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()
def setup_class(cls): params = Configuration(common.TEST_CONF_ROIPAC).__dict__ params[cf.TEMP_MLOOKED_DIR] = os.path.join(params[cf.OUT_DIR], cf.TEMP_MLOOKED_DIR) conv2tif.main(params) prepifg.main(params) params[cf.REF_EST_METHOD] = 2 xlks, _, crop = cf.transform_params(params) dest_paths, headers = common.repair_params_for_correct_tests(params[cf.OUT_DIR], params) correct._copy_mlooked(params) copied_dest_paths = [os.path.join(params[cf.TEMP_MLOOKED_DIR], os.path.basename(d)) for d in dest_paths] del dest_paths # start run_pyrate copy ifgs = pre_prepare_ifgs(copied_dest_paths, params) mst_grid = tests.common.mst_calculation(copied_dest_paths, params) refx, refy = pyrate.core.refpixel.ref_pixel_calc_wrapper(params) params[cf.REFX] = refx params[cf.REFY] = refy params[cf.ORBFIT_OFFSET] = True # Estimate and remove orbit errors pyrate.core.orbital.remove_orbital_error(ifgs, params) ifgs = prepare_ifgs_without_phase(copied_dest_paths, params) for ifg in ifgs: ifg.close() correct._update_params_with_tiles(params) _, ifgs = pyrate.core.ref_phs_est.ref_phase_est_wrapper(params) 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 copied_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() cls.params = params
def setup_class(cls): params = Configuration(common.TEST_CONF_ROIPAC).__dict__ cls.tmp_dir = tempfile.mkdtemp() common.copytree(common.SML_TEST_TIF, cls.tmp_dir) tifs = glob.glob(os.path.join(cls.tmp_dir, "*.tif")) for t in tifs: os.chmod(t, 0o644) small_ifgs = common.small_data_setup(datafiles=tifs) ifg_paths = [i.data_path for i in small_ifgs] cls.ifg_ret = common.pre_prepare_ifgs(ifg_paths, params=params) for i in cls.ifg_ret: i.close() nan_conversion = params[C.NAN_CONVERSION] # prepare a second set cls.tmp_dir2 = tempfile.mkdtemp() common.copytree(common.SML_TEST_TIF, cls.tmp_dir2) tifs = glob.glob(os.path.join(cls.tmp_dir2, "*.tif")) for t in tifs: os.chmod(t, 0o644) small_ifgs = common.small_data_setup(datafiles=tifs) ifg_paths = [i.data_path for i in small_ifgs] cls.ifgs = [shared.Ifg(p) for p in ifg_paths] for i in cls.ifgs: i.open(readonly=False) if nan_conversion: # nan conversion happens here in networkx mst i.nodata_value = params[C.NO_DATA_VALUE] i.convert_to_nans() if not i.mm_converted: i.convert_to_mm() i.close()
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')
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)
def setUpClass(cls): params = cf.get_config_params(common.TEST_CONF_ROIPAC) cls.temp_out_dir = tempfile.mkdtemp() sys.argv = ['run_prepifg.py', common.TEST_CONF_ROIPAC] params[cf.OUT_DIR] = cls.temp_out_dir run_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]) 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 = run_pyrate._ref_pixel_calc(dest_paths, params) # Estimate and remove orbit errors pyrate.orbital.remove_orbital_error(ifgs, params) ifgs = common.prepare_ifgs_without_phase(dest_paths, params) _, ifgs = rpe.estimate_ref_phase(ifgs, params, refx, refy) r_dist = covariance.RDist(ifgs[0])() maxvar = [covariance.cvd(i, params, r_dist)[0] for i in ifgs] vcmt = covariance.get_vcmt(ifgs, maxvar) 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) params[cf.PARALLEL] = 2 cls.tsincr_2, cls.tscum_2, cls.tsvel_2 = \ common.calculate_time_series(ifgs, params, vcmt, mst=mst_grid) # load the matlab data ts_dir = os.path.join(common.SML_TEST_DIR, 'matlab_time_series') tsincr_path = os.path.join(ts_dir, 'ts_incr_interp0_method1.csv') ts_incr = np.genfromtxt(tsincr_path) # the matlab tsvel return is a bit pointless and not tested here # tserror is not returned # tserr_path = os.path.join(SML_TIME_SERIES_DIR, # 'ts_error_interp0_method1.csv') # ts_err = np.genfromtxt(tserr_path, delimiter=',') 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')
def setup_class(cls): roipac_params = Configuration(TEST_CONF_ROIPAC).__dict__ from copy import deepcopy params = deepcopy(roipac_params) shared.mkdir_p(params[C.TMPDIR]) params[C.REF_EST_METHOD] = 2 conv2tif.main(params) params = deepcopy(roipac_params) prepifg.main(params) params = deepcopy(roipac_params) base_ifg_paths = [ c.unwrapped_path for c in params[C.INTERFEROGRAM_FILES] ] dest_paths = [c.converted_path for c in params[C.INTERFEROGRAM_FILES]] params[C.INTERFEROGRAM_FILES] = [ MultiplePaths(d, params) for d in dest_paths ] for p in params[C.INTERFEROGRAM_FILES]: # hack p.sampled_path = p.converted_path 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) correct._copy_mlooked(params) correct._update_params_with_tiles(params) correct._create_ifg_dict(params) pyrate.core.refpixel.ref_pixel_calc_wrapper(params) params[C.ORBFIT_OFFSET] = True pyrate.core.orbital.remove_orbital_error(ifgs, params) ifgs = prepare_ifgs_without_phase(dest_paths, params) for ifg in ifgs: ifg.close() for p in params[C.INTERFEROGRAM_FILES]: # hack p.tmp_sampled_path = p.sampled_path _, cls.ifgs = pyrate.core.ref_phs_est.ref_phase_est_wrapper(params) 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() cls.params = params
def setup_class(cls): params = Configuration(common.TEST_CONF_ROIPAC).__dict__ conv2tif.main(params) prepifg.main(params) for p in params[cf.INTERFEROGRAM_FILES]: # hack p.tmp_sampled_path = p.sampled_path Path(p.sampled_path).chmod( 0o664 ) # assign write permission as conv2tif output is readonly params[cf.REF_EST_METHOD] = 2 params[cf.PARALLEL] = False params[cf.ORBFIT_OFFSET] = True dest_paths, headers = common.repair_params_for_correct_tests( params[cf.OUT_DIR], params) # 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 = ref_pixel_calc_wrapper(params) # Estimate and remove orbit errors 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() for p in params[cf.INTERFEROGRAM_FILES]: p.tmp_sampled_path = p.sampled_path params[cf.REFX], params[cf.REFY] = refx, refy params['rows'], params['cols'] = 3, 2 correct._update_params_with_tiles(params) cls.ref_phs, cls.ifgs = ref_phase_est_wrapper(params) cls.params = params
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)
def setUpClass(cls): params = cf.get_config_params(common.TEST_CONF_ROIPAC) cls.temp_out_dir = tempfile.mkdtemp() sys.argv = ['run_prepifg.py', common.TEST_CONF_ROIPAC] params[cf.OUT_DIR] = cls.temp_out_dir run_prepifg.main(params) params[cf.OUT_DIR] = cls.temp_out_dir params[cf.REF_EST_METHOD] = 1 params[cf.PARALLEL] = False xlks, ylks, crop = cf.transform_params(params) base_ifg_paths = cf.original_ifg_paths(params[cf.IFG_FILE_LIST]) 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) # Estimate reference pixel location refx, refy = run_pyrate._ref_pixel_calc(dest_paths, params) # Estimate and remove orbit errors pyrate.orbital.remove_orbital_error(ifgs, params) for i in ifgs: i.close() ifgs = common.pre_prepare_ifgs(dest_paths, params) cls.ref_phs, cls.ifgs = estimate_ref_phase(ifgs, params, refx, refy) # end run_pyrate copy # manually close for windows compatibility for i in ifgs: i.close()
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()
def setUpClass(cls): params = cf.get_config_params(TEST_CONF_ROIPAC) cls.temp_out_dir = tempfile.mkdtemp() sys.argv = ['run_prepifg.py', TEST_CONF_ROIPAC] 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]) run_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]) dest_paths = cf.get_dest_paths(base_ifg_paths, crop, params, xlks) # start run_pyrate copy ifgs = pre_prepare_ifgs(dest_paths, params) mst_grid = tests.common.mst_calculation(dest_paths, params) refx, refy = run_pyrate._ref_pixel_calc(dest_paths, params) # Estimate and remove orbit errors pyrate.orbital.remove_orbital_error(ifgs, params) ifgs = prepare_ifgs_without_phase(dest_paths, params) _, ifgs = rpe.estimate_ref_phase(ifgs, params, refx, refy) r_dist = vcm_module.RDist(ifgs[0])() maxvar = [vcm_module.cvd(i, params, r_dist)[0] for i in ifgs] vcmt = vcm_module.get_vcmt(ifgs, maxvar) # 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) matlab_linrate_dir = os.path.join(SML_TEST_DIR, 'matlab_linrate') cls.rate_matlab = np.genfromtxt(os.path.join(matlab_linrate_dir, 'stackmap.csv'), delimiter=',') cls.error_matlab = np.genfromtxt(os.path.join(matlab_linrate_dir, 'errormap.csv'), delimiter=',') cls.samples_matlab = np.genfromtxt(os.path.join( matlab_linrate_dir, 'coh_sta.csv'), delimiter=',')
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')
def setup_class(cls): params = Configuration(common.TEST_CONF_ROIPAC).__dict__ params[cf.TEMP_MLOOKED_DIR] = os.path.join(params[cf.OUT_DIR], cf.TEMP_MLOOKED_DIR) conv2tif.main(params) prepifg.main(params) params[cf.REF_EST_METHOD] = 2 xlks, _, crop = cf.transform_params(params) dest_paths, headers = common.repair_params_for_correct_tests( params[cf.OUT_DIR], params) correct._copy_mlooked(params) copied_dest_paths = [ os.path.join(params[cf.TEMP_MLOOKED_DIR], os.path.basename(d)) for d in dest_paths ] del dest_paths # start run_pyrate copy ifgs = common.pre_prepare_ifgs(copied_dest_paths, params) mst_grid = common.mst_calculation(copied_dest_paths, params) refx, refy = pyrate.core.refpixel.ref_pixel_calc_wrapper(params) params[cf.REFX] = refx params[cf.REFY] = refy params[cf.ORBFIT_OFFSET] = True # Estimate and remove orbit errors pyrate.core.orbital.remove_orbital_error(ifgs, params) ifgs = common.prepare_ifgs_without_phase(copied_dest_paths, params) for ifg in ifgs: ifg.close() correct._update_params_with_tiles(params) _, ifgs = pyrate.core.ref_phs_est.ref_phase_est_wrapper(params) 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 copied_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') cls.params = params
def test_timeseries_linrate_mpi(mpisync, tempdir, modify_config, ref_est_method, row_splits, col_splits, get_crop, orbfit_lks, orbfit_method, orbfit_degrees): params = modify_config outdir = mpiops.run_once(tempdir) params[cf.OUT_DIR] = outdir params[cf.TMPDIR] = os.path.join(params[cf.OUT_DIR], cf.TMPDIR) params[cf.DEM_HEADER_FILE] = SML_TEST_DEM_HDR_GAMMA params[cf.REF_EST_METHOD] = ref_est_method params[cf.IFG_CROP_OPT] = get_crop params[cf.ORBITAL_FIT_LOOKS_Y] = orbfit_lks params[cf.ORBITAL_FIT_LOOKS_X] = orbfit_lks params[cf.ORBITAL_FIT_METHOD] = orbfit_method params[cf.ORBITAL_FIT_DEGREE] = orbfit_degrees xlks, ylks, crop = cf.transform_params(params) if xlks * col_splits > 45 or ylks * row_splits > 70: print('skipping test because lks and col_splits are not compatible') return # skip some tests in travis to run CI faster if TRAVIS and (xlks % 2 or row_splits % 2 or col_splits % 2 or orbfit_lks % 2): print('Skipping in travis env for faster CI run') return print("xlks={}, ref_est_method={}, row_splits={}, col_splits={}, " "get_crop={}, orbfit_lks={}, orbfit_method={}, " "rank={}".format(xlks, ref_est_method, row_splits, col_splits, get_crop, orbfit_lks, orbfit_method, orbfit_degrees, mpiops.rank)) base_unw_paths = cf.original_ifg_paths(params[cf.IFG_FILE_LIST]) # dest_paths are tifs that have been geotif converted and multilooked dest_paths = cf.get_dest_paths(base_unw_paths, crop, params, xlks) # run prepifg, create the dest_paths files if mpiops.rank == 0: run_prepifg.gamma_prepifg(base_unw_paths, params) mpiops.comm.barrier() (refpx, refpy), maxvar, vcmt = run_pyrate.process_ifgs(ifg_paths=dest_paths, params=params, rows=row_splits, cols=col_splits) tiles = mpiops.run_once(pyrate.shared.get_tiles, dest_paths[0], rows=row_splits, cols=col_splits) postprocessing._postprocess_linrate(row_splits, col_splits, params) postprocessing._postprocess_timeseries(row_splits, col_splits, params) ifgs_mpi_out_dir = params[cf.OUT_DIR] ifgs_mpi = small_data_setup(datafiles=dest_paths) # single process timeseries/linrate calculation if mpiops.rank == 0: params_old = modify_config params_old[cf.OUT_DIR] = tempdir() params_old[cf.REF_EST_METHOD] = ref_est_method params_old[cf.IFG_CROP_OPT] = get_crop params_old[cf.ORBITAL_FIT_LOOKS_Y] = orbfit_lks params_old[cf.ORBITAL_FIT_LOOKS_X] = orbfit_lks params_old[cf.ORBITAL_FIT_METHOD] = orbfit_method params_old[cf.ORBITAL_FIT_DEGREE] = orbfit_degrees xlks, ylks, crop = cf.transform_params(params_old) base_unw_paths = cf.original_ifg_paths(params_old[cf.IFG_FILE_LIST]) dest_paths = cf.get_dest_paths(base_unw_paths, crop, params_old, xlks) run_prepifg.gamma_prepifg(base_unw_paths, params_old) ifgs = pre_prepare_ifgs(dest_paths, params_old) mst_grid = tests.common.mst_calculation(dest_paths, params_old) refy, refx = refpixel.ref_pixel(ifgs, params_old) assert (refx == refpx) and (refy == refpy) # both must match pyrate.orbital.remove_orbital_error(ifgs, params_old) ifgs = common.prepare_ifgs_without_phase(dest_paths, params_old) rpe.estimate_ref_phase(ifgs, params_old, refx, refy) ifgs = pre_prepare_ifgs(dest_paths, params_old) r_dist = covariance.RDist(ifgs[0])() maxvar_s = [covariance.cvd(i, params_old, r_dist)[0] for i in ifgs] vcmt_s = covariance.get_vcmt(ifgs, maxvar) tsincr, tscum, _ = tests.common.compute_time_series( ifgs, mst_grid, params, vcmt) rate, error, samples = tests.common.calculate_linear_rate( ifgs, params_old, vcmt, mst_grid) mst_mpi = reconstruct_mst(ifgs[0].shape, tiles, params[cf.TMPDIR]) np.testing.assert_array_almost_equal(mst_grid, mst_mpi) tsincr_mpi, tscum_mpi = reconstruct_times_series( ifgs[0].shape, tiles, params[cf.TMPDIR]) rate_mpi, error_mpi, samples_mpi = \ [reconstruct_linrate(ifgs[0].shape, tiles, params[cf.TMPDIR], t) for t in ['linrate', 'linerror', 'linsamples']] np.testing.assert_array_almost_equal(maxvar, maxvar_s) np.testing.assert_array_almost_equal(vcmt, vcmt_s) for i, j in zip(ifgs, ifgs_mpi): np.testing.assert_array_almost_equal(i.phase_data, j.phase_data) np.testing.assert_array_almost_equal(tsincr, tsincr_mpi, decimal=4) np.testing.assert_array_almost_equal(tscum, tscum_mpi, decimal=4) np.testing.assert_array_almost_equal(rate, rate_mpi, decimal=4) np.testing.assert_array_almost_equal(error, error_mpi, decimal=4) np.testing.assert_array_almost_equal(samples, samples_mpi, decimal=4) # assert linear rate output tifs are same _tifs_same(ifgs_mpi_out_dir, params_old[cf.OUT_DIR], 'linrate.tif') _tifs_same(ifgs_mpi_out_dir, params_old[cf.OUT_DIR], 'linerror.tif') _tifs_same(ifgs_mpi_out_dir, params_old[cf.OUT_DIR], 'linsamples.tif') # assert time series output tifs are same epochlist = algorithm.get_epochs(ifgs)[0] for i in range(tsincr.shape[2]): _tifs_same(ifgs_mpi_out_dir, params_old[cf.OUT_DIR], 'tsincr' + '_' + str(epochlist.dates[i + 1]) + ".tif") # 12 timeseries outputs assert i + 1 == tsincr.shape[2] shutil.rmtree(ifgs_mpi_out_dir) # remove mpi out dir shutil.rmtree(params_old[cf.OUT_DIR]) # remove serial out dir
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 = 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 = 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 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()