from __future__ import absolute_import, division, print_function from iotbx.shelx import hklf from cctbx.array_family import flex from libtbx.test_utils import Exception_not_expected, approx_equal from libtbx.test_utils import Exception_expected, show_diff from six.moves import cStringIO as StringIO def exercise_hklf_reader(): s = (' 1 2 -1 -23.34 4.56 1\n' ' 2 -3 9 12.45 6.12 2\r\n' '99999999999999999.9999999.999999\n' '-999-999-999-9999.99-9999.99-999\r\n' ' 0 0 0 0.00 0.00 0\n') r = hklf.reader(file_object=StringIO(s)) assert list(r.indices()) == [ (1, 2, -1), (2, -3, 9), (9999, 9999, 9999), (-999, -999, -999), ] assert approx_equal(r.data(), [-23.34, 12.45, 99999.99, -9999.99, ]) assert approx_equal(r.sigmas(), [4.56, 6.12, 99999.99, -9999.99, ]) assert approx_equal(r.batch_numbers(), [1, 2, 9999, -999, ]) assert approx_equal(r.alphas(), [1, 2, 9999, -999, ]) for ma in r.as_miller_arrays(): assert ma.indices().all_eq(r.indices()) assert ma.anomalous_flag() is False ma = r.as_miller_arrays()[0] assert ma.data().all_approx_equal(r.data()) assert ma.sigmas().all_approx_equal(r.sigmas()) ma = r.as_miller_arrays()[1] assert ma.data().all_eq(r.alphas()) assert ma.sigmas() is None s = (' 0 2 3 1816.00 20.00\n' ' 0 2 415508.00 138.00\n' ' 0 2 5 4776.00 40.00\n') r = hklf.reader(file_object=StringIO(s)) assert list(r.indices()) == [ (0,2,3), (0,2,4), (0,2,5) ] assert r.batch_numbers() is None assert r.alphas() is None assert r.wavelengths() is None for end_line in (True, False): for something_after_end_line in (True, False): s = (' 1 2 -1 23.34 4.56\n' ' 2 -3 9 12.45 6.12\r\n' '99999999999999999.9999999.99\n' '-999-999-999-9999.99-9999.99\n') if end_line: s += ' 0 0 0 0.00 0.00\n' if something_after_end_line: s += ' -5 1 0 123.45 66.12\n' s = (s) r = hklf.reader(file_object=StringIO(s)) assert approx_equal(r.sigmas(), [4.56, 6.12, 99999.99, -9999.99, ]) assert r.batch_numbers() is None assert r.alphas() is None assert r.wavelengths() is None s = '' try: r = hklf.reader(file_object=StringIO(s)) except RuntimeError: pass else: raise Exception_expected s = (' 1 2 -1 23.34 4.56 1\n' ' 2 -3 a9 12.45 6.12 2\n' ' 0 0 0 0.00 0.00 0\n') try: r = hklf.reader(file_object=StringIO(s)) except Exception: pass else: raise Exception_expected s = (' 1 2 -1 23.34 4.56 1 45.36\n' ' 2 -3 9 -12.45 -6.12 2 54.63\n' ' 0 0 0 0.00 0.00 0 0\n') r = hklf.reader(file_object=StringIO(s)) assert list(r.indices()) == [ (1, 2, -1), (2, -3, 9)] assert approx_equal(r.data(), [23.34, -12.45]) assert approx_equal(r.sigmas(), [4.56, -6.12]) assert approx_equal(r.batch_numbers(), [1, 2]) assert approx_equal(r.wavelengths(), [45.36, 54.63]) s = (' 1 2 -1 23. 4. 2\n' ' -2 1 3 -1. 3. 1\n' ' 0 0 0 0. 0. 0\n') r = hklf.reader(file_object=StringIO(s)) assert list(r.indices()) == [(1, 2, -1), (-2, 1, 3)] assert approx_equal(r.data(), [23, -1]) assert approx_equal(r.sigmas(), [4, 3]) assert approx_equal(r.alphas(), [2, 1]) assert r.wavelengths() is None s = (' 3 2 -1 32. 5.\n' ' 0 0 0\n') r = hklf.reader(file_object=StringIO(s)) assert list(r.indices()) == [(3, 2, -1)] assert approx_equal(r.data(), [32]) assert approx_equal(r.sigmas(), [5]) assert r.alphas() is None assert r.wavelengths() is None s = ( """King Arthur: [after Arthur's cut off both of the Black Knight's arms] Look, you stupid Bastard. You've got no arms left. Black Knight: Yes I have. King Arthur: *Look*! Black Knight: It's just a flesh wound.""") try: r = hklf.reader(file_object=StringIO(s)) except RuntimeError: pass else: raise Exception_expected def exercise_miller_export_as_shelx_hklf(): s = """\ 1 2 -1 23.34 4.56 2 -3 9 12.45 6.12 99999999999999999.9999999.99 -999-999-999-9999.99-9999.99 3 4 5999999.99999999. 3 4 5-99999.9-999999. """ ma = hklf.reader(file_object=StringIO(s)).as_miller_arrays()[0] sio = StringIO() ma.export_as_shelx_hklf(file_object=sio) ma2 = hklf.reader(file_object=StringIO(sio.getvalue())).as_miller_arrays()[0] assert approx_equal(ma.indices(), ma2.indices()) assert approx_equal(ma.data(), ma2.data()) assert approx_equal(ma.sigmas(), ma2.sigmas()) assert ma.anomalous_flag() is False assert ma2.anomalous_flag() is False # ma = ma.select(flex.size_t([0])) def check(d, s, f, exception_expected=True): if (s is not None): s = flex.double([s]) ma2 = ma.array(data=flex.double([d]), sigmas=s) sio = StringIO() ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True) assert not show_diff(sio.getvalue(), """\ 1 2 -1%s 0 0 0 0.00 0.00 """ % f) if exception_expected: try: ma2.export_as_shelx_hklf(sio) except RuntimeError: pass else: raise Exception_expected else: try: ma2.export_as_shelx_hklf(sio) except RuntimeError: raise Exception_not_expected check(-12345678, 1, "-999999. 0.08") check(-12345678, None, "-999999. 0.00") check(2, -12345678, " 0.16-999999.") # Should negative sigma be allowed? check(123456789, 30, "9999999. 2.43") check(123456789, None, "9999999. 0.00") check(40, 123456789, " 3.249999999.") check(-23456789, 123456789, "-999999.5263153.") check(123456789, -23456789, "5263153.-999999.") # Numbers that would be formatted as integers should end with "." check(-123456, 1, "-123456. 1.00", exception_expected=False) check(1234567, 10, "1234567. 10.00", exception_expected=False) # ma = hklf.reader(file_object=StringIO(s)).as_miller_arrays()[0] ma = ma.select(flex.size_t([0,1])) ma2 = ma.array(data=flex.double([123456789, -23456789])) sio = StringIO() ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True) assert not show_diff(sio.getvalue(), """\ 1 2 -15263153. 0.00 2 -3 9-999999. 0.00 0 0 0 0.00 0.00 """) ma2 = ma.array(data=flex.double([-23456789, 823456789])) sio = StringIO() ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True) assert not show_diff(sio.getvalue(), """\ 1 2 -1-284858. 0.00 2 -3 99999999. 0.00 0 0 0 0.00 0.00 """) # Test that setting the scale range works. ma2.export_as_shelx_hklf( sio, scale_range=(-9999., 9999.), normalise_if_format_overflow=True) # Test that ignoring the scale range and normalising out-of-range values anyway works. ma2.export_as_shelx_hklf(sio, full_dynamic_range=True) def run(): exercise_hklf_reader() exercise_miller_export_as_shelx_hklf() print("OK") if __name__ == '__main__': run()