import numpy as np import pytest from astropy.io import ascii from astropy.io.ascii.qdp import _get_lines_from_file, _read_table_qdp, _write_table_qdp from astropy.table import Column, MaskedColumn, Table from astropy.utils.exceptions import AstropyUserWarning def test_get_tables_from_qdp_file(tmp_path): example_qdp = """ ! Swift/XRT hardness ratio of trigger: XXXX, name: BUBU X-2 ! Columns are as labelled READ TERR 1 READ SERR 2 ! WT -- hard data !MJD Err (pos) Err(neg) Rate Error 53000.123456 2.37847222222222e-05 -2.37847222222222e-05 -0.212439 0.212439 55045.099887 1.14467592592593e-05 -1.14467592592593e-05 0.000000 0.000000 NO NO NO NO NO ! WT -- soft data !MJD Err (pos) Err(neg) Rate Error 53000.123456 2.37847222222222e-05 -2.37847222222222e-05 0.726155 0.583890 55045.099887 1.14467592592593e-05 -1.14467592592593e-05 2.410935 1.393592 NO NO NO NO NO ! WT -- hardness ratio !MJD Err (pos) Err(neg) Rate Error 53000.123456 2.37847222222222e-05 -2.37847222222222e-05 -0.292553 -0.374935 55045.099887 1.14467592592593e-05 -1.14467592592593e-05 0.000000 -nan """ path = tmp_path / "test.qdp" with open(path, "w") as fp: print(example_qdp, file=fp) table0 = _read_table_qdp(fp.name, names=["MJD", "Rate"], table_id=0) assert table0.meta["initial_comments"][0].startswith("Swift") assert table0.meta["comments"][0].startswith("WT -- hard data") table2 = _read_table_qdp(fp.name, names=["MJD", "Rate"], table_id=2) assert table2.meta["initial_comments"][0].startswith("Swift") assert table2.meta["comments"][0].startswith("WT -- hardness") assert np.isclose(table2["MJD_nerr"][0], -2.37847222222222e-05) def lowercase_header(value): """Make every non-comment line lower case.""" lines = [] for line in value.splitlines(): if not line.startswith("!"): line = line.lower() lines.append(line) return "\n".join(lines) @pytest.mark.parametrize("lowercase", [False, True]) def test_roundtrip(tmp_path, lowercase): example_qdp = """ ! Swift/XRT hardness ratio of trigger: XXXX, name: BUBU X-2 ! Columns are as labelled READ TERR 1 READ SERR 2 ! WT -- hard data !MJD Err (pos) Err(neg) Rate Error 53000.123456 2.37847222222222e-05 -2.37847222222222e-05 NO 0.212439 55045.099887 1.14467592592593e-05 -1.14467592592593e-05 0.000000 0.000000 NO NO NO NO NO ! WT -- soft data !MJD Err (pos) Err(neg) Rate Error 53000.123456 2.37847222222222e-05 -2.37847222222222e-05 0.726155 0.583890 55045.099887 1.14467592592593e-05 -1.14467592592593e-05 2.410935 1.393592 NO NO NO NO NO ! WT -- hardness ratio !MJD Err (pos) Err(neg) Rate Error 53000.123456 2.37847222222222e-05 -2.37847222222222e-05 -0.292553 -0.374935 55045.099887 1.14467592592593e-05 -1.14467592592593e-05 0.000000 NO ! Add command, just to raise the warning. READ TERR 1 ! WT -- whatever !MJD Err (pos) Err(neg) Rate Error 53000.123456 2.37847222222222e-05 -2.37847222222222e-05 -0.292553 -0.374935 NO 1.14467592592593e-05 -1.14467592592593e-05 0.000000 NO """ if lowercase: example_qdp = lowercase_header(example_qdp) path = str(tmp_path / "test.qdp") path2 = str(tmp_path / "test2.qdp") with open(path, "w") as fp: print(example_qdp, file=fp) with pytest.warns(AstropyUserWarning) as record: table = _read_table_qdp(path, names=["MJD", "Rate"], table_id=0) assert np.any( [ "This file contains multiple command blocks" in r.message.args[0] for r in record ] ) _write_table_qdp(table, path2) new_table = _read_table_qdp(path2, names=["MJD", "Rate"], table_id=0) for col in new_table.colnames: is_masked = np.array([np.ma.is_masked(val) for val in new_table[col]]) if np.any(is_masked): # All NaN values are read as such. assert np.ma.is_masked(table[col][is_masked]) is_nan = np.array( [(not np.ma.is_masked(val) and np.isnan(val)) for val in new_table[col]] ) # All non-NaN values are the same assert np.allclose(new_table[col][~is_nan], table[col][~is_nan]) if np.any(is_nan): # All NaN values are read as such. assert np.isnan(table[col][is_nan]) assert np.allclose(new_table["MJD_perr"], [2.378472e-05, 1.1446759e-05]) for meta_name in ["initial_comments", "comments"]: assert meta_name in new_table.meta def test_read_example(): example_qdp = """ ! Initial comment line 1 ! Initial comment line 2 READ TERR 1 READ SERR 3 ! Table 0 comment !a a(pos) a(neg) b c ce d 53000.5 0.25 -0.5 1 1.5 3.5 2 54000.5 1.25 -1.5 2 2.5 4.5 3 NO NO NO NO NO ! Table 1 comment !a a(pos) a(neg) b c ce d 54000.5 2.25 -2.5 NO 3.5 5.5 5 55000.5 3.25 -3.5 4 4.5 6.5 nan """ dat = ascii.read(example_qdp, format="qdp", table_id=1, names=["a", "b", "c", "d"]) t = Table.read( example_qdp, format="ascii.qdp", table_id=1, names=["a", "b", "c", "d"] ) assert np.allclose(t["a"], [54000, 55000]) assert t["c_err"][0] == 5.5 assert np.ma.is_masked(t["b"][0]) assert np.isnan(t["d"][1]) for col1, col2 in zip(t.itercols(), dat.itercols()): assert np.allclose(col1, col2, equal_nan=True) def test_roundtrip_example(tmp_path): example_qdp = """ ! Initial comment line 1 ! Initial comment line 2 READ TERR 1 READ SERR 3 ! Table 0 comment !a a(pos) a(neg) b c ce d 53000.5 0.25 -0.5 1 1.5 3.5 2 54000.5 1.25 -1.5 2 2.5 4.5 3 NO NO NO NO NO ! Table 1 comment !a a(pos) a(neg) b c ce d 54000.5 2.25 -2.5 NO 3.5 5.5 5 55000.5 3.25 -3.5 4 4.5 6.5 nan """ test_file = tmp_path / "test.qdp" t = Table.read( example_qdp, format="ascii.qdp", table_id=1, names=["a", "b", "c", "d"] ) t.write(test_file, err_specs={"terr": [1], "serr": [3]}) t2 = Table.read(test_file, names=["a", "b", "c", "d"], table_id=0) for col1, col2 in zip(t.itercols(), t2.itercols()): assert np.allclose(col1, col2, equal_nan=True) def test_roundtrip_example_comma(tmp_path): example_qdp = """ ! Initial comment line 1 ! Initial comment line 2 READ TERR 1 READ SERR 3 ! Table 0 comment !a,a(pos),a(neg),b,c,ce,d 53000.5,0.25,-0.5,1,1.5,3.5,2 54000.5,1.25,-1.5,2,2.5,4.5,3 NO,NO,NO,NO,NO ! Table 1 comment !a,a(pos),a(neg),b,c,ce,d 54000.5,2.25,-2.5,NO,3.5,5.5,5 55000.5,3.25,-3.5,4,4.5,6.5,nan """ test_file = tmp_path / "test.qdp" t = Table.read( example_qdp, format="ascii.qdp", table_id=1, names=["a", "b", "c", "d"], sep="," ) t.write(test_file, err_specs={"terr": [1], "serr": [3]}) t2 = Table.read(test_file, names=["a", "b", "c", "d"], table_id=0) # t.values_equal(t2) for col1, col2 in zip(t.itercols(), t2.itercols()): assert np.allclose(col1, col2, equal_nan=True) def test_read_write_simple(tmp_path): test_file = tmp_path / "test.qdp" t1 = Table() t1.add_column(Column(name="a", data=[1, 2, 3, 4])) t1.add_column( MaskedColumn( data=[4.0, np.nan, 3.0, 1.0], name="b", mask=[False, False, False, True] ) ) t1.write(test_file, format="ascii.qdp") with pytest.warns(UserWarning) as record: t2 = Table.read(test_file, format="ascii.qdp") assert np.any( [ "table_id not specified. Reading the first available table" in r.message.args[0] for r in record ] ) assert np.allclose(t2["col1"], t1["a"]) assert np.all(t2["col1"] == t1["a"]) good = ~np.isnan(t1["b"]) assert np.allclose(t2["col2"][good], t1["b"][good]) def test_read_write_simple_specify_name(tmp_path): test_file = tmp_path / "test.qdp" t1 = Table() t1.add_column(Column(name="a", data=[1, 2, 3])) # Give a non-None err_specs t1.write(test_file, format="ascii.qdp") t2 = Table.read(test_file, table_id=0, format="ascii.qdp", names=["a"]) assert np.all(t2["a"] == t1["a"]) def test_get_lines_from_qdp(tmp_path): test_file = str(tmp_path / "test.qdp") text_string = "A\nB" text_output = _get_lines_from_file(text_string) with open(test_file, "w") as fobj: print(text_string, file=fobj) file_output = _get_lines_from_file(test_file) list_output = _get_lines_from_file(["A", "B"]) for i, line in enumerate(["A", "B"]): assert file_output[i] == line assert list_output[i] == line assert text_output[i] == line