def test_rotation_scan_i04(master_h5):
assert FormatNexusEigerDLS16M.understand(master_h5)
expts = ExperimentListFactory.from_filenames(
[master_h5], format_kwargs={"dynamic_shadowing": True})
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatNexusEigerDLS16M
detector = imageset.get_detector()
gonio = imageset.get_goniometer()
scan = imageset.get_scan()
beam = imageset.get_beam()
panel = detector[0]
assert panel.get_pixel_size() == (0.075, 0.075)
assert panel.get_image_size() == (4148, 4362)
assert panel.get_trusted_range() == (-1, 65535)
assert panel.get_fast_axis() == (1, 0, 0)
assert panel.get_slow_axis() == (0, -1, 0)
assert panel.get_origin() == pytest.approx(
(-166.07661632390744, 172.5371934106162, -200.0))
assert panel.get_distance() == 200
assert len(gonio.get_axes()) == 3
expected_axes = ((1, 0, 0), (0, 0, -1), (1, 0, 0))
for a1, a2 in zip(gonio.get_axes(), expected_axes):
assert a1 == pytest.approx(a2, abs=5e-2)
assert gonio.get_scan_axis() == 2
assert scan.get_oscillation() == (0, 0.2)
assert scan.get_image_range() == (1, 900)
assert beam.get_wavelength() == pytest.approx(0.979499)
assert beam.get_s0() == pytest.approx((0, 0, -1 / beam.get_wavelength()))
def test_masked_i03_16bit(master_h5):
assert FormatNexusEigerDLS16M.understand(master_h5)
expts = ExperimentListFactory.from_filenames([master_h5])
imageset = expts[0].imageset
assert flex.min(imageset[0][0]) == -1.0
assert flex.max(imageset[0][0]) != 0xFFFF
def test_grid_scan_i04():
master_h5 = "/dls/i04/data/2019/cm23004-1/20190109/Eiger/grid/Thaum/Thau_5/Thau_5_1_master.h5"
assert FormatNexusEigerDLS16M.understand(master_h5)
expts = ExperimentListFactory.from_filenames([master_h5])
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatNexusEigerDLS16M
detector = imageset.get_detector()
gonio = imageset.get_goniometer()
scan = imageset.get_scan()
beam = imageset.get_beam()
panel = detector[0]
assert panel.get_pixel_size() == (0.075, 0.075)
assert panel.get_image_size() == (4148, 4362)
assert panel.get_trusted_range() == (-1, 65535)
assert panel.get_fast_axis() == (1, 0, 0)
assert panel.get_slow_axis() == (0, -1, 0)
assert panel.get_origin() == pytest.approx(
(-167.44717577120824, 172.46833023184868, -350.0))
assert panel.get_distance() == 350
assert len(gonio.get_axes()) == 3
expected_axes = ((1, 0, 0), (0, 0, -1), (1, 0, 0))
for a1, a2 in zip(gonio.get_axes(), expected_axes):
assert a1 == pytest.approx(a2, abs=5e-2)
# assert gonio.get_scan_axis() == 2
if scan:
osc = scan.get_oscillation()
assert osc[0] == osc[1]
assert beam.get_wavelength() == pytest.approx(0.979499)
assert beam.get_s0() == pytest.approx((0, 0, -1 / beam.get_wavelength()))
def test_units():
master_h5 = "/dls/i04/data/2019/cm23004-1/20190114/Eiger/grid/Se_Thaum/Se_Thaum_12/Se_Thaum_12_2_master.h5"
assert FormatNexusEigerDLS16M.understand(master_h5)
datablocks = DataBlockFactory.from_filenames([master_h5])
imageset = datablocks[0].extract_imagesets()[0]
assert imageset.get_format_class() == FormatNexusEigerDLS16M
detector = imageset.get_detector()
scan = imageset.get_scan()
beam = imageset.get_beam()
panel = detector[0]
assert panel.get_pixel_size() == (0.075, 0.075)
assert panel.get_fast_axis() == (1, 0, 0)
assert panel.get_slow_axis() == (0, -1, 0)
# XXX Need to check and update expected values here, however the ones
# dxtbx is currently generating from the file are very wrong
assert panel.get_origin() == pytest.approx(
(-167.35570274412459, 172.4729262553403, -339.9887931971389))
assert panel.get_distance() == pytest.approx(339.9887931971389)
assert scan is None
assert beam.get_wavelength() == pytest.approx(0.979499)
assert beam.get_s0() == pytest.approx((0, 0, -1 / beam.get_wavelength()))
assert panel.get_beam_centre_px(beam.get_s0()) == pytest.approx(
(2231.41, 2299.64))
def test_screening(dials_data):
master_h5 = dials_data("thaumatin_eiger_screen").join("Therm_6_1_master.h5").strpath
assert FormatNexusEigerDLS16M.understand(master_h5)
expts = ExperimentListFactory.from_filenames([master_h5])
assert len(expts) == 3
imagesets = expts[0].imageset
assert imagesets[0].get_format_class() == FormatNexusEigerDLS16M
def test_screening():
master_h5 = "/dls/i04/data/2019/cm23004-1/20190109/Eiger/gw-screen/Thaum/Thau_3/Thau_3_1_master.h5"
assert FormatNexusEigerDLS16M.understand(master_h5)
datablocks = DataBlockFactory.from_filenames([master_h5])
imagesets = datablocks[0].extract_imagesets()
assert len(imagesets) == 3
assert imagesets[0].get_format_class() == FormatNexusEigerDLS16M
def test_do_not_understand_i24(tmp_path):
nxs = tmp_path / "data.nxs"
with h5py.File(nxs, mode="w") as fh:
entry = fh.create_group("entry")
instrument = entry.create_group("instrument")
instrument.attrs["short_name"] = np.string_("DLS I24")
name = instrument.create_dataset(
"name", data=np.string_("DIAMOND BEAMLINE I24")
)
name.attrs["short_name"] = np.string_("DLS I24")
assert not FormatNexusEigerDLS16M.understand(nxs)
def test_understand_legacy(beamline, tmp_path):
# See https://jira.diamond.ac.uk/browse/MXGDA-3624
nxs = tmp_path / "data.nxs"
with h5py.File(nxs, mode="w") as fh:
entry = fh.create_group("entry")
instrument = entry.create_group("instrument")
instrument.attrs["short_name"] = np.string_(f"{beamline}")
name = instrument.create_dataset("name", data=np.string_(f"{beamline}"))
name.attrs["short_name"] = np.string_(f"{beamline}")
assert FormatNexusEigerDLS16M.understand(nxs)
assert FormatNexusEigerDLS.understand(nxs)
def test_rotation_scan_i03_2019_run_4(master_h5):
assert FormatNexusEigerDLS16M.understand(master_h5)
expts = ExperimentListFactory.from_filenames(
[master_h5], format_kwargs={"dynamic_shadowing": True})
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatNexusEigerDLS16M
gonio = imageset.get_goniometer()
assert list(gonio.get_angles()) == pytest.approx([45.0, 45.0, 45.0])
assert list(gonio.get_axes().as_double()) == pytest.approx(
[1.0, -0.0025, 0.0056, -0.006, -0.0264, -0.9996, 1.0, 0.0, 0.0])
assert list(gonio.get_names()) == ["phi", "chi", "omega"]
assert imageset.has_dynamic_mask()
masker = imageset.masker()
assert isinstance(masker, SmarGonShadowMasker)
assert masker.get_mask(imageset.get_detector(), 0)[0].count(False) == 0
masker.get_mask(imageset.get_detector(), 50)[0].count(False) == 486717
assert masker.get_mask(imageset.get_detector(),
100)[0].count(False) == 1092226
def test_do_not_understand_name_none(tmp_path):
nxs = tmp_path / "data.nxs"
with h5py.File(nxs, mode="w") as fh:
entry = fh.create_group("entry")
entry.create_group("instrument")
assert not FormatNexusEigerDLS16M.understand(nxs)