Пример #1
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    def setUpClass(cls):

        params = Configuration(TEST_CONF_ROIPAC).__dict__
        cls.temp_out_dir = tempfile.mkdtemp()
        sys.argv = ['prepifg.py', TEST_CONF_ROIPAC]
        params[cf.OUT_DIR] = cls.temp_out_dir
        params[cf.TMPDIR] = os.path.join(cls.temp_out_dir, cf.TMPDIR)
        shared.mkdir_p(params[cf.TMPDIR])
        params[cf.REF_EST_METHOD] = 2
        conv2tif.main(params)
        prepifg.main(params)
        cls.params = params
        xlks, ylks, crop = cf.transform_params(params)
        base_ifg_paths = cf.original_ifg_paths(params[cf.IFG_FILE_LIST],
                                               params[cf.OBS_DIR])
        dest_paths = cf.get_dest_paths(base_ifg_paths, crop, params, xlks)
        ifgs = common.pre_prepare_ifgs(dest_paths, params)
        refx, refy = process._ref_pixel_calc(dest_paths, params)
        pyrate.core.orbital.remove_orbital_error(ifgs, params)
        ifgs = prepare_ifgs_without_phase(dest_paths, params)
        for ifg in ifgs:
            ifg.close()
        _, cls.ifgs = process._ref_phase_estimation(dest_paths, params, refx, refy)
        ifgs[0].open()
        r_dist = RDist(ifgs[0])()
        ifgs[0].close()
        # Calculate interferogram noise
        cls.maxvar = [cvd(i, params, r_dist, calc_alpha=True,
                          save_acg=True, write_vals=True)[0] for i in dest_paths]
        cls.vcmt = get_vcmt(ifgs, cls.maxvar)
        for ifg in ifgs:
            ifg.close()
Пример #2
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    def test_small_test_data_ref_chipsize_15(self):

        refx, refy = process._ref_pixel_calc(self.ifg_paths,
                                             self.params_chipsize_15)
        self.assertEqual(refx, 7)
        self.assertEqual(refy, 7)
        self.assertAlmostEqual(0.5, self.params_alt_ref_frac[cf.REF_MIN_FRAC])
Пример #3
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def test_vcm_legacy_vs_mpi(mpisync, tempdir, roipac_or_gamma_conf):
    params = configuration.Configuration(roipac_or_gamma_conf).__dict__
    LEGACY_VCM_DIR = os.path.join(SML_TEST_DIR, 'vcm')
    legacy_vcm = np.genfromtxt(os.path.join(LEGACY_VCM_DIR, 'vcmt.csv'),
                               delimiter=',')
    tmpdir = Path(mpiops.run_once(tempdir))
    mpiops.run_once(common.copytree, params[cf.OBS_DIR], tmpdir)
    params[cf.OUT_DIR] = tmpdir.joinpath('out')
    params[cf.PARALLEL] = False
    xlks, ylks, crop = cf.transform_params(params)
    base_unw_paths = cf.original_ifg_paths(params[cf.IFG_FILE_LIST],
                                           params[cf.OBS_DIR])
    # dest_paths are tifs that have been geotif converted and multilooked
    dest_paths = cf.get_dest_paths(base_unw_paths, crop, params, xlks)

    # run conv2tif and prepifg, create the dest_paths files
    conv2tif.main(params)
    prepifg.main(params)

    tiles = pyrate.core.shared.get_tiles(dest_paths[0], rows=1, cols=1)
    preread_ifgs = process._create_ifg_dict(dest_paths,
                                            params=params,
                                            tiles=tiles)
    refpx, refpy = process._ref_pixel_calc(dest_paths, params)
    process._orb_fit_calc(dest_paths, params)
    process._ref_phase_estimation(dest_paths, params, refpx, refpy)

    maxvar, vcmt = process._maxvar_vcm_calc(dest_paths, params, preread_ifgs)
    np.testing.assert_array_almost_equal(maxvar, legacy_maxvar, decimal=4)
    np.testing.assert_array_almost_equal(legacy_vcm, vcmt, decimal=3)
    mpiops.run_once(shutil.rmtree, tmpdir)
Пример #4
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    def setUpClass(cls):
        params = Configuration(common.TEST_CONF_ROIPAC).__dict__
        cls.temp_out_dir = tempfile.mkdtemp()
        sys.argv = ['prepifg.py', common.TEST_CONF_ROIPAC]
        params[cf.OUT_DIR] = cls.temp_out_dir
        conv2tif.main(params)
        prepifg.main(params)

        params[cf.REF_EST_METHOD] = 2

        xlks, ylks, crop = cf.transform_params(params)

        base_ifg_paths = cf.original_ifg_paths(params[cf.IFG_FILE_LIST],
                                               params[cf.OBS_DIR])

        dest_paths = cf.get_dest_paths(base_ifg_paths, crop, params, xlks)
        # start run_pyrate copy
        ifgs = common.pre_prepare_ifgs(dest_paths, params)
        mst_grid = common.mst_calculation(dest_paths, params)
        refx, refy = process._ref_pixel_calc(dest_paths, params)
        # Estimate and remove orbit errors
        pyrate.core.orbital.remove_orbital_error(ifgs, params)
        ifgs = common.prepare_ifgs_without_phase(dest_paths, params)
        for ifg in ifgs:
            ifg.close()
        _, ifgs = process._ref_phase_estimation(dest_paths, params, refx, refy)
        ifgs[0].open()
        r_dist = covariance.RDist(ifgs[0])()
        ifgs[0].close()
        maxvar = [covariance.cvd(i, params, r_dist)[0] for i in dest_paths]
        for ifg in ifgs:
            ifg.open()
        vcmt = covariance.get_vcmt(ifgs, maxvar)

        for ifg in ifgs:
            ifg.close()
            ifg.open()
            ifg.nodata_value = 0.0

        params[cf.TIME_SERIES_METHOD] = 1
        params[cf.PARALLEL] = 0
        # Calculate time series
        cls.tsincr_0, cls.tscum_0, _ = common.calculate_time_series(
            ifgs, params, vcmt, mst=mst_grid)

        params[cf.PARALLEL] = 1
        cls.tsincr_1, cls.tscum_1, cls.tsvel_1 = common.calculate_time_series(
            ifgs, params, vcmt, mst=mst_grid)

        # load the legacy data
        ts_dir = os.path.join(common.SML_TEST_DIR, 'time_series')
        tsincr_path = os.path.join(ts_dir, 'ts_incr_interp0_method1.csv')
        ts_incr = np.genfromtxt(tsincr_path)

        tscum_path = os.path.join(ts_dir, 'ts_cum_interp0_method1.csv')
        ts_cum = np.genfromtxt(tscum_path)
        cls.ts_incr = np.reshape(ts_incr,
                                 newshape=cls.tsincr_0.shape,
                                 order='F')
        cls.ts_cum = np.reshape(ts_cum, newshape=cls.tscum_0.shape, order='F')
Пример #5
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    def test_more_small_test_data_ref_pixel(self):

        refx, refy = process._ref_pixel_calc(self.ifg_paths,
                                             self.params_alt_ref_frac)
        self.assertEqual(refx, 38)
        self.assertEqual(refy, 58)
        self.assertAlmostEqual(0.5, self.params_alt_ref_frac[cf.REF_MIN_FRAC])
Пример #6
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 def test_small_test_data_ref_pixel_lat_lon_provided(self):
     self.params[cf.REFX], self.params[
         cf.REFY] = 150.941666654, -34.218333314
     refx, refy = process._ref_pixel_calc(self.ifg_paths, self.params)
     self.assertEqual(refx, 38)
     self.assertEqual(refy, 58)
     self.assertAlmostEqual(0.8, self.params[cf.REF_MIN_FRAC])
Пример #7
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def test_vcm_legacy_vs_mpi(mpisync, tempdir, roipac_or_gamma_conf):

    params = configuration.Configuration(roipac_or_gamma_conf).__dict__
    LEGACY_VCM_DIR = os.path.join(SML_TEST_DIR, 'vcm')
    legacy_vcm = np.genfromtxt(os.path.join(LEGACY_VCM_DIR, 'vcmt.csv'), delimiter=',')
    tmpdir = Path(mpiops.run_once(tempdir))
    mpiops.run_once(common.copytree, params[cf.OBS_DIR], tmpdir)
    params[cf.OUT_DIR] = tmpdir.joinpath('out')
    params[cf.PARALLEL] = 0
    output_conf = Path(tmpdir).joinpath('conf.cfg')
    cf.write_config_file(params=params, output_conf_file=output_conf)
    params = configuration.Configuration(output_conf).__dict__

    dest_paths = [p.sampled_path for p in params[cf.INTERFEROGRAM_FILES]]
    # run conv2tif and prepifg, create the dest_paths files
    conv2tif.main(params)
    params[cf.INTERFEROGRAM_FILES].pop()
    prepifg.main(params)
    params[cf.INTERFEROGRAM_FILES].pop()
    preread_ifgs = process._create_ifg_dict(dest_paths, params=params)
    refpx, refpy = process._ref_pixel_calc(dest_paths, params)
    process._orb_fit_calc(params[cf.INTERFEROGRAM_FILES], params)
    process._ref_phase_estimation(dest_paths, params, refpx, refpy)

    maxvar, vcmt = process._maxvar_vcm_calc(dest_paths, params, preread_ifgs)

    # phase data after ref pixel has changed due to commit bf2f7ebd
    # Legacy tests won't match anymore
    np.testing.assert_array_almost_equal(maxvar, legacy_maxvar, decimal=4)
    np.testing.assert_array_almost_equal(legacy_vcm, vcmt, decimal=3)
    mpiops.run_once(shutil.rmtree, tmpdir)
Пример #8
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 def test_small_test_data_ref_all_1(self):
     refx, refy = process._ref_pixel_calc(self.ifg_paths,
                                          self.params_all_1s)
     self.assertAlmostEqual(0.7, self.params_all_1s[cf.REF_MIN_FRAC])
     self.assertEqual(1, self.params_all_1s[cf.REFNX])
     self.assertEqual(1, self.params_all_1s[cf.REFNY])
     self.assertEqual(refx, 2)
     self.assertEqual(refy, 2)
Пример #9
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 def test_metadata(self):
     refx, refy = process._ref_pixel_calc(self.ifg_paths,
                                          self.params_chipsize_15)
     for i in self.ifg_paths:
         ifg = shared.Ifg(i)
         ifg.open(readonly=True)
         md = ifg.meta_data
         for k, v in zip([
                 ifc.PYRATE_REFPIX_X, ifc.PYRATE_REFPIX_Y,
                 ifc.PYRATE_REFPIX_LAT, ifc.PYRATE_REFPIX_LON,
                 ifc.PYRATE_MEAN_REF_AREA, ifc.PYRATE_STDDEV_REF_AREA
         ], [str(refx), str(refy), 0, 0, 0, 0]):
             assert k in md  # metadata present
             # assert values
         ifg.close()
Пример #10
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    def setUpClass(cls):
        params = Configuration(common.TEST_CONF_ROIPAC).__dict__
        shutil.rmtree(params[cf.OUT_DIR])
        params = Configuration(common.TEST_CONF_ROIPAC).__dict__
        cls.temp_out_dir = tempfile.mkdtemp()
        sys.argv = ['prepifg.py', common.TEST_CONF_ROIPAC]
        params[cf.OUT_DIR] = cls.temp_out_dir
        params[cf.TMPDIR] = cls.temp_out_dir
        conv2tif.main(params)
        prepifg.main(params)

        params[cf.REF_EST_METHOD] = 1
        params[cf.PARALLEL] = True

        xlks, ylks, crop = cf.transform_params(params)

        base_ifg_paths = [
            c.unwrapped_path for c in params[cf.INTERFEROGRAM_FILES]
        ]
        headers = [roipac.roipac_header(i, params) for i in base_ifg_paths]
        dest_paths = [
            Path(cls.temp_out_dir).joinpath(Path(
                c.sampled_path).name).as_posix()
            for c in params[cf.INTERFEROGRAM_FILES][:-2]
        ]

        # start run_pyrate copy
        ifgs = common.pre_prepare_ifgs(dest_paths, params)
        mst_grid = common.mst_calculation(dest_paths, params)
        # Estimate reference pixel location
        refx, refy = process._ref_pixel_calc(dest_paths, params)

        # Estimate and remove orbit errors
        pyrate.core.orbital.remove_orbital_error(ifgs, params, headers)

        for i in ifgs:
            i.close()

        ifgs = common.pre_prepare_ifgs(dest_paths, params)

        for i in ifgs:
            i.close()

        cls.ref_phs, cls.ifgs = process._ref_phase_estimation(
            dest_paths, params, refx, refy)
Пример #11
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 def setUpClass(cls):
     params = Configuration(TEST_CONF_ROIPAC).__dict__
     cls.temp_out_dir = tempfile.mkdtemp()
     sys.argv = ['prepifg.py', TEST_CONF_ROIPAC]
     params[cf.OUT_DIR] = cls.temp_out_dir
     params[cf.TMPDIR] = os.path.join(cls.temp_out_dir, cf.TMPDIR)
     shared.mkdir_p(params[cf.TMPDIR])
     params[cf.REF_EST_METHOD] = 2
     conv2tif.main(params)
     prepifg.main(params)
     cls.params = params
     base_ifg_paths = [
         c.unwrapped_path for c in params[cf.INTERFEROGRAM_FILES]
     ]
     dest_paths = [c.converted_path for c in params[cf.INTERFEROGRAM_FILES]]
     dest_paths = dest_paths[:-2]
     for i in dest_paths:
         Path(i).chmod(
             0o664
         )  # assign write permission as conv2tif output is readonly
     ifgs = common.pre_prepare_ifgs(dest_paths, params)
     refx, refy = process._ref_pixel_calc(dest_paths, params)
     headers = [roipac.roipac_header(i, cls.params) for i in base_ifg_paths]
     pyrate.core.orbital.remove_orbital_error(ifgs, params, headers)
     ifgs = prepare_ifgs_without_phase(dest_paths, params)
     for ifg in ifgs:
         ifg.close()
     _, cls.ifgs = process._ref_phase_estimation(dest_paths, params, refx,
                                                 refy)
     ifgs[0].open()
     r_dist = RDist(ifgs[0])()
     ifgs[0].close()
     # Calculate interferogram noise
     cls.maxvar = [
         cvd(i,
             params,
             r_dist,
             calc_alpha=True,
             save_acg=True,
             write_vals=True)[0] for i in dest_paths
     ]
     cls.vcmt = get_vcmt(ifgs, cls.maxvar)
     for ifg in ifgs:
         ifg.close()
Пример #12
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def test_vcm_legacy_vs_mpi(mpisync, tempdir, get_config):
    from tests.common import SML_TEST_DIR, TEST_CONF_ROIPAC

    params_dict = get_config(TEST_CONF_ROIPAC)
    LEGACY_VCM_DIR = os.path.join(SML_TEST_DIR, 'vcm')
    legacy_vcm = np.genfromtxt(os.path.join(LEGACY_VCM_DIR, 'vcmt.csv'),
                               delimiter=',')
    if mpiops.rank == 0:
        outdir = tempdir()
    else:
        outdir = None
    outdir = mpiops.comm.bcast(outdir, root=0)
    params_dict[cf.OUT_DIR] = outdir
    params_dict[cf.PARALLEL] = False
    xlks, ylks, crop = cf.transform_params(params_dict)
    base_unw_paths = cf.original_ifg_paths(params_dict[cf.IFG_FILE_LIST],
                                           params_dict[cf.OBS_DIR])
    # dest_paths are tifs that have been geotif converted and multilooked
    dest_paths = cf.get_dest_paths(base_unw_paths, crop, params_dict, xlks)

    # run prepifg, create the dest_paths files
    if mpiops.rank == 0:
        conv2tif.main(params_dict)
        prepifg.main(params_dict)

    mpiops.comm.barrier()

    tiles = pyrate.core.shared.get_tiles(dest_paths[0], rows=1, cols=1)
    preread_ifgs = process._create_ifg_dict(dest_paths,
                                            params=params_dict,
                                            tiles=tiles)
    refpx, refpy = process._ref_pixel_calc(dest_paths, params_dict)
    process._orb_fit_calc(dest_paths, params_dict)
    process._ref_phase_estimation(dest_paths, params_dict, refpx, refpy)

    maxvar, vcmt = process._maxvar_vcm_calc(dest_paths, params_dict,
                                            preread_ifgs)
    np.testing.assert_array_almost_equal(maxvar, legacy_maxvar, decimal=4)
    np.testing.assert_array_almost_equal(legacy_vcm, vcmt, decimal=3)
    if mpiops.rank == 0:
        shutil.rmtree(outdir)
        common.remove_tifs(params_dict[cf.OBS_DIR])
Пример #13
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    def setUpClass(cls):

        params = cf.get_config_params(common.TEST_CONF_ROIPAC)
        cls.temp_out_dir = tempfile.mkdtemp()
        sys.argv = ['prepifg.py', common.TEST_CONF_ROIPAC]
        params[cf.OUT_DIR] = cls.temp_out_dir
        params[cf.TMPDIR] = cls.temp_out_dir
        conv2tif.main(params)
        prepifg.main(params)

        params[cf.OUT_DIR] = cls.temp_out_dir
        params[cf.REF_EST_METHOD] = 2
        params[cf.PARALLEL] = True

        xlks, ylks, crop = cf.transform_params(params)

        base_ifg_paths = cf.original_ifg_paths(params[cf.IFG_FILE_LIST],
                                               params[cf.OBS_DIR])

        dest_paths = cf.get_dest_paths(base_ifg_paths, crop, params, xlks)

        # start run_pyrate copy
        ifgs = common.pre_prepare_ifgs(dest_paths, params)
        # Estimate reference pixel location
        refx, refy = process._ref_pixel_calc(dest_paths, params)

        # Estimate and remove orbit errors
        pyrate.core.orbital.remove_orbital_error(ifgs, params)

        for i in ifgs:
            i.close()

        ifgs = common.pre_prepare_ifgs(dest_paths, params)

        for i in ifgs:
            i.close()

        cls.ref_phs, cls.ifgs = process._ref_phase_estimation(
            dest_paths, params, refx, refy)
Пример #14
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    def setUpClass(cls):
        params = Configuration(common.TEST_CONF_ROIPAC).__dict__
        cls.temp_out_dir = tempfile.mkdtemp()
        params[cf.OUT_DIR] = cls.temp_out_dir
        params[cf.PARALLEL] = 0
        conv2tif.main(params)
        prepifg.main(params)

        params[cf.REF_EST_METHOD] = 2

        base_ifg_paths = [
            c.unwrapped_path for c in params[cf.INTERFEROGRAM_FILES]
        ]
        headers = [roipac.roipac_header(i, params) for i in base_ifg_paths]
        dest_paths = [
            Path(cls.temp_out_dir).joinpath(Path(
                c.sampled_path).name).as_posix()
            for c in params[cf.INTERFEROGRAM_FILES][:-2]
        ]
        # start run_pyrate copy
        ifgs = common.pre_prepare_ifgs(dest_paths, params)
        mst_grid = common.mst_calculation(dest_paths, params)

        refx, refy = process._ref_pixel_calc(dest_paths, params)

        # Estimate and remove orbit errors
        pyrate.core.orbital.remove_orbital_error(ifgs, params, headers)
        ifgs = common.prepare_ifgs_without_phase(dest_paths, params)
        for ifg in ifgs:
            ifg.close()
        _, ifgs = process._ref_phase_estimation(dest_paths, params, refx, refy)
        ifgs[0].open()
        r_dist = covariance.RDist(ifgs[0])()
        ifgs[0].close()
        # Calculate interferogram noise
        maxvar = [covariance.cvd(i, params, r_dist)[0] for i in dest_paths]
        for ifg in ifgs:
            ifg.open()
        vcmt = covariance.get_vcmt(ifgs, maxvar)
        for ifg in ifgs:
            ifg.close()
            ifg.open()
            ifg.nodata_value = 0.0

        params[cf.TIME_SERIES_METHOD] = 2
        params[cf.PARALLEL] = 1
        # Calculate time series
        cls.tsincr, cls.tscum, _ = common.calculate_time_series(ifgs,
                                                                params,
                                                                vcmt,
                                                                mst=mst_grid)

        params[cf.PARALLEL] = 0
        # Calculate time series serailly by the pixel
        cls.tsincr_0, cls.tscum_0, _ = common.calculate_time_series(
            ifgs, params, vcmt, mst=mst_grid)

        # copy legacy data
        SML_TIME_SERIES_DIR = os.path.join(common.SML_TEST_DIR, 'time_series')
        tsincr_path = os.path.join(SML_TIME_SERIES_DIR,
                                   'ts_incr_interp0_method2.csv')
        ts_incr = np.genfromtxt(tsincr_path)

        tscum_path = os.path.join(SML_TIME_SERIES_DIR,
                                  'ts_cum_interp0_method2.csv')
        ts_cum = np.genfromtxt(tscum_path)

        cls.ts_incr = np.reshape(ts_incr,
                                 newshape=cls.tsincr_0.shape,
                                 order='F')
        cls.ts_cum = np.reshape(ts_cum, newshape=cls.tscum_0.shape, order='F')
Пример #15
0
    def setUpClass(cls):
        params = cf.get_config_params(TEST_CONF_ROIPAC)
        cls.temp_out_dir = tempfile.mkdtemp()

        params[cf.OUT_DIR] = cls.temp_out_dir
        params[cf.TMPDIR] = os.path.join(params[cf.OUT_DIR], cf.TMPDIR)
        shared.mkdir_p(params[cf.TMPDIR])
        conv2tif.main(params)
        prepifg.main(params)

        params[cf.REF_EST_METHOD] = 2

        xlks, _, crop = cf.transform_params(params)

        base_ifg_paths = cf.original_ifg_paths(params[cf.IFG_FILE_LIST],
                                               params[cf.OBS_DIR])

        dest_paths = cf.get_dest_paths(base_ifg_paths, crop, params, xlks)
        print(f"base_ifg_paths={base_ifg_paths}")
        print(f"dest_paths={dest_paths}")
        # start run_pyrate copy
        ifgs = pre_prepare_ifgs(dest_paths, params)
        mst_grid = tests.common.mst_calculation(dest_paths, params)

        refx, refy = process._ref_pixel_calc(dest_paths, params)

        # Estimate and remove orbit errors
        pyrate.core.orbital.remove_orbital_error(ifgs, params)
        ifgs = prepare_ifgs_without_phase(dest_paths, params)
        for ifg in ifgs:
            ifg.close()
        _, ifgs = process._ref_phase_estimation(dest_paths, params, refx, refy)
        ifgs[0].open()
        r_dist = vcm_module.RDist(ifgs[0])()
        ifgs[0].close()
        maxvar = [vcm_module.cvd(i, params, r_dist)[0] for i in dest_paths]
        for ifg in ifgs:
            ifg.open()
        vcmt = vcm_module.get_vcmt(ifgs, maxvar)
        for ifg in ifgs:
            ifg.close()
            ifg.open()

        # Calculate linear rate map
        params[cf.PARALLEL] = 1
        cls.rate, cls.error, cls.samples = tests.common.calculate_linear_rate(
            ifgs, params, vcmt, mst_mat=mst_grid)

        params[cf.PARALLEL] = 2
        cls.rate_2, cls.error_2, cls.samples_2 = \
            tests.common.calculate_linear_rate(ifgs, params, vcmt,
                                               mst_mat=mst_grid)

        params[cf.PARALLEL] = 0
        # Calculate linear rate map
        cls.rate_s, cls.error_s, cls.samples_s = \
            tests.common.calculate_linear_rate(ifgs, params, vcmt,
                                               mst_mat=mst_grid)

        linrate_dir = os.path.join(SML_TEST_DIR, 'linrate')

        cls.rate_container = np.genfromtxt(os.path.join(
            linrate_dir, 'stackmap.csv'),
                                           delimiter=',')
        cls.error_container = np.genfromtxt(os.path.join(
            linrate_dir, 'errormap.csv'),
                                            delimiter=',')

        cls.samples_container = np.genfromtxt(os.path.join(
            linrate_dir, 'coh_sta.csv'),
                                              delimiter=',')

        for ifg in ifgs:
            ifg.close()
Пример #16
0
    def setUpClass(cls):
        params = Configuration(TEST_CONF_ROIPAC).__dict__
        cls.temp_out_dir = tempfile.mkdtemp()

        params[cf.OUT_DIR] = cls.temp_out_dir
        params[cf.TMPDIR] = os.path.join(params[cf.OUT_DIR], cf.TMPDIR)
        shared.mkdir_p(params[cf.TMPDIR])
        conv2tif.main(params)
        prepifg.main(params)

        params[cf.REF_EST_METHOD] = 2

        xlks, _, crop = cf.transform_params(params)

        base_ifg_paths = [
            c.unwrapped_path for c in params[cf.INTERFEROGRAM_FILES]
        ]
        headers = [roipac.roipac_header(i, params) for i in base_ifg_paths]
        dest_paths = [
            Path(cls.temp_out_dir).joinpath(Path(
                c.sampled_path).name).as_posix()
            for c in params[cf.INTERFEROGRAM_FILES][:-2]
        ]
        # start run_pyrate copy
        ifgs = pre_prepare_ifgs(dest_paths, params)
        mst_grid = tests.common.mst_calculation(dest_paths, params)

        refx, refy = process._ref_pixel_calc(dest_paths, params)

        # Estimate and remove orbit errors
        pyrate.core.orbital.remove_orbital_error(ifgs, params, headers)
        ifgs = prepare_ifgs_without_phase(dest_paths, params)
        for ifg in ifgs:
            ifg.close()
        _, ifgs = process._ref_phase_estimation(dest_paths, params, refx, refy)
        ifgs[0].open()
        r_dist = vcm_module.RDist(ifgs[0])()
        ifgs[0].close()
        maxvar = [vcm_module.cvd(i, params, r_dist)[0] for i in dest_paths]
        for ifg in ifgs:
            ifg.open()
        vcmt = vcm_module.get_vcmt(ifgs, maxvar)
        for ifg in ifgs:
            ifg.close()
            ifg.open()

        # Calculate stacked rate map
        params[cf.PARALLEL] = 1
        cls.rate, cls.error, cls.samples = tests.common.calculate_stack_rate(
            ifgs, params, vcmt, mst_mat=mst_grid)

        # Calculate stacked rate map
        params[cf.PARALLEL] = 0
        cls.rate_s, cls.error_s, cls.samples_s = tests.common.calculate_stack_rate(
            ifgs, params, vcmt, mst_mat=mst_grid)

        stackrate_dir = os.path.join(SML_TEST_DIR, 'stackrate')

        cls.rate_container = np.genfromtxt(os.path.join(
            stackrate_dir, 'stackmap.csv'),
                                           delimiter=',')
        cls.error_container = np.genfromtxt(os.path.join(
            stackrate_dir, 'errormap.csv'),
                                            delimiter=',')
        cls.samples_container = np.genfromtxt(os.path.join(
            stackrate_dir, 'coh_sta.csv'),
                                              delimiter=',')

        for ifg in ifgs:
            ifg.close()