from __future__ import division, absolute_import, print_function import warnings import numpy as np from numpy.testing import ( run_module_suite, TestCase, assert_, assert_equal, assert_almost_equal, assert_raises ) # Test data _ndat = np.array([[0.6244, np.nan, 0.2692, 0.0116, np.nan, 0.1170], [0.5351, 0.9403, np.nan, 0.2100, 0.4759, 0.2833], [np.nan, np.nan, np.nan, 0.1042, np.nan, 0.5954], [0.1610, np.nan, np.nan, 0.1859, 0.3146, np.nan]]) # Rows of _ndat with nans removed _rdat = [np.array([ 0.6244, 0.2692, 0.0116, 0.1170]), np.array([ 0.5351, 0.9403, 0.2100, 0.4759, 0.2833]), np.array([ 0.1042, 0.5954]), np.array([ 0.1610, 0.1859, 0.3146])] class TestNanFunctions_MinMax(TestCase): nanfuncs = [np.nanmin, np.nanmax] stdfuncs = [np.min, np.max] def test_mutation(self): # Check that passed array is not modified. ndat = _ndat.copy() for f in self.nanfuncs: f(ndat) assert_equal(ndat, _ndat) def test_keepdims(self): mat = np.eye(3) for nf, rf in zip(self.nanfuncs, self.stdfuncs): for axis in [None, 0, 1]: tgt = rf(mat, axis=axis, keepdims=True) res = nf(mat, axis=axis, keepdims=True) assert_(res.ndim == tgt.ndim) def test_out(self): mat = np.eye(3) for nf, rf in zip(self.nanfuncs, self.stdfuncs): resout = np.zeros(3) tgt = rf(mat, axis=1) res = nf(mat, axis=1, out=resout) assert_almost_equal(res, resout) assert_almost_equal(res, tgt) def test_dtype_from_input(self): codes = 'efdgFDG' for nf, rf in zip(self.nanfuncs, self.stdfuncs): for c in codes: mat = np.eye(3, dtype=c) tgt = rf(mat, axis=1).dtype.type res = nf(mat, axis=1).dtype.type assert_(res is tgt) # scalar case tgt = rf(mat, axis=None).dtype.type res = nf(mat, axis=None).dtype.type assert_(res is tgt) def test_result_values(self): for nf, rf in zip(self.nanfuncs, self.stdfuncs): tgt = [rf(d) for d in _rdat] res = nf(_ndat, axis=1) assert_almost_equal(res, tgt) def test_allnans(self): mat = np.array([np.nan]*9).reshape(3, 3) for f in self.nanfuncs: for axis in [None, 0, 1]: with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') assert_(np.isnan(f(mat, axis=axis)).all()) assert_(len(w) == 1, 'no warning raised') assert_(issubclass(w[0].category, RuntimeWarning)) # Check scalars with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') assert_(np.isnan(f(np.nan))) assert_(len(w) == 1, 'no warning raised') assert_(issubclass(w[0].category, RuntimeWarning)) def test_masked(self): mat = np.ma.fix_invalid(_ndat) msk = mat._mask.copy() for f in [np.nanmin]: res = f(mat, axis=1) tgt = f(_ndat, axis=1) assert_equal(res, tgt) assert_equal(mat._mask, msk) assert_(not np.isinf(mat).any()) def test_scalar(self): for f in self.nanfuncs: assert_(f(0.) == 0.) def test_matrices(self): # Check that it works and that type and # shape are preserved mat = np.matrix(np.eye(3)) for f in self.nanfuncs: res = f(mat, axis=0) assert_(isinstance(res, np.matrix)) assert_(res.shape == (1, 3)) res = f(mat, axis=1) assert_(isinstance(res, np.matrix)) assert_(res.shape == (3, 1)) res = f(mat) assert_(np.isscalar(res)) class TestNanFunctions_ArgminArgmax(TestCase): nanfuncs = [np.nanargmin, np.nanargmax] def test_mutation(self): # Check that passed array is not modified. ndat = _ndat.copy() for f in self.nanfuncs: f(ndat) assert_equal(ndat, _ndat) def test_result_values(self): for f, fcmp in zip(self.nanfuncs, [np.greater, np.less]): for row in _ndat: with warnings.catch_warnings(record=True): warnings.simplefilter('always') ind = f(row) val = row[ind] # comparing with NaN is tricky as the result # is always false except for NaN != NaN assert_(not np.isnan(val)) assert_(not fcmp(val, row).any()) assert_(not np.equal(val, row[:ind]).any()) def test_allnans(self): mat = np.array([np.nan]*9).reshape(3, 3) for f in self.nanfuncs: for axis in [None, 0, 1]: assert_raises(ValueError, f, mat, axis=axis) assert_raises(ValueError, f, np.nan) def test_empty(self): mat = np.zeros((0, 3)) for f in self.nanfuncs: for axis in [0, None]: assert_raises(ValueError, f, mat, axis=axis) for axis in [1]: res = f(mat, axis=axis) assert_equal(res, np.zeros(0)) def test_scalar(self): for f in self.nanfuncs: assert_(f(0.) == 0.) def test_matrices(self): # Check that it works and that type and # shape are preserved mat = np.matrix(np.eye(3)) for f in self.nanfuncs: res = f(mat, axis=0) assert_(isinstance(res, np.matrix)) assert_(res.shape == (1, 3)) res = f(mat, axis=1) assert_(isinstance(res, np.matrix)) assert_(res.shape == (3, 1)) res = f(mat) assert_(np.isscalar(res)) class TestNanFunctions_IntTypes(TestCase): int_types = (np.int8, np.int16, np.int32, np.int64, np.uint8, np.uint16, np.uint32, np.uint64) mat = np.array([127, 39, 93, 87, 46]) def integer_arrays(self): for dtype in self.int_types: yield self.mat.astype(dtype) def test_nanmin(self): tgt = np.min(self.mat) for mat in self.integer_arrays(): assert_equal(np.nanmin(mat), tgt) def test_nanmax(self): tgt = np.max(self.mat) for mat in self.integer_arrays(): assert_equal(np.nanmax(mat), tgt) def test_nanargmin(self): tgt = np.argmin(self.mat) for mat in self.integer_arrays(): assert_equal(np.nanargmin(mat), tgt) def test_nanargmax(self): tgt = np.argmax(self.mat) for mat in self.integer_arrays(): assert_equal(np.nanargmax(mat), tgt) def test_nansum(self): tgt = np.sum(self.mat) for mat in self.integer_arrays(): assert_equal(np.nansum(mat), tgt) def test_nanmean(self): tgt = np.mean(self.mat) for mat in self.integer_arrays(): assert_equal(np.nanmean(mat), tgt) def test_nanvar(self): tgt = np.var(self.mat) for mat in self.integer_arrays(): assert_equal(np.nanvar(mat), tgt) tgt = np.var(mat, ddof=1) for mat in self.integer_arrays(): assert_equal(np.nanvar(mat, ddof=1), tgt) def test_nanstd(self): tgt = np.std(self.mat) for mat in self.integer_arrays(): assert_equal(np.nanstd(mat), tgt) tgt = np.std(self.mat, ddof=1) for mat in self.integer_arrays(): assert_equal(np.nanstd(mat, ddof=1), tgt) class TestNanFunctions_Sum(TestCase): def test_mutation(self): # Check that passed array is not modified. ndat = _ndat.copy() np.nansum(ndat) assert_equal(ndat, _ndat) def test_keepdims(self): mat = np.eye(3) for axis in [None, 0, 1]: tgt = np.sum(mat, axis=axis, keepdims=True) res = np.nansum(mat, axis=axis, keepdims=True) assert_(res.ndim == tgt.ndim) def test_out(self): mat = np.eye(3) resout = np.zeros(3) tgt = np.sum(mat, axis=1) res = np.nansum(mat, axis=1, out=resout) assert_almost_equal(res, resout) assert_almost_equal(res, tgt) def test_dtype_from_dtype(self): mat = np.eye(3) codes = 'efdgFDG' for c in codes: tgt = np.sum(mat, dtype=np.dtype(c), axis=1).dtype.type res = np.nansum(mat, dtype=np.dtype(c), axis=1).dtype.type assert_(res is tgt) # scalar case tgt = np.sum(mat, dtype=np.dtype(c), axis=None).dtype.type res = np.nansum(mat, dtype=np.dtype(c), axis=None).dtype.type assert_(res is tgt) def test_dtype_from_char(self): mat = np.eye(3) codes = 'efdgFDG' for c in codes: tgt = np.sum(mat, dtype=c, axis=1).dtype.type res = np.nansum(mat, dtype=c, axis=1).dtype.type assert_(res is tgt) # scalar case tgt = np.sum(mat, dtype=c, axis=None).dtype.type res = np.nansum(mat, dtype=c, axis=None).dtype.type assert_(res is tgt) def test_dtype_from_input(self): codes = 'efdgFDG' for c in codes: mat = np.eye(3, dtype=c) tgt = np.sum(mat, axis=1).dtype.type res = np.nansum(mat, axis=1).dtype.type assert_(res is tgt) # scalar case tgt = np.sum(mat, axis=None).dtype.type res = np.nansum(mat, axis=None).dtype.type assert_(res is tgt) def test_result_values(self): tgt = [np.sum(d) for d in _rdat] res = np.nansum(_ndat, axis=1) assert_almost_equal(res, tgt) def test_allnans(self): # Check for FutureWarning with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') res = np.nansum([np.nan]*3, axis=None) assert_(res == 0, 'result is not 0') assert_(len(w) == 0, 'warning raised') # Check scalar res = np.nansum(np.nan) assert_(res == 0, 'result is not 0') assert_(len(w) == 0, 'warning raised') # Check there is no warning for not all-nan np.nansum([0]*3, axis=None) assert_(len(w) == 0, 'unwanted warning raised') def test_empty(self): mat = np.zeros((0, 3)) tgt = [0]*3 res = np.nansum(mat, axis=0) assert_equal(res, tgt) tgt = [] res = np.nansum(mat, axis=1) assert_equal(res, tgt) tgt = 0 res = np.nansum(mat, axis=None) assert_equal(res, tgt) def test_scalar(self): assert_(np.nansum(0.) == 0.) def test_matrices(self): # Check that it works and that type and # shape are preserved mat = np.matrix(np.eye(3)) res = np.nansum(mat, axis=0) assert_(isinstance(res, np.matrix)) assert_(res.shape == (1, 3)) res = np.nansum(mat, axis=1) assert_(isinstance(res, np.matrix)) assert_(res.shape == (3, 1)) res = np.nansum(mat) assert_(np.isscalar(res)) class TestNanFunctions_MeanVarStd(TestCase): nanfuncs = [np.nanmean, np.nanvar, np.nanstd] stdfuncs = [np.mean, np.var, np.std] def test_mutation(self): # Check that passed array is not modified. ndat = _ndat.copy() for f in self.nanfuncs: f(ndat) assert_equal(ndat, _ndat) def test_dtype_error(self): for f in self.nanfuncs: for dtype in [np.bool_, np.int_, np.object]: assert_raises( TypeError, f, _ndat, axis=1, dtype=np.int) def test_out_dtype_error(self): for f in self.nanfuncs: for dtype in [np.bool_, np.int_, np.object]: out = np.empty(_ndat.shape[0], dtype=dtype) assert_raises( TypeError, f, _ndat, axis=1, out=out) def test_keepdims(self): mat = np.eye(3) for nf, rf in zip(self.nanfuncs, self.stdfuncs): for axis in [None, 0, 1]: tgt = rf(mat, axis=axis, keepdims=True) res = nf(mat, axis=axis, keepdims=True) assert_(res.ndim == tgt.ndim) def test_out(self): mat = np.eye(3) for nf, rf in zip(self.nanfuncs, self.stdfuncs): resout = np.zeros(3) tgt = rf(mat, axis=1) res = nf(mat, axis=1, out=resout) assert_almost_equal(res, resout) assert_almost_equal(res, tgt) def test_dtype_from_dtype(self): mat = np.eye(3) codes = 'efdgFDG' for nf, rf in zip(self.nanfuncs, self.stdfuncs): for c in codes: tgt = rf(mat, dtype=np.dtype(c), axis=1).dtype.type res = nf(mat, dtype=np.dtype(c), axis=1).dtype.type assert_(res is tgt) # scalar case tgt = rf(mat, dtype=np.dtype(c), axis=None).dtype.type res = nf(mat, dtype=np.dtype(c), axis=None).dtype.type assert_(res is tgt) def test_dtype_from_char(self): mat = np.eye(3) codes = 'efdgFDG' for nf, rf in zip(self.nanfuncs, self.stdfuncs): for c in codes: tgt = rf(mat, dtype=c, axis=1).dtype.type res = nf(mat, dtype=c, axis=1).dtype.type assert_(res is tgt) # scalar case tgt = rf(mat, dtype=c, axis=None).dtype.type res = nf(mat, dtype=c, axis=None).dtype.type assert_(res is tgt) def test_dtype_from_input(self): codes = 'efdgFDG' for nf, rf in zip(self.nanfuncs, self.stdfuncs): for c in codes: mat = np.eye(3, dtype=c) tgt = rf(mat, axis=1).dtype.type res = nf(mat, axis=1).dtype.type assert_(res is tgt, "res %s, tgt %s" % (res, tgt)) # scalar case tgt = rf(mat, axis=None).dtype.type res = nf(mat, axis=None).dtype.type assert_(res is tgt) def test_ddof(self): nanfuncs = [np.nanvar, np.nanstd] stdfuncs = [np.var, np.std] for nf, rf in zip(nanfuncs, stdfuncs): for ddof in [0, 1]: tgt = [rf(d, ddof=ddof) for d in _rdat] res = nf(_ndat, axis=1, ddof=ddof) assert_almost_equal(res, tgt) def test_ddof_too_big(self): nanfuncs = [np.nanvar, np.nanstd] stdfuncs = [np.var, np.std] dsize = [len(d) for d in _rdat] for nf, rf in zip(nanfuncs, stdfuncs): for ddof in range(5): with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') tgt = [ddof >= d for d in dsize] res = nf(_ndat, axis=1, ddof=ddof) assert_equal(np.isnan(res), tgt) if any(tgt): assert_(len(w) == 1) assert_(issubclass(w[0].category, RuntimeWarning)) else: assert_(len(w) == 0) def test_result_values(self): for nf, rf in zip(self.nanfuncs, self.stdfuncs): tgt = [rf(d) for d in _rdat] res = nf(_ndat, axis=1) assert_almost_equal(res, tgt) def test_allnans(self): mat = np.array([np.nan]*9).reshape(3, 3) for f in self.nanfuncs: for axis in [None, 0, 1]: with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') assert_(np.isnan(f(mat, axis=axis)).all()) assert_(len(w) == 1) assert_(issubclass(w[0].category, RuntimeWarning)) # Check scalar assert_(np.isnan(f(np.nan))) assert_(len(w) == 2) assert_(issubclass(w[0].category, RuntimeWarning)) def test_empty(self): mat = np.zeros((0, 3)) for f in self.nanfuncs: for axis in [0, None]: with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') assert_(np.isnan(f(mat, axis=axis)).all()) assert_(len(w) == 1) assert_(issubclass(w[0].category, RuntimeWarning)) for axis in [1]: with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') assert_equal(f(mat, axis=axis), np.zeros([])) assert_(len(w) == 0) def test_scalar(self): for f in self.nanfuncs: assert_(f(0.) == 0.) def test_matrices(self): # Check that it works and that type and # shape are preserved mat = np.matrix(np.eye(3)) for f in self.nanfuncs: res = f(mat, axis=0) assert_(isinstance(res, np.matrix)) assert_(res.shape == (1, 3)) res = f(mat, axis=1) assert_(isinstance(res, np.matrix)) assert_(res.shape == (3, 1)) res = f(mat) assert_(np.isscalar(res)) if __name__ == "__main__": run_module_suite()