def understand(image_file):
is_nexus = FormatHDF5EigerNearlyNexus.understand(image_file)
if not is_nexus:
return False
# Get the file handle
with h5py.File(image_file, "r") as handle:
if "/entry/instrument/detector/detector_number" in handle and handle[
"/entry/instrument/detector/detector_number"][()] in [
b"E-32-0114", b"E-32-0112", b"E-18-0103"
]:
return True
return False
def test_semi_synthetic_dectris_eiger_nearly_nexus(dials_data, tmpdir):
master_h5 = dials_data("image_examples").join(
"dectris_eiger_master.h5").strpath
if not os.access(master_h5, os.R_OK):
pytest.skip("Test images not available")
assert FormatHDF5EigerNearlyNexus.understand(master_h5)
expts = ExperimentListFactory.from_filenames([master_h5])
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatHDF5EigerNearlyNexus
image = imageset.get_raw_data(0)[0]
assert min(image) == 0
assert max(image) == 65535
detector = imageset.get_detector()
gonio = imageset.get_goniometer()
scan = imageset.get_scan()
beam = imageset.get_beam()
panel = detector[0]
assert panel.get_pixel_size() == pytest.approx((0.075, 0.075))
assert panel.get_image_size() == (3110, 3269)
assert panel.get_trusted_range() == (-1, 12440)
assert panel.get_fast_axis() == (1, 0, 0)
assert panel.get_slow_axis() == (0, -1, 0)
assert panel.get_thickness() == pytest.approx(0.45)
assert panel.get_mu() == pytest.approx(3.96764, abs=1e-4)
assert panel.get_material() == "Si"
assert panel.get_origin() == pytest.approx((-120.556, 118.982, -134.255),
abs=1e-3)
assert panel.get_distance() == pytest.approx(134.255)
assert isinstance(gonio, Goniometer)
assert gonio.get_rotation_axis() == (1, 0, 0)
assert gonio.get_fixed_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert gonio.get_setting_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert scan.get_oscillation() == pytest.approx((0, 0))
assert scan.get_image_range() == (1, 1)
assert beam.get_wavelength() == pytest.approx(0.980112, abs=1e-5)
assert beam.get_s0() == pytest.approx((0, 0, -1 / beam.get_wavelength()))
def test_biomax_vertical_goniometer_at_diamond(tmpdir):
master_h5 = (
"/dls/science/groups/scisoft/DIALS/"
"regression-test-data/biomax-eiger-moche/tau1-tau_1_master.h5")
if not os.access(master_h5, os.R_OK):
pytest.skip("Test data not available")
assert FormatHDF5EigerNearlyNexus.understand(master_h5)
expts = ExperimentListFactory.from_filenames([master_h5])
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatHDF5EigerNearlyNexus
gonio = imageset.get_goniometer()
assert isinstance(gonio, Goniometer)
assert gonio.get_rotation_axis() == (0, 1, 0)
def test_soleil_Proxima2A_zenodo_1443110_data03():
# https://zenodo.org/record/1221344#.XEHr_5ynx2Q
master_h5 = "/dls/mx-scratch/rjgildea/zenodo/1221344/200Hz/3_5_200Hz_1_master.h5"
if not os.access(master_h5, os.R_OK):
pytest.skip("Test images not available")
assert FormatHDF5EigerNearlyNexus.understand(master_h5)
expts = ExperimentListFactory.from_filenames([master_h5])
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatHDF5EigerNearlyNexus
detector = imageset.get_detector()
gonio = imageset.get_goniometer()
scan = imageset.get_scan()
beam = imageset.get_beam()
panel = detector[0]
assert panel.get_pixel_size() == pytest.approx((0.075, 0.075))
assert panel.get_image_size() == (3110, 3269)
assert panel.get_trusted_range() == (-1, 12440)
assert panel.get_fast_axis() == (1, 0, 0)
assert panel.get_slow_axis() == (0, -1, 0)
assert panel.get_thickness() == pytest.approx(0.45)
assert panel.get_mu() == pytest.approx(3.96763)
assert panel.get_material() == "Si"
assert panel.get_origin() == pytest.approx((-120.556, 118.982, -134.255),
abs=1e-3)
assert panel.get_distance() == pytest.approx(134.255)
assert isinstance(gonio, Goniometer)
assert gonio.get_rotation_axis() == (1, 0, 0)
assert gonio.get_fixed_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert gonio.get_setting_rotation() == (1, 0, 0, 0, 1, 0, 0, 0, 1)
assert scan.get_oscillation() == pytest.approx((0, 0.5))
assert scan.get_image_range() == (1, 800)
assert beam.get_wavelength() == pytest.approx(0.980112, abs=1e-5)
assert beam.get_s0() == pytest.approx((0, 0, -1 / beam.get_wavelength()))