solarwindpy 0.0.1.dev0__py3-none-any.whl → 0.1.1__py3-none-any.whl

tests/core/test_alfvenic_turbulence.py

@@ -0,0 +1,544 @@
+#!/usr/bin/env python
+"""Tests for Alfvenic turbulence calculations."""
+
+
+import numpy as np
+import pandas as pd
+import logging
+import pytest
+
+import pandas.testing as pdt
+
+from abc import ABC, abstractproperty
+
+from scipy import constants
+from scipy.constants import physical_constants
+
+# import test_base as base
+from . import test_base as base
+
+from solarwindpy import alfvenic_turbulence as turb
+
+pd.set_option("mode.chained_assignment", "raise")
+
+
+class AlfvenicTrubulenceTestBase(ABC):
+    #    def setUp(self):
+    #        self.object_testing.set_agg("mean")
+    #        self.object_testing.update_rolling(window=2,
+    #                                           min_periods=1,
+    #                                           center=True)
+    #
+    @classmethod
+    def set_object_testing(cls):
+        species = cls().species.split("+")
+
+        data = (
+            pd.concat(
+                {s: cls().data.xs(s, axis=1, level="S") for s in species},
+                axis=1,
+                names=["S"],
+            )
+            .swaplevel(i="M", j="S", axis=1)
+            .swaplevel(i="S", j="C", axis=1)
+            .sort_index(axis=1)
+        )
+
+        tkb = ["x", "y", "z"]
+        b = cls().data.xs("b", axis=1, level="M").xs("", axis=1, level="S").loc[:, tkb]
+
+        tkv = pd.IndexSlice["v", ["x", "y", "z"], species]
+        v = cls().data.loc[:, tkv]
+
+        # Do the following so `n` only has one level in MultiIndex.
+        n = cls().data.loc[:, "n"].loc[:, ""].loc[:, species]
+
+        m = cls().mass_in_mp
+        r = n.multiply(m)
+        rtot = r.sum(axis=1)
+
+        vcom = (
+            v.multiply(r, axis=1, level="S")
+            .T.groupby(level="C")
+            .sum()
+            .T
+            # sum(axis=1, level="C")
+            .divide(rtot, axis=0)
+        )
+
+        coef = 1e-9 / (np.sqrt(constants.mu_0 * constants.m_p * 1e6) * 1e3)
+        b_ca_units = coef * b.divide(np.sqrt(rtot), axis=0)
+
+        # Have **kwargs pass to rolling(**kwargs) with window, min_periods, and
+        # center taken from kwargs.pop("window", 2), etc.
+        test_window = "365d"
+        test_periods = 1
+        module = turb.AlfvenicTurbulence(
+            vcom,
+            b,
+            rtot,
+            "+".join(species),
+            window=test_window,
+            min_periods=test_periods,
+        )
+
+        data = pd.concat(
+            {"v": vcom, "b": b_ca_units, "r": rtot.to_frame(name="+".join(species))},
+            axis=1,
+            names=["M", "C"],
+        ).sort_index(axis=1)
+        # rolled = data.rolling(window=2, min_periods=1, center=True).agg("mean")
+        rolled = data.rolling(window=test_window, min_periods=test_periods).agg("mean")
+        deltas = data.subtract(rolled, axis=1)
+
+        data.name = "measurements"
+        deltas.name = "deltas"
+
+        #         print("",
+        #               "<Test>",
+        #               "<species>: %s" % species,
+        #               "<m>: %s" % m,
+        #               "<n>", type(n), n,
+        #               "<r>", type(r), r,
+        #               "<rtot>", type(rtot), rtot,
+        #               "<v>", type(v), v,
+        #               "<vcom>", type(vcom), vcom,
+        #               "<b>", type(b), b,
+        #               "<coeff>: %s" % coef,
+        #               "<b_ca_units>", type(b_ca_units), b_ca_units,
+        #               "<data>", type(data), data,
+        #               sep="\n",
+        #               end="\n\n")
+
+        # pdb.set_trace()
+        cls.object_testing = module
+        cls.data = deltas
+        cls.unrolled_data = data
+        cls.test_window = test_window
+        cls.test_periods = test_periods
+
+    @abstractproperty
+    def species(self):
+        pass
+
+    @property
+    def mass(self):
+        trans = {
+            "a": "alpha particle",
+            "p": "proton",
+            "p1": "proton",
+            "p2": "proton",
+            "e": "electron",
+        }
+        m = {
+            s: physical_constants["%s mass" % trans[s]][0]
+            for s in self.species.split("+")
+        }
+        return pd.Series(m)
+
+    @property
+    def mass_in_mp(self):
+        trans = {
+            "a": physical_constants["alpha particle-proton mass ratio"][0],
+            "p": 1,
+            "p1": 1,
+            "p2": 1,
+            "e": physical_constants["electron-proton mass ratio"][0],
+        }
+        return pd.Series({s: trans[s] for s in self.species.split("+")})
+
+    def test_str(self):
+        self.assertEqual("AlfvenicTurbulence", self.object_testing.__class__.__name__)
+
+    def test_species(self):
+        self.assertEqual(self.species, self.object_testing.species)
+
+    def test__clean_species_for_setting(self):
+        test_fcn = self.object_testing._clean_species_for_setting
+        for stest in (
+            "a",
+            "p1",
+            "p2",
+            "a,p1",
+            "a,p2",
+            "p2,p1",
+            "p1,p2",
+            "a,p1+p2",
+            "p2,a+p2",
+            "p1,a+p2",
+            "a,a+p1+p2",
+            "p1,a+p1+p2",
+            "p2,a+p1+p2",
+        ):
+            self.assertEqual(stest, test_fcn(stest))
+
+        with self.assertRaises(ValueError):
+            test_fcn("a,p1,p2")
+        with self.assertRaises(TypeError):
+            test_fcn("a", "p1", "p2")
+
+    def test_data(self):
+        data = self.data.drop("r", axis=1, level="M")
+        ot = self.object_testing
+
+        pdt.assert_frame_equal(data, ot.data)
+
+    def test_meaurements(self):
+        measurements = self.unrolled_data.drop("r", axis=1, level="M")
+        ot = self.object_testing
+        pdt.assert_frame_equal(measurements, ot.measurements)
+
+    def test_averaging_info(self):
+        ot = self.object_testing
+        avg = ot.averaging_info
+        expected = turb.AlvenicTurbAveraging(self.test_window, self.test_periods)
+        self.assertEqual(expected, avg)
+
+    #    def test_auto_reindex(self):
+    #
+    #        v = self.unrolled_data.loc[:, "v"].drop(1, axis=0)
+    #        b = self.unrolled_data.loc[:, "b"].drop(1, axis=0)
+    #        r = self.unrolled_data.loc[:, ("r", self.species)].drop(1, axis=0)
+    #
+    #        idx_with_skip = pd.Int64Index([0, 2])
+    #        pdt.assert_index_equal(idx_with_skip, v.index)
+    #        pdt.assert_index_equal(idx_with_skip, b.index)
+    #        pdt.assert_index_equal(idx_with_skip, r.index)
+    #        pdt.assert_index_equal(v.index, b.index)
+    #        pdt.assert_index_equal(v.index, r.index)
+    #
+    #        # `unrolled_data` stores [b] = km/s. Need to get back to nT.
+    #        coef = 1e-9 / (np.sqrt(constants.mu_0 * constants.m_p * 1e6) * 1e3)
+    #        b_nT = b.multiply(np.sqrt(r), axis=0) / coef
+    #
+    #        chk = turb.AlfvenicTurbulence(
+    #            v,
+    #            b_nT,
+    #            r,
+    #            self.species,
+    #            auto_reindex=True,
+    #            window=2,
+    #            min_periods=1,
+    #            center=True,
+    #        )
+    #
+    #        idx = pd.RangeIndex(start=v.index.min(), stop=v.index.max() + 1, step=1)
+    #        pdt.assert_index_equal(idx, chk.v.index)
+    #        pdt.assert_index_equal(idx, chk.b.index)
+    #        pdt.assert_index_equal(chk.v.index, chk.b.index)
+    #
+    #        nans = pd.DataFrame(
+    #            {
+    #                "x": pd.Series([False, True, False]),
+    #                "y": pd.Series([False, True, False]),
+    #                "z": pd.Series([False, True, False]),
+    #            }
+    #        )
+    #        nans.columns.names = ["C"]
+    #
+    #        v = v.reindex(idx, axis=0)
+    #        b = b.reindex(idx, axis=0)
+    #
+    #        pdt.assert_frame_equal(nans, chk.v.isna())
+    #        pdt.assert_frame_equal(nans, chk.b.isna())
+    #
+    #        # TODO: I don't think I want to test values here, so I've removed this
+    #        #       code. All this function tests is if things automatically
+    #        #       reindex correctly.
+    #        # Rolled values will average with NaN -> zero.
+    #        # v = v.mask(~nans, 0.0)
+    #        # b = b.mask(~nans, 0.0)
+    #
+    #    #        pdb.set_trace()
+    #    #
+    #    #        pdt.assert_frame_equal(v, chk.v)
+    #    #        pdt.assert_frame_equal(b, chk.b)
+
+    def test_bfield(self):
+        # Test in Alfven units
+        b = self.data.loc[:, "b"]
+
+        ot = self.object_testing
+        pdt.assert_frame_equal(b, ot.bfield)
+        pdt.assert_frame_equal(ot.bfield, ot.b)
+
+    def test_velocity(self):
+        v = self.data.loc[:, "v"]
+
+        ot = self.object_testing
+        pdt.assert_frame_equal(v, ot.velocity)
+        pdt.assert_frame_equal(ot.v, ot.velocity)
+
+    def test_z_plus(self):
+        v = self.data.loc[:, "v"]
+        b = self.data.loc[:, "b"]
+        zp = v.add(b, axis=1)
+
+        ot = self.object_testing
+        pdt.assert_frame_equal(zp, ot.z_plus)
+        pdt.assert_frame_equal(ot.zp, ot.z_plus)
+
+    def test_z_minus(self):
+        v = self.data.loc[:, "v"]
+        b = self.data.loc[:, "b"]
+        zm = v.subtract(b, axis=1)
+
+        ot = self.object_testing
+        pdt.assert_frame_equal(zm, ot.z_minus)
+        pdt.assert_frame_equal(ot.zm, ot.z_minus)
+
+    def test_e_plus(self):
+        v = self.data.loc[:, "v"]
+        b = self.data.loc[:, "b"]
+        zp = v.add(b, axis=1)
+        ep = 0.5 * zp.pow(2).sum(axis=1)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(ep, ot.e_plus)
+        pdt.assert_series_equal(ot.ep, ot.e_plus)
+
+    def test_e_minus(self):
+        v = self.data.loc[:, "v"]
+        b = self.data.loc[:, "b"]
+        zm = v.subtract(b, axis=1)
+        em = 0.5 * zm.pow(2).sum(axis=1)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(em, ot.e_minus)
+        pdt.assert_series_equal(ot.em, ot.e_minus)
+
+    def test_kinetic_energy(self):
+        v = self.data.loc[:, "v"]
+        ev = 0.5 * v.pow(2).sum(axis=1)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(ev, ot.kinetic_energy)
+        pdt.assert_series_equal(ot.kinetic_energy, ot.ev)
+
+    def test_magnetic_energy(self):
+        b = self.data.loc[:, "b"]
+        eb = 0.5 * b.pow(2).sum(axis=1)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(eb, ot.magnetic_energy)
+        pdt.assert_series_equal(ot.magnetic_energy, ot.eb)
+
+    def test_total_energy(self):
+        tk = ["v", "b"]
+        etot = 0.5 * self.data.loc[:, tk].pow(2).sum(axis=1)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(etot, ot.total_energy)
+        pdt.assert_series_equal(ot.total_energy, ot.etot)
+
+    def test_residual_energy(self):
+        v = self.data.loc[:, "v"]
+        ev = 0.5 * v.pow(2).sum(axis=1)
+        b = self.data.loc[:, "b"]
+        eb = 0.5 * b.pow(2).sum(axis=1)
+        eres = ev.subtract(eb, axis=0)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(eres, ot.residual_energy)
+        pdt.assert_series_equal(ot.residual_energy, ot.eres)
+
+    def test_normalized_residual_energy(self):
+        v = self.data.loc[:, "v"]
+        ev = 0.5 * v.pow(2).sum(axis=1)
+        b = self.data.loc[:, "b"]
+        eb = 0.5 * b.pow(2).sum(axis=1)
+        etot = ev.add(eb, axis=0)
+        eres = ev.subtract(eb, axis=0)
+        eres_norm = eres.divide(etot, axis=0)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(eres_norm, ot.normalized_residual_energy)
+        pdt.assert_series_equal(ot.normalized_residual_energy, ot.eres_norm)
+
+    def test_sigma_r(self):
+        ot = self.object_testing
+        pdt.assert_series_equal(ot.sigma_r, ot.normalized_residual_energy)
+
+    def test_cross_helicity(self):
+        v = self.data.loc[:, "v"]
+        b = self.data.loc[:, "b"]
+        ch = 0.5 * v.multiply(b, axis=1).sum(axis=1)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(ch, ot.cross_helicity)
+
+    def test_normalized_cross_helicity(self):
+        v = self.data.loc[:, "v"]
+        b = self.data.loc[:, "b"]
+        ch = 0.5 * v.multiply(b, axis=1).sum(axis=1)
+        ev = 0.5 * v.pow(2).sum(axis=1)
+        eb = 0.5 * b.pow(2).sum(axis=1)
+        etot = ev.add(eb, axis=0)
+        normalized_cross_helicity = 2.0 * ch.divide(etot, axis=0)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(normalized_cross_helicity, ot.normalized_cross_helicity)
+        pdt.assert_series_equal(ot.sigma_c, ot.normalized_cross_helicity)
+
+    def test_alfven_ratio(self):
+        v = self.data.loc[:, "v"]
+        b = self.data.loc[:, "b"]
+        ev = 0.5 * v.pow(2).sum(axis=1)
+        eb = 0.5 * b.pow(2).sum(axis=1)
+        rA = ev.divide(eb, axis=0)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(rA, ot.alfven_ratio)
+        pdt.assert_series_equal(ot.alfven_ratio, ot.rA)
+
+    def test_elsasser_ratio(self):
+        v = self.data.loc[:, "v"]
+        b = self.data.loc[:, "b"]
+        zp = v.add(b, axis=1)
+        zm = v.subtract(b, axis=1)
+        ep = 0.5 * zp.pow(2).sum(axis=1)
+        em = 0.5 * zm.pow(2).sum(axis=1)
+        rE = em.divide(ep, axis=0)
+
+        ot = self.object_testing
+        pdt.assert_series_equal(rE, ot.elsasser_ratio)
+        pdt.assert_series_equal(ot.elsasser_ratio, ot.rE)
+
+    def test_eq(self):
+        ot = self.object_testing
+        # ID should be equal.
+        self.assertEqual(ot, ot)
+        # Data and type should be equal.
+
+        data = self.unrolled_data
+        v = data.loc[:, "v"]
+        r = data.loc[:, ("r", self.species)]
+        b = data.loc[:, "b"]
+        coef = 1e-9 / (np.sqrt(constants.mu_0 * constants.m_p * 1e6) * 1e3)
+        # `unrolled_data` stores [b] = km/s. Need to get back to nT.
+        b_nT = b.multiply(np.sqrt(r), axis=0) / coef
+        new_object = ot.__class__(
+            v,
+            b_nT,
+            r,
+            ot.species,
+            window=self.test_window,
+            min_periods=self.test_periods,
+        )
+
+        print_inline_debug = False
+        if print_inline_debug:
+            print(
+                "<Test>",
+                "<object_testing>",
+                type(ot),
+                ot,
+                id(ot),
+                ot.species,
+                ot.data,
+                "<new_object>",
+                type(new_object),
+                id(new_object),
+                new_object,
+                new_object.species,
+                new_object.data,
+                "",
+                sep="\n",
+                end="\n\n",
+            )
+
+        self.assertEqual(ot.species, new_object.species)
+        pdt.assert_frame_equal(ot.data, new_object.data)
+        try:
+            self.assertEqual(ot, new_object)
+        except AssertionError as e0:
+            try:
+                pdt.assert_frame_equal(ot.data.round(15), new_object.data.round(15))
+            except AssertionError as e1:  # noqa: F841
+                raise (e0)
+
+
+#     def test_neq(self):
+#         object_testing = self.object_testing
+#         # Data isn't equal
+#         self.assertNotEqual(object_testing,
+#                             object_testing.__class__(object_testing.data * 4))
+#          # Type isn't equal
+#         for other in ([], tuple(), np.array([]), pd.Series(), pd.DataFrame()):
+#             self.assertNotEqual(object_testing, other)
+
+
+#####
+# Tests
+#####
+# @unittest.skip
+class TestPlasmaAlpha(base.AlphaTest, AlfvenicTrubulenceTestBase, base.SWEData):
+    pass
+
+
+# @unittest.skip
+class TestAlfvenicTrubulenceP1(base.P1Test, AlfvenicTrubulenceTestBase, base.SWEData):
+    pass
+
+
+# @unittest.skip
+class TestAlfvenicTrubulenceP2(base.P2Test, AlfvenicTrubulenceTestBase, base.SWEData):
+    pass
+
+
+# @unittest.skip
+class TestAlfvenicTrubulenceAlphaP1(
+    base.AlphaP1Test, AlfvenicTrubulenceTestBase, base.SWEData
+):
+    pass
+
+
+# @unittest.skip
+class TestAlfvenicTrubulenceAlphaP2(
+    base.AlphaP2Test, AlfvenicTrubulenceTestBase, base.SWEData
+):
+    pass
+
+
+# @unittest.skip
+class TestAlfvenicTrubulenceP1P2(
+    base.P1P2Test, AlfvenicTrubulenceTestBase, base.SWEData
+):
+    pass
+
+
+# @unittest.skip
+class TestAlfvenicTrubulenceAlphaP1P2(
+    base.AlphaP1P2Test, AlfvenicTrubulenceTestBase, base.SWEData
+):
+    pass
+
+
+def test_set_data_requires_datetimeindex():
+    """``set_data`` raises ``TypeError`` for non-``DatetimeIndex`` inputs."""
+
+    idx = pd.RangeIndex(3)
+    v = pd.DataFrame(np.arange(9).reshape(3, 3), index=idx, columns=["x", "y", "z"])
+    b = pd.DataFrame(
+        np.arange(9).reshape(3, 3) / 10.0, index=idx, columns=["x", "y", "z"]
+    )
+    rho = pd.Series(np.arange(3), index=idx)
+
+    with pytest.raises(TypeError):
+        turb.AlfvenicTurbulence(v, b, rho, "p1")
+
+
+def test_set_data_warns_on_mismatched_index(caplog):
+    """Mismatched indices trigger a warning."""
+
+    v_idx = pd.date_range("2020-01-01", periods=3, freq="H")
+    b_idx = pd.date_range("2020-01-02", periods=3, freq="H")
+    v = pd.DataFrame(np.arange(9).reshape(3, 3), index=v_idx, columns=["x", "y", "z"])
+    b = pd.DataFrame(
+        np.arange(9).reshape(3, 3) / 10.0, index=b_idx, columns=["x", "y", "z"]
+    )
+    rho = pd.Series(np.arange(3), index=v_idx)
+
+    with caplog.at_level(logging.WARNING):
+        turb.AlfvenicTurbulence(v, b, rho, "p1")
+    assert "v and b have unequal indices" in caplog.text

tests/core/test_base.py

@@ -0,0 +1,112 @@
+#!/usr/bin/env python
+"""Tests for basic synthetic data setup."""
+import numpy as np
+import pandas as pd
+from pathlib import Path
+from unittest import TestCase
+
+pd.set_option("mode.chained_assignment", "raise")
+
+DATA_PATH = Path(__file__).parent.parent / "data"
+
+
+class TestData(object):
+    def __init__(self):
+        self.set_plasma_data()
+        self.set_spacecraft_data()
+
+    @property
+    def epoch(self):
+        path = DATA_PATH / "epoch.csv"
+        epoch = pd.read_csv(path)["epoch"].map(pd.to_datetime)
+        epoch.name = "epoch"
+        return epoch
+
+    @property
+    def spacecraft_data(self):
+        return self._spacecraft_data
+
+    @property
+    def plasma_data(self):
+        return self._plasma_data
+
+    @property
+    def combined_data(self):
+        sc = pd.concat(
+            {"sc": self.spacecraft_data}, axis=1, names=["S"], sort=True
+        ).reorder_levels(["M", "C", "S"], axis=1)
+        out = pd.concat([self.plasma_data, sc], axis=1, sort=True)
+        return out
+
+    def set_spacecraft_data(self):
+        path = DATA_PATH / "spacecraft.csv"
+        test_data = pd.read_csv(path)
+        test_data.columns = pd.MultiIndex.from_tuples(
+            [tuple(c.split("|")) for c in test_data.columns]
+        )
+        test_data.columns.names = ["M", "C", "S"]
+        test_data = test_data.astype(np.float64).sort_index(axis=1)
+        test_data.index = self.epoch
+        self._spacecraft_data = test_data.xs("", axis=1, level="S")
+
+    def set_plasma_data(self):
+        path = DATA_PATH / "plasma.csv"
+        test_plasma = pd.read_csv(path)
+        test_plasma.columns = pd.MultiIndex.from_tuples(
+            [tuple(c.split("|")) for c in test_plasma.columns]
+        )
+        test_plasma = test_plasma.astype(np.float64)
+        test_plasma.columns.names = ["M", "C", "S"]
+        test_plasma.index = self.epoch
+        test_plasma = test_plasma.sort_index(axis=1)
+        self._plasma_data = test_plasma
+
+
+class SWEData(TestCase):
+    @classmethod
+    def setUpClass(cls):
+        data = TestData()
+        cls.data = data.plasma_data.sort_index(axis=1)
+        cls.set_object_testing()
+
+
+class AlphaTest(object):
+    @property
+    def species(self):
+        return "a"
+
+
+class P1Test(object):
+    @property
+    def species(self):
+        return "p1"
+
+
+class P2Test(object):
+    @property
+    def species(self):
+        return "p2"
+
+
+class AlphaP1Test(object):
+    @property
+    def species(self):
+        return "a+p1"
+
+
+class AlphaP2Test(object):
+    @property
+    def species(self):
+        return "a+p2"
+
+
+class P1P2Test(object):
+    @property
+    def species(self):
+        return "p1+p2"
+
+
+class AlphaP1P2Test(object):
+    @property
+    def species(self):
+        return "a+p1+p2"

tests/core/test_base_head_tail.py

@@ -0,0 +1,29 @@
+import pandas as pd
+import pandas.testing as pdt
+from unittest import TestCase
+
+from solarwindpy.core import base
+
+pd.set_option("mode.chained_assignment", "raise")
+
+
+class DummyBase(base.Base):
+    def set_data(self, new: pd.DataFrame) -> None:
+        super().set_data(new)
+        self._data = new
+
+
+class TestBaseHeadTail(TestCase):
+    @classmethod
+    def setUpClass(cls):
+        cls.df = pd.DataFrame(
+            {"a": range(5)},
+            index=pd.date_range("2020-01-01", periods=5, name="epoch"),
+        )
+        cls.instance = DummyBase(cls.df)
+
+    def test_head(self):
+        pdt.assert_frame_equal(self.df.head(), self.instance.head())
+
+    def test_tail(self):
+        pdt.assert_frame_equal(self.df.tail(), self.instance.tail())

tests/core/test_base_mi_tuples.py

@@ -0,0 +1,11 @@
+import pandas as pd
+import pandas.testing as pdt
+
+from solarwindpy.core.base import Base
+
+
+def test_mi_tuples_returns_index_with_names():
+    tuples = (("v", "x", "p"), ("b", "y", ""))
+    result = Base.mi_tuples(tuples)
+    expected = pd.MultiIndex.from_tuples(tuples, names=["M", "C", "S"])
+    pdt.assert_index_equal(result, expected)