagger.getFlags() f = flagger.getFlags() assert f is not origin f = flagger.isFlagged() assert f is not origin f = flagger.setFlags(field).getFlags() assert f is not origin f = flagger.clearFlags(field).getFlags() assert f is not origin LOC_ILOC_FUNCS = [ 'isFlagged', 'getFlags' ] @pytest.mark.parametrize('data', DATASETS) @pytest.mark.parametrize('flagger', TESTFLAGGERS) @pytest.mark.parametrize('flaggerfunc', LOC_ILOC_FUNCS) def test_loc(data, flagger, flaggerfunc): flagger.initFlags(data) flags = flagger.getFlags() sl = slice('2011-01-02', '2011-01-05') chunk = data.loc[sl, field] d = data.loc[sl] m = data.index.get_loc(d.index[0]) M = data.index.get_loc(d.index[-1]) mask = np.full(len(data), False) mask[m:M] = True flagger_func = getattr(flagger, flaggerfunc) # masked mflags0 = flagger_func(field, loc=mask) mflags1 = flagger_func().loc[mask, field] mflags2 = flagger_func(field).loc[mask] mflags3 = flagger_func(loc=mask)[field] assert (mflags0 == mflags1).all() assert (mflags0 == mflags2).all() assert (mflags0 == mflags3).all() # indexed iflags0 = flagger_func(field, loc=chunk.index) iflags1 = flagger_func().loc[chunk.index, field] iflags2 = flagger_func(field).loc[chunk.index] iflags3 = flagger_func(loc=chunk.index)[field] assert (iflags0 == iflags1).all() assert (iflags0 == iflags2).all() assert (iflags0 == iflags3).all() # sliced sflags0 = flagger_func(field, loc=sl) sflags1 = flagger_func().loc[sl, field] sflags2 = flagger_func(field).loc[sl] sflags3 = flagger_func(loc=sl)[field] assert (sflags0 == sflags1).all() assert (sflags0 == sflags2).all() assert (sflags0 == sflags3).all() assert (sflags0 == iflags0).all() @pytest.mark.parametrize('data', DATASETS) @pytest.mark.parametrize('flagger', TESTFLAGGERS) @pytest.mark.parametrize('flaggerfunc', LOC_ILOC_FUNCS) def test_iloc(data, flagger, flaggerfunc): flagger.initFlags(data) flags = flagger.getFlags() M = len(data.index) - 1 if M < 3: return m = M // 3 M = m * 2 array = data.reset_index(drop=True).index.values[m:M] sl = slice(m, M) mask = np.full(len(data), False) mask[sl] = True flagger_func = getattr(flagger, flaggerfunc) # masked mflags0 = flagger_func(field, iloc=mask) mflags1 = flagger_func().iloc[mask, 0] mflags2 = flagger_func(field).iloc[mask] mflags3 = flagger_func(iloc=mask)[field] assert (mflags0 == mflags1).all() assert (mflags0 == mflags2).all() assert (mflags0 == mflags3).all() # indexed iflags0 = flagger_func(field, iloc=array) iflags1 = flagger_func().iloc[array, 0] iflags2 = flagger_func(field).iloc[array] iflags3 = flagger_func(iloc=array)[field] assert (iflags0 == iflags1).all() assert (iflags0 == iflags2).all() assert (iflags0 == iflags3).all() # sliced sflags0 = flagger_func(field, iloc=sl) sflags1 = flagger_func().iloc[sl, 0] sflags2 = flagger_func(field).iloc[sl] sflags3 = flagger_func(iloc=sl)[field] assert (sflags0 == sflags1).all() assert (sflags0 == sflags2).all() assert (sflags0 == sflags3).all() assert (sflags0 == iflags0).all() assert (sflags0 == mflags0).all() @pytest.mark.parametrize('data', DATASETS) @pytest.mark.parametrize('flagger', TESTFLAGGERS) def test_classicUseCases(data, flagger): flagger.initFlags(data) flags = flagger.getFlags() # data-mask, same length than flags d = data[field] mask = d < (d.max() - d.min()) // 2 flagger.clearFlags(field) flagged = flagger.setFlags(field, loc=mask, flag=flagger.BAD).isFlagged(field) assert (flagged == mask).all() # some fun with numpy but not same dimensions.. pass indices to iloc indices = np.arange(0, len(data)) mask = indices % 3 == 0 indices = indices[mask] flagger.clearFlags(field) flagged = flagger.setFlags(field, iloc=indices, flag=flagger.BAD).isFlagged(field) assert (flagged.iloc[indices] == flagged[flagged]).all()