def run_process(self, iterable):
# Create ExperimentList objects from image paths (doing it in the processor
# because I can't have Python objects in the INFO JSON file)
adj_iterable = []
imageseq = None
crystal = None
for entry in iterable:
path = str(entry[1])
if path.endswith('.h5'):
exp_idx = entry[0]
img_idx = entry[2]
if imageseq is None:
exps = ExLF.from_filenames(filenames=[path])
imageseq = exps.imagesets()[0]
crystal = exps[0].crystal
one_image = imageseq.partial_set(img_idx, img_idx + 1)
one_exp = ExLF.from_imageset_and_crystal(imageset=one_image,
crystal=crystal)
adj_iterable.append([exp_idx, path, img_idx, one_exp])
else:
# Create ExperimentList object from CBF
expr = ExLF.from_filenames(filenames=[path])
exp_entry = [entry[0], entry[1], 0, expr]
adj_iterable.append(exp_entry)
# Run a multiprocessing job
img_objects = parallel_map(iterable=adj_iterable,
func=self.import_and_process,
callback=self.callback,
processes=self.params.mp.n_processors)
return img_objects
def test_no_abs_via_scheme(registry, monkeypatch):
# Tries to construct these and relies on pickleable
monkeypatch.setattr(dxtbx.imageset, "ImageSetData", Mock())
monkeypatch.setattr(dxtbx.imageset, "ImageSet", Mock())
_hits = []
class SufficientError(Exception):
"""Stop when we've reached the test point"""
class SchemeHandler(Format):
schemes = ["scheme"]
@classmethod
def understand(cls, endpoint):
return True
def _start(self):
assert self._image_file == "scheme://something"
_hits.append(self._image_file)
# The second reconstruction call had the issue
if len(_hits) == 2:
raise SufficientError
registry.register(SchemeHandler)
with pytest.raises(SufficientError):
# We don't want to try doing everything here, just check construction
ExperimentListFactory.from_filenames(["scheme://something"])
assert _hits == ["scheme://something", "scheme://something"]
def make_experiments(filename, data=None):
# make experiments
e_start = time.time()
if data:
FormatEigerStream.injected_data = data
experiments = ExperimentListFactory.from_filenames([filename])
else:
experiments = ExperimentListFactory.from_filenames([filename])
e_time = time.time() - e_start
return experiments, e_time
def test_load_models(dials_regression):
pytest.importorskip("h5py")
filename = os.path.join(
dials_regression,
"image_examples",
"SACLA_MPCCD_Cheetah",
"run266702-0-subset.h5",
)
# Test different ways of loading the data
waves1, waves2, waves3, waves4, waves5 = [], [], [], [], []
oris1, oris2, oris3, oris4, oris5 = [], [], [], [], []
img = dxtbx.load(filename)
# Test using dxtbx directly
for i in range(img.get_num_images()):
waves1.append(img.get_beam(i).get_wavelength())
oris1.append(img.get_detector(i)[0].get_origin())
# Test using the imageset clases
imageset = img.get_imageset(filename)
for i in range(len(imageset)):
waves2.append(imageset.get_beam(i).get_wavelength())
oris2.append(imageset.get_detector(i)[0].get_origin())
# Test using imageset subsets
imageset = img.get_imageset(filename)
for i in range(len(imageset)):
subset = imageset[i:i + 1]
waves3.append(subset.get_beam(0).get_wavelength())
oris3.append(subset.get_detector(0)[0].get_origin())
# Test using pre-loaded experiments
experiments = ExperimentListFactory.from_filenames([filename])
for experiment in experiments:
waves4.append(experiment.beam.get_wavelength())
oris4.append(experiment.detector[0].get_origin())
# Test using post-loaded experiments
experiments = ExperimentListFactory.from_filenames([filename],
load_models=False)
for experiment in experiments:
assert experiment.beam is None and experiment.detector is None
experiment.load_models()
waves5.append(experiment.beam.get_wavelength())
oris5.append(experiment.detector[0].get_origin())
for w1, w2, w3, w4, w5 in zip(waves1, waves2, waves3, waves4, waves5):
assert w1 == w2 == w3 == w4 == w5
for o1, o2, o3, o4, o5 in zip(oris1, oris2, oris3, oris4, oris5):
assert o1 == o2 == o3 == o4 == o5
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_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_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_dlsnxs2cbf(dials_data, tmp_path):
screen = dials_data("thaumatin_eiger_screen")
master = screen.join("Therm_6_1_master.h5")
result = procrunner.run(["dxtbx.dlsnxs2cbf", master, "junk_%04d.cbf"],
working_directory=tmp_path)
assert not result.returncode and not result.stderr
output_files = ["junk_%04d.cbf" % j for j in (1, 2, 3)]
for file in output_files:
assert file.encode("latin-1") in result.stdout
assert tmp_path.joinpath(file).is_file()
expts = ExperimentListFactory.from_filenames(
str(tmp_path / file) for file in output_files)
assert all(imgset.get_format_class() == FormatCBFMiniEigerDLS16MSN160
for imgset in expts.imagesets())
with h5py.File(master) as fh:
for i, imgset in enumerate(expts.imagesets()):
original = fh["/entry/data/data_000001"][i][()]
sel = np.where(original < original.max())
np.testing.assert_equal(
fh["/entry/data/data_000001"][i][sel],
imgset.get_raw_data(0)[0].as_numpy_array()[sel],
)
def test_vmxi_thaumatin(dials_data):
master_h5 = dials_data("vmxi_thaumatin") / "image_15799_master.h5"
expts = ExperimentListFactory.from_filenames([master_h5.strpath])
to_xds = xds.to_xds(expts[0].imageset)
s = to_xds.XDS_INP()
assert "DETECTOR=EIGER" in s
assert "SENSOR_THICKNESS= 0.450" in s
def test_experimentlist_imagesequence_stills(dials_data):
filenames = [
str(dials_data("thaumatin_grid_scan") / f"thau_3_2_{i:04d}.cbf.bz2")
for i in range(1, 4)
]
experiments = ExperimentListFactory.from_filenames(filenames)
assert len(experiments) == 3
assert len(experiments.imagesets()) == 1
# Convert experiment list to dict
d = experiments.to_dict()
# Decode the dict to get a new experiment list
experiments2 = ExperimentListDict(d).decode()
# Verify that this experiment is as we expect
assert len(experiments2) == 3
assert len(experiments2.imagesets()) == 1
assert len(experiments2.goniometers()) == 1
assert len(experiments2.detectors()) == 1
assert len(experiments2.beams()) == 1
assert len(experiments2.scans()) == 3
for expt in experiments2:
assert expt.imageset is experiments2.imagesets()[0]
def test_experimentlist_imagesequence_stills():
filenames = [
"/Users/rjgildea/tmp/118/Puck3_10_1_000%i.cbf.gz" % i
for i in range(1, 4)
]
for f in filenames:
if not os.path.exists(f):
pytest.skip("%s does not exist" % f)
experiments = ExperimentListFactory.from_filenames(filenames)
assert len(experiments) == 3
assert len(experiments.imagesets()) == 1
# Convert experiment list to dict
d = experiments.to_dict()
# Decode the dict to get a new experiment list
experiments2 = ExperimentListDict(d).decode()
# Verify that this experiment is as we expect
assert len(experiments2) == 3
assert len(experiments2.imagesets()) == 1
assert len(experiments2.goniometers()) == 1
assert len(experiments2.detectors()) == 1
assert len(experiments2.beams()) == 1
assert len(experiments2.scans()) == 3
for expt in experiments2:
assert expt.imageset is experiments2.imagesets()[0]
def test_spring8_ccp4_2018_zenodo_1443110_data03():
# https://zenodo.org/record/1443110#.XD8bD5ynzmE
master_h5 = "/dls/mx-scratch/rjgildea/zenodo/spring8-ccp4-2018/1443110/ccp4school2018_bl41xu/05/data03/data03_master.h5"
assert FormatHDF5EigerNearlyNexusSPring8.understand(master_h5)
expts = ExperimentListFactory.from_filenames([master_h5])
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatHDF5EigerNearlyNexusSPring8
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() == (4150, 4371)
assert panel.get_trusted_range() == (-1, 2.094707e06)
assert panel.get_fast_axis() == (1, 0, 0)
assert panel.get_slow_axis() == (0, -1, 0)
assert panel.get_origin() == pytest.approx((-151.939, 169.629, -180),
abs=1e-3)
assert panel.get_distance() == pytest.approx(180)
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((-10, 1))
assert scan.get_image_range() == (1, 180)
assert beam.get_wavelength() == pytest.approx(1.28241, abs=1e-5)
assert beam.get_s0() == pytest.approx((0, 0, -1 / beam.get_wavelength()))
def _extract_or_read_imagesets(params):
"""
Return a list of ImageSets, importing them via alternative means if necessary.
The "Alternative Means" means via params.input.template or .directory,
if the images to import haven't been specified directly.
Args:
params: The phil.scope_extract from dials.import
Returns: A list of ImageSet objects
"""
# Get the experiments
experiments = flatten_experiments(params.input.experiments)
# Check we have some filenames
if len(experiments) == 0:
# FIXME Should probably make this smarter since it requires editing here
# and in dials.import phil scope
try:
format_kwargs = {
"dynamic_shadowing": params.format.dynamic_shadowing,
"multi_panel": params.format.multi_panel,
}
except AttributeError:
format_kwargs = None
# Check if a template has been set and print help if not, otherwise try to
# import the images based on the template input
if len(params.input.template) > 0:
importer = ExperimentListTemplateImporter(
params.input.template,
image_range=params.geometry.scan.image_range,
format_kwargs=format_kwargs,
)
experiments = importer.experiments
if len(experiments) == 0:
raise Sorry("No experiments found matching template %s" %
params.input.experiments)
elif len(params.input.directory) > 0:
experiments = ExperimentListFactory.from_filenames(
params.input.directory, format_kwargs=format_kwargs)
if len(experiments) == 0:
raise Sorry("No experiments found in directories %s" %
params.input.directory)
else:
raise Sorry("No experiments found")
# TODO (Nick): This looks redundant as the experiments are immediately discarded.
# verify this, and remove if it is.
if params.identifier_type:
generate_experiment_identifiers(experiments, params.identifier_type)
# Get a list of all imagesets
imageset_list = experiments.imagesets()
# Return the experiments
return imageset_list
def test_DLS_I03_smargon(dials_data, tmpdir):
filename_gz = (dials_data("image_examples").join(
"DLS_I03_smargon_0001.cbf.gz").strpath)
# The need to manually extract the file will be removed by
# https://github.com/cctbx/dxtbx/pull/80
filename = tmpdir.join(os.path.split(filename_gz[:-3])[-1]).strpath
with open(filename, "wb") as f:
with gzip.open(filename_gz, "rb") as fgz:
f.write(fgz.read())
assert FormatCBFFullPilatusDLS6MSN126.understand(filename)
expts = ExperimentListFactory.from_filenames(
[filename], format_kwargs={"dynamic_shadowing": True})
assert len(expts) == 1
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatCBFFullPilatusDLS6MSN126
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, 0.0, 0.0, 0.0, 0.0, -1.0, 1.0, 0.0, 0.0])
assert list(gonio.get_names()) == ["GON_PHI", "GON_CHI", "GON_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
assert masker.get_mask(imageset.get_detector(),
100)[0].count(False) == 261588
def do_import(filename, load_models=True):
logger.info("Loading %s" % os.path.basename(filename))
experiments = ExperimentListFactory.from_filenames([filename],
load_models=False)
if len(experiments) == 0:
try:
experiments = ExperimentListFactory.from_json_file(filename)
except ValueError:
raise Abort("Could not load %s" % filename)
if len(experiments) == 0:
raise Abort("Could not load %s" % filename)
from dxtbx.imageset import ImageSetFactory
for experiment in experiments:
if load_models:
experiment.load_models()
imageset = ImageSetFactory.imageset_from_anyset(experiment.imageset)
imageset.set_scan(None)
imageset.set_goniometer(None)
experiment.imageset = imageset
experiment.scan = None
experiment.goniometer = None
return experiments
def test_create_multiple_blocks(multiple_block_filenames):
experiments = ExperimentListFactory.from_filenames(
multiple_block_filenames)
assert len(experiments) == 24
imagesets = experiments.imagesets()
assert len(imagesets) == 24
assert [len(im) for im in imagesets] == [9] + [1] * 23
def test_VMXi_rotation_scan():
master_h5 = "/dls/mx/data/mx21314/mx21314-27/VMXi-AB0816/well_7/images/image_14364_master.h5"
assert FormatNexus.understand(master_h5)
expts = ExperimentListFactory.from_filenames([master_h5])
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatNexus
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() == (2068, 2162)
assert panel.get_trusted_range() == (-1, 4096)
assert panel.get_fast_axis() == (1, 0, 0)
assert panel.get_slow_axis() == (0, -1, 0)
assert panel.get_origin() == pytest.approx(
(-78.05999999999999, 87.03, -194.5039999999999))
assert panel.get_distance() == pytest.approx(194.504)
assert isinstance(gonio, Goniometer)
assert gonio.get_rotation_axis() == (0, 1, 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((-30, 0.1))
assert scan.get_image_range() == (1, 600)
assert beam.get_wavelength() == pytest.approx(0.979492)
assert beam.get_s0() == pytest.approx((0, 0, -1 / beam.get_wavelength()))
def test_multi_panel(dials_data, tmpdir):
filename = dials_data("x4wide") / "X4_wide_M1S4_2_0001.cbf"
assert FormatCBFMiniPilatus.understand(filename.strpath)
expts = ExperimentListFactory.from_filenames(
[filename.strpath], format_kwargs={"multi_panel": True})
assert len(expts) == 1
assert len(expts[0].detector) == 60
assert len(expts[0].imageset.get_raw_data(0)) == 60
expected_xoffset = [-212.47848, -127.51048, -42.54248, 42.42552, 127.39352]
expected_yoffset = [
220.00176,
183.53776,
147.07376,
110.60976,
74.14576,
37.68176,
1.21776,
-35.24624,
-71.71024,
-108.17424,
-144.63824,
-181.10224,
]
for i, p in enumerate(expts[0].detector):
assert p.get_image_size() == (487, 195)
origin = p.get_origin()
assert origin[0] == pytest.approx(expected_xoffset[i % 5])
assert origin[1] == pytest.approx(expected_yoffset[i // 5])
assert origin[2] == pytest.approx(-190.18)
def test_dynamic_shadowing(path, count_only_shadow, count_mask_shadow,
count_mask_no_shadow, dials_regression):
path = os.path.join(dials_regression, path)
assert os.path.exists(path), path
for shadowing in (libtbx.Auto, True, False):
format_kwargs = {"dynamic_shadowing": shadowing}
experiments = ExperimentListFactory.from_filenames(
[path], format_kwargs=format_kwargs)
imageset = experiments.imagesets()[0]
detector = imageset.get_detector()
scan = imageset.get_scan()
masker = imageset.masker()
if shadowing is not False:
assert masker is not None
mask = masker.get_mask(detector, scan.get_oscillation()[0])
assert len(mask) == len(detector)
# only shadowed pixels masked
assert mask[0].count(False) == count_only_shadow, (
mask[0].count(False),
count_only_shadow,
)
mask = imageset.get_mask(0)
# dead pixels, pixels in gaps, etc also masked
if shadowing is libtbx.Auto or shadowing is True:
assert mask[0].count(False) == count_mask_shadow, (
mask[0].count(False),
count_mask_shadow,
)
else:
assert mask[0].count(False) == count_mask_no_shadow, (
mask[0].count(False),
count_mask_no_shadow,
)
def run(args=None):
args = args or sys.argv[1:]
user_phil = []
files = []
for arg in args:
if os.path.isfile(arg):
files.append(arg)
else:
try:
user_phil.append(parse(arg))
except Exception:
raise Sorry("Unrecognized argument %s" % arg)
params = phil_scope.fetch(sources=user_phil).extract()
fig = plt.figure()
colormap = plt.cm.gist_ncar
colors = [colormap(i) for i in np.linspace(0, 0.9, len(files))]
for file_name, color in zip(files, colors):
# read the data and get the detector models
try:
datablocks = DataBlockFactory.from_json_file(file_name,
check_format=False)
detectors = sum((db.unique_detectors() for db in datablocks), [])
except Exception:
try:
experiments = ExperimentListFactory.from_json_file(
file_name, check_format=False)
except ValueError:
experiments = ExperimentListFactory.from_filenames([file_name])
detectors = experiments.detectors()
if not params.plot_all_detectors:
detectors = detectors[0:1]
for detector in detectors:
# plot the hierarchy
if params.orthographic:
ax = fig.gca()
else:
ax = fig.gca(projection="3d")
plot_group(
detector.hierarchy(),
color,
ax,
orthographic=params.orthographic,
show_origin_vectors=params.show_origin_vectors,
panel_numbers=params.panel_numbers,
)
plt.xlabel("x")
plt.ylabel("y")
if params.orthographic:
plt.axes().set_aspect("equal", "datalim")
if params.pdf_file:
pp = PdfPages(params.pdf_file)
for i in plt.get_fignums():
pp.savefig(plt.figure(i))
pp.close()
else:
plt.show()
def test_MPCCD_RECONST_MODE(dials_data, monkeypatch):
for MPCCD_RECONST_MODE in (0, 1):
if MPCCD_RECONST_MODE:
monkeypatch.setenv("MPCCD_RECONST_MODE", str(MPCCD_RECONST_MODE))
else:
monkeypatch.delenv("MPCCD_RECONST_MODE", raising=False)
master_h5 = (dials_data("image_examples").join(
"SACLA-MPCCD-Phase3-21528-5images.h5").strpath)
expts = ExperimentListFactory.from_filenames([master_h5])
imageset = expts[0].imageset
# Horrible hack to work around format_instance caching
imageset.reader().nullify_format_instance()
raw_data = imageset.get_raw_data(0)
mmm = raw_data[0].as_double().as_1d().min_max_mean()
mmm.show()
if MPCCD_RECONST_MODE:
assert mmm.min == -1
assert mmm.max == 14102
assert mmm.mean == pytest.approx(2.93752665030144)
else:
assert mmm.min == 0
assert mmm.max == 3610.0
assert mmm.mean == pytest.approx(3.397266387939453)
# Horrible hack to work around format_instance caching
# This is needed to prevent an incorrect format_instance affecting
# other tests that are run after this one.
imageset.reader().nullify_format_instance()
def test_HDF5_format_caching(dials_data, clear_cache):
"""
xfail: see https://github.com/cctbx/dxtbx/issues/245
"""
img_file = "SACLA-MPCCD-Phase3-21528-5images.h5"
master_h5 = dials_data("image_examples").join(img_file).strpath
expts1 = ExperimentListFactory.from_filenames([master_h5])
expts1[0].imageset.get_mask(0)
if clear_cache:
expts1[0].imageset.reader().nullify_format_instance()
expts2 = ExperimentListFactory.from_filenames([master_h5])
for e1, e2 in zip(expts1, expts2):
assert (e1.imageset.get_beam().get_wavelength() ==
e2.imageset.get_beam().get_wavelength())
def test_MPCCD_Phase3_21528(dials_data):
master_h5 = (dials_data("image_examples").join(
"SACLA-MPCCD-Phase3-21528-5images.h5").strpath)
assert FormatHDF5SaclaMPCCD.understand(master_h5)
expts = ExperimentListFactory.from_filenames([master_h5])
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatHDF5SaclaMPCCD
detector = imageset.get_detector()
beam = imageset.get_beam()
assert len(detector) == 8
panel = detector[0]
assert panel.get_pixel_size() == pytest.approx((0.05, 0.05))
assert panel.get_image_size() == (512, 1024)
assert panel.get_trusted_range() == (-1.0, 65535.0)
assert panel.get_fast_axis() == pytest.approx(
(-0.0026929852392799875, -0.9999963739086762, 0.0))
assert panel.get_slow_axis() == pytest.approx(
(-0.9999963739086762, 0.0026929852392799875, 0.0))
assert panel.get_thickness() == pytest.approx(0.3)
assert panel.get_mu() == 0
assert panel.get_material() == ""
assert panel.get_origin() == pytest.approx(
(-1.8203499755859376, 51.6243984375, -99.5))
assert panel.get_distance() == pytest.approx(99.5)
assert imageset.get_goniometer() is None
assert imageset.get_scan() is None
assert beam.get_wavelength() == pytest.approx(1.2452863763694901)
assert beam.get_sample_to_source_direction() == (0, 0, 1)
imageset.reader().nullify_format_instance()
def test_spring8_ccp4_2018_zenodo_1443110_data03(dials_data):
master_h5 = (dials_data("spring8_ccp4_2018").join(
"ccp4school2018_bl41xu", "05", "data03", "data03_master.h5").strpath)
assert FormatHDF5EigerNearlyNexusSPring8.understand(master_h5)
expts = ExperimentListFactory.from_filenames([master_h5])
imageset = expts[0].imageset
assert imageset.get_format_class() == FormatHDF5EigerNearlyNexusSPring8
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() == (4150, 4371)
assert panel.get_trusted_range() == (-1, 2.094707e06)
assert panel.get_fast_axis() == (1, 0, 0)
assert panel.get_slow_axis() == (0, -1, 0)
assert panel.get_origin() == pytest.approx((-151.939, 169.629, -180),
abs=1e-3)
assert panel.get_distance() == pytest.approx(180)
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((-10, 1))
assert scan.get_image_range() == (1, 180)
assert beam.get_wavelength() == pytest.approx(1.28241, abs=1e-5)
assert beam.get_s0() == pytest.approx((0, 0, -1 / beam.get_wavelength()))
def test_create_single_sequence(single_sequence_filenames):
experiments = ExperimentListFactory.from_filenames(
single_sequence_filenames)
assert len(experiments) == 1
imagesets = experiments.imagesets()
assert imagesets[0].get_format_class()
assert len(imagesets) == 1
assert len(imagesets[0]) == 9
def test_slice_experiments_centroid_test_data(dials_data):
files = dials_data("centroid_test_data").listdir("*.cbf", sort=True)
experiments = ExperimentListFactory.from_filenames(f.strpath for f in files)
sliced_image_range = [(1, 3)]
sliced_experiments = slice_experiments(experiments, sliced_image_range)
assert sliced_experiments[0].scan.get_image_range() == sliced_image_range[0]
# for some reason the sliced_experiments is not copyable
assert copy.deepcopy(sliced_experiments)
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 run_process(self, iterable):
# Create ExperimentList objects from image paths (doing it in the processor
# because I can't have Python objects in the INFO JSON file)
adj_iterable = []
crystal = None
for entry in iterable:
path = str(entry[1])
if path.endswith(".h5"):
exp_idx = entry[0]
img_idx = entry[2]
# Generate a list of single images if at img_idx = 0
if img_idx == 0:
imageseqs = []
exps = ExLF.from_filenames(filenames=[path])
crystal = exps[0].crystal
# flatten all imagesets into a single imagesequence
for iset in exps.imagesets():
if iset.size() == 1:
imageseqs.append(iset)
else:
for i in range(iset.size()):
one_image = imageseq.partial_set(i, i + 1)
imageseqs.append(i)
# Create ExperimentList object from extracted imageset
current_image = imageseqs[img_idx]
one_exp = ExLF.from_imageset_and_crystal(
imageset=current_image, crystal=crystal
)
adj_iterable.append([exp_idx, path, img_idx, one_exp])
else:
# Create ExperimentList object from CBF
expr = ExLF.from_filenames(filenames=[path])
exp_entry = [entry[0], entry[1], 0, expr]
adj_iterable.append(exp_entry)
# Run a multiprocessing job
img_objects = parallel_map(
iterable=adj_iterable,
func=self.import_and_process,
callback=self.callback,
processes=self.params.mp.n_processors,
)
return img_objects
def test_slice_experiments_centroid_test_data_starting_from_2(dials_data):
files = dials_data("centroid_test_data").listdir("*.cbf", sort=True)[1:]
experiments = ExperimentListFactory.from_filenames(f.strpath
for f in files)
sliced_image_range = [(2, 4)]
sliced_experiments = slice_experiments(experiments, sliced_image_range)
assert sliced_experiments[0].scan.get_image_range(
) == sliced_image_range[0]
def test_single_panel(dials_data, tmpdir):
filename = dials_data("x4wide") / "X4_wide_M1S4_2_0001.cbf"
assert FormatCBFMiniPilatus.understand(filename.strpath)
expts = ExperimentListFactory.from_filenames([filename.strpath])
assert len(expts) == 1
assert len(expts[0].detector) == 1
assert len(expts[0].imageset.get_raw_data(0)) == 1
