pyramid/tests/test_phasemap.py

-# -*- coding: utf-8 -*-
-"""Testcase for the phasemap module."""
-
-import os
-import unittest
-
-import numpy as np
-from numpy.testing import assert_allclose
-
-from pyramid.phasemap import PhaseMap
-from pyramid import load_phasemap
-
-
-class TestCasePhaseMap(unittest.TestCase):
-    def setUp(self):
-        self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemap')
-        phase = np.zeros((4, 4))
-        phase[1:-1, 1:-1] = 1
-        mask = phase.astype(dtype=np.bool)
-        confidence = np.ones((4, 4))
-        self.phasemap = PhaseMap(10.0, phase, mask, confidence)
-
-    def tearDown(self):
-        self.path = None
-        self.phasemap = None
-
-    def test_copy(self):
-        phasemap = self.phasemap
-        phasemap_copy = self.phasemap.copy()
-        assert phasemap == self.phasemap, 'Unexpected behaviour in copy()!'
-        assert phasemap_copy != self.phasemap, 'Unexpected behaviour in copy()!'
-
-    def test_scale_down(self):
-        self.phasemap.scale_down()
-        reference = 1 / 4. * np.ones((2, 2))
-        assert_allclose(self.phasemap.phase, reference,
-                        err_msg='Unexpected behavior in scale_down()!')
-        assert_allclose(self.phasemap.mask, np.zeros((2, 2), dtype=np.bool),
-                        err_msg='Unexpected behavior in scale_down()!')
-        assert_allclose(self.phasemap.confidence, np.ones((2, 2)),
-                        err_msg='Unexpected behavior in scale_down()!')
-        assert_allclose(self.phasemap.a, 20,
-                        err_msg='Unexpected behavior in scale_down()!')
-
-    def test_scale_up(self):
-        self.phasemap.scale_up()
-        reference = np.zeros((8, 8))
-        reference[2:-2, 2:-2] = 1
-        assert_allclose(self.phasemap.phase, reference,
-                        err_msg='Unexpected behavior in scale_up()!')
-        assert_allclose(self.phasemap.mask, reference.astype(dtype=np.bool),
-                        err_msg='Unexpected behavior in scale_up()!')
-        assert_allclose(self.phasemap.confidence, np.ones((8, 8)),
-                        err_msg='Unexpected behavior in scale_up()!')
-        assert_allclose(self.phasemap.a, 5,
-                        err_msg='Unexpected behavior in scale_up()!')
-
-    def test_load_from_txt(self):
-        phasemap = load_phasemap(os.path.join(self.path, 'ref_phasemap.txt'))
-        assert_allclose(self.phasemap.phase, phasemap.phase,
-                        err_msg='Unexpected behavior in load_from_txt()!')
-        assert_allclose(phasemap.a, self.phasemap.a,
-                        err_msg='Unexpected behavior in load_from_txt()!')
-
-    def test_load_from_hdf5(self):
-        phasemap = load_phasemap(os.path.join(self.path, 'ref_phasemap.hdf5'))
-        assert_allclose(self.phasemap.phase, phasemap.phase,
-                        err_msg='Unexpected behavior in load_from_netcdf4()!')
-        assert_allclose(self.phasemap.mask, phasemap.mask,
-                        err_msg='Unexpected behavior in load_from_netcdf4()!')
-        assert_allclose(self.phasemap.confidence, phasemap.confidence,
-                        err_msg='Unexpected behavior in load_from_netcdf4()!')
-        assert_allclose(phasemap.a, self.phasemap.a,
-                        err_msg='Unexpected behavior in load_from_netcdf4()!')

pyramid/tests/test_phasemap/ref_phasemap.txt

-PYRAMID-PHASEMAP: ref_phase_map
-grid spacing = 10.0 nm
-0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00
-0.000000e+00	1.000000e+00	1.000000e+00	0.000000e+00
-0.000000e+00	1.000000e+00	1.000000e+00	0.000000e+00
-0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00

pyramid/tests/test_phasemapper.py

-# -*- coding: utf-8 -*-
-"""Testcase for the phasemapper module."""
-
-import os
-import unittest
-
-import numpy as np
-from numpy.testing import assert_allclose
-
-from pyramid.kernel import Kernel
-from pyramid.phasemapper import PhaseMapperRDFC, PhaseMapperFDFC, PhaseMapperMIP, PhaseMapperCharge
-from pyramid import load_phasemap, load_vectordata, load_scalardata
-
-
-class TestCasePhaseMapperRDFC(unittest.TestCase):
-    def setUp(self):
-        self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
-        self.mag_proj = load_vectordata(os.path.join(self.path, 'mag_proj.hdf5'))
-        self.mapper = PhaseMapperRDFC(Kernel(self.mag_proj.a, self.mag_proj.dim[1:]))
-
-    def tearDown(self):
-        self.path = None
-        self.mag_proj = None
-        self.mapper = None
-
-    def test_PhaseMapperRDFC_call(self):
-        phase_ref = load_phasemap(os.path.join(self.path, 'phasemap.hdf5'))
-        phasemap = self.mapper(self.mag_proj)
-        assert_allclose(phasemap.phase, phase_ref.phase, atol=1E-7,
-                        err_msg='Unexpected behavior in __call__()!')
-        assert_allclose(phasemap.a, phase_ref.a, err_msg='Unexpected behavior in __call__()!')
-
-    def test_PhaseMapperRDFC_jac_dot(self):
-        phase = self.mapper(self.mag_proj).phase
-        mag_proj_vec = self.mag_proj.field[:2, ...].ravel()
-        phase_jac = self.mapper.jac_dot(mag_proj_vec).reshape(self.mapper.kernel.dim_uv)
-        assert_allclose(phase, phase_jac, atol=1E-7,
-                        err_msg='Inconsistency between __call__() and jac_dot()!')
-        n = self.mapper.n
-        jac = np.array([self.mapper.jac_dot(np.eye(n)[:, i]) for i in range(n)]).T
-        jac_ref = np.load(os.path.join(self.path, 'jac.npy'))
-        assert_allclose(jac, jac_ref, atol=1E-7,
-                        err_msg='Unexpected behaviour in the the jacobi matrix!')
-
-    def test_PhaseMapperRDFC_jac_T_dot(self):
-        m = self.mapper.m
-        jac_T = np.array([self.mapper.jac_T_dot(np.eye(m)[:, i]) for i in range(m)]).T
-        jac_T_ref = np.load(os.path.join(self.path, 'jac.npy')).T
-        assert_allclose(jac_T, jac_T_ref, atol=1E-7,
-                        err_msg='Unexpected behaviour in the the transposed jacobi matrix!')
-
-
-class TestCasePhaseMapperFDFCpad0(unittest.TestCase):
-    def setUp(self):
-        self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
-        self.mag_proj = load_vectordata(os.path.join(self.path, 'mag_proj.hdf5'))
-        self.mapper = PhaseMapperFDFC(self.mag_proj.a, self.mag_proj.dim[1:], padding=0)
-
-    def tearDown(self):
-        self.path = None
-        self.mag_proj = None
-        self.mapper = None
-
-    def test_PhaseMapperFDFC_call(self):
-        phase_ref = load_phasemap(os.path.join(self.path, 'phasemap_fc.hdf5'))
-        phasemap = self.mapper(self.mag_proj)
-        assert_allclose(phasemap.phase, phase_ref.phase, atol=1E-7,
-                        err_msg='Unexpected behavior in __call__()!')
-        assert_allclose(phasemap.a, phase_ref.a, err_msg='Unexpected behavior in __call__()!')
-
-    def test_PhaseMapperFDFC_jac_dot(self):
-        phase = self.mapper(self.mag_proj).phase
-        mag_proj_vec = self.mag_proj.field[:2, ...].ravel()
-        phase_jac = self.mapper.jac_dot(mag_proj_vec).reshape(self.mapper.dim_uv)
-        assert_allclose(phase, phase_jac, atol=1E-7,
-                        err_msg='Inconsistency between __call__() and jac_dot()!')
-        n = self.mapper.n
-        jac = np.array([self.mapper.jac_dot(np.eye(n)[:, i]) for i in range(n)]).T
-        jac_ref = np.load(os.path.join(self.path, 'jac_fc.npy'))
-        assert_allclose(jac, jac_ref, atol=1E-7,
-                        err_msg='Unexpected behaviour in the the jacobi matrix!')
-
-    def test_PhaseMapperFDFC_jac_T_dot(self):
-        self.assertRaises(NotImplementedError, self.mapper.jac_T_dot, None)
-
-
-class TestCasePhaseMapperFDFCpad1(unittest.TestCase):
-    def setUp(self):
-        self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
-        self.mag_proj = load_vectordata(os.path.join(self.path, 'mag_proj.hdf5'))
-        self.mapper = PhaseMapperFDFC(self.mag_proj.a, self.mag_proj.dim[1:], padding=1)
-
-    def tearDown(self):
-        self.path = None
-        self.mag_proj = None
-        self.mapper = None
-
-    def test_PhaseMapperFDFC_call(self):
-        phase_ref = load_phasemap(os.path.join(self.path, 'phasemap_fc_pad1.hdf5'))
-        phasemap = self.mapper(self.mag_proj)
-        assert_allclose(phasemap.phase, phase_ref.phase, atol=1E-7,
-                        err_msg='Unexpected behavior in __call__()!')
-        assert_allclose(phasemap.a, phase_ref.a, err_msg='Unexpected behavior in __call__()!')
-
-    def test_PhaseMapperFDFC_jac_dot(self):
-        phase = self.mapper(self.mag_proj).phase
-        mag_proj_vec = self.mag_proj.field[:2, ...].ravel()
-        phase_jac = self.mapper.jac_dot(mag_proj_vec).reshape(self.mapper.dim_uv)
-        assert_allclose(phase, phase_jac, atol=1E-7,
-                        err_msg='Inconsistency between __call__() and jac_dot()!')
-        n = self.mapper.n
-        jac = np.array([self.mapper.jac_dot(np.eye(n)[:, i]) for i in range(n)]).T
-        jac_ref = np.load(os.path.join(self.path, 'jac_fc_pad1.npy'))
-        assert_allclose(jac, jac_ref, atol=1E-7,
-                        err_msg='Unexpected behaviour in the the jacobi matrix!')
-
-    def test_PhaseMapperFDFC_jac_T_dot(self):
-        self.assertRaises(NotImplementedError, self.mapper.jac_T_dot, None)
-
-
-class TestCasePhaseMapperFDFCpad10(unittest.TestCase):
-    def setUp(self):
-        self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
-        self.mag_proj = load_vectordata(os.path.join(self.path, 'mag_proj.hdf5'))
-        self.mapper = PhaseMapperFDFC(self.mag_proj.a, self.mag_proj.dim[1:], padding=200)
-
-    def tearDown(self):
-        self.path = None
-        self.mag_proj = None
-        self.mapper = None
-
-    def test_PhaseMapperFDFC_call(self):
-        phase_ref = load_phasemap(os.path.join(self.path, 'phasemap_fc_pad10.hdf5'))
-        phasemap = self.mapper(self.mag_proj)
-        assert_allclose(phasemap.phase, phase_ref.phase, atol=1E-7,
-                        err_msg='Unexpected behavior in __call__()!')
-        assert_allclose(phasemap.a, phase_ref.a, err_msg='Unexpected behavior in __call__()!')
-
-    def test_PhaseMapperFDFC_jac_dot(self):
-        phase = self.mapper(self.mag_proj).phase
-        mag_proj_vec = self.mag_proj.field[:2, ...].ravel()
-        phase_jac = self.mapper.jac_dot(mag_proj_vec).reshape(self.mapper.dim_uv)
-        assert_allclose(phase, phase_jac, atol=1E-7,
-                        err_msg='Inconsistency between __call__() and jac_dot()!')
-        n = self.mapper.n
-        jac = np.array([self.mapper.jac_dot(np.eye(n)[:, i]) for i in range(n)]).T
-        jac_ref = np.load(os.path.join(self.path, 'jac_fc_pad10.npy'))
-        assert_allclose(jac, jac_ref, atol=1E-7,
-                        err_msg='Unexpected behaviour in the the jacobi matrix!')
-
-    def test_PhaseMapperFDFC_jac_T_dot(self):
-        self.assertRaises(NotImplementedError, self.mapper.jac_T_dot, None)
-
-
-class TestCasePhaseMapperMIP(unittest.TestCase):
-    def setUp(self):
-        self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
-        self.elec_proj = load_scalardata(os.path.join(self.path, 'elec_proj.hdf5'))
-        self.mapper = PhaseMapperMIP(self.elec_proj.a, self.elec_proj.dim[1:])
-
-    def tearDown(self):
-        self.path = None
-        self.elec_proj = None
-        self.mapper = None
-
-    def test_call(self):
-        phase_ref = load_phasemap(os.path.join(self.path, 'phasemap_elec.hdf5'))
-        phasemap = self.mapper(self.elec_proj)
-        assert_allclose(phasemap.phase, phase_ref.phase, atol=1E-7,
-                        err_msg='Unexpected behavior in __call__()!')
-        assert_allclose(phasemap.a, phase_ref.a, err_msg='Unexpected behavior in __call__()!')
-
-    def test_jac_dot(self):
-        self.assertRaises(NotImplementedError, self.mapper.jac_dot, None)
-
-    def test_jac_T_dot(self):
-        self.assertRaises(NotImplementedError, self.mapper.jac_T_dot, None)
-
-
-class TestCasePhaseMapperCharge(unittest.TestCase):
-    def setUp(self):
-        self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
-        self.charge_proj = load_scalardata(os.path.join(self.path, 'charge_proj.hdf5'))
-        self.mapper = PhaseMapperCharge(self.charge_proj.a, self.charge_proj.dim[1:],
-                                        electrode_vec=[8, 8], v_acc=300000)
-
-    def tearDown(self):
-        self.path = None
-        self.charge_proj = None
-        self.mapper = None
-
-    def test_call(self):
-        charge_phase_ref = load_phasemap(os.path.join(self.path, 'charge_phase_ref.hdf5'))
-        phasemap = self.mapper(self.charge_proj)
-        assert_allclose(phasemap.phase, charge_phase_ref.phase, atol=1E-7,
-                        err_msg='Unexpected behavior in __call__()!')
-        assert_allclose(phasemap.a, charge_phase_ref.a, err_msg='Unexpected behavior in __call__()!')
-
-    def test_jac_dot(self):
-        self.assertRaises(NotImplementedError, self.mapper.jac_dot, None)
-
-    def test_jac_T_dot(self):
-        self.assertRaises(NotImplementedError, self.mapper.jac_T_dot, None)