def test_experimentlist_dumper_dump_empty_sweep(tmpdir):
tmpdir.chdir()
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model import Crystal
from dxtbx.format.Format import Format
filenames = ["filename_%01d.cbf" % (i+1) for i in range(0, 2)]
imageset = Format.get_imageset(
filenames,
beam = Beam((1, 0, 0)),
detector = Detector(),
goniometer = Goniometer(),
scan = Scan((1,2), (0.0, 1.0)),
as_sweep=True)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
dump = ExperimentListDumper(experiments)
filename = 'temp.json'
dump.as_json(filename)
experiments2 = ExperimentListFactory.from_json_file(filename,
check_format=False)
check(experiments, experiments2)
def test_experimentlist_factory_from_datablock():
filenames = ["filename_%01d.cbf" % (i + 1) for i in range(0, 2)]
imageset = Format.get_imageset(
filenames,
beam=Beam(),
detector=Detector(),
goniometer=Goniometer(),
scan=Scan((1, 2), (0, 1)),
as_sequence=True,
)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
datablock = DataBlockFactory.from_imageset(imageset)
assert datablock[0].format_class()
experiments = ExperimentListFactory.from_datablock_and_crystal(
datablock, crystal)
assert len(experiments) == 1
assert experiments[0].imageset
assert experiments[0].beam
assert experiments[0].detector is not None
assert experiments[0].goniometer
assert experiments[0].scan
assert experiments[0].crystal
def test_experimentlist_factory_from_datablock():
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.datablock import DataBlockFactory
from dxtbx.model import Crystal
from dxtbx.format.Format import Format
filenames = ["filename_%01d.cbf" % (i+1) for i in range(0, 2)]
imageset = Format.get_imageset(
filenames,
beam = Beam(),
detector = Detector(),
goniometer = Goniometer(),
scan = Scan((1,2), (0,1)),
as_sweep=True)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
datablock = DataBlockFactory.from_imageset(imageset)
experiments = ExperimentListFactory.from_datablock_and_crystal(
datablock, crystal)
assert len(experiments) == 1
assert experiments[0].imageset is not None
assert experiments[0].beam is not None
assert experiments[0].detector is not None
assert experiments[0].goniometer is not None
assert experiments[0].scan is not None
assert experiments[0].crystal is not None
def tst_from_null_sweep(self):
from dxtbx.format.Format import Format
from dxtbx.imageset import ImageSweep
from dxtbx.model import Beam, Detector, Goniometer, Scan
filenames = ["template_%2d.cbf" % (i+1) for i in range(0, 10)]
sweep = Format.get_imageset(
filenames,
beam = Beam((0, 0, 1)),
detector = Detector(),
goniometer = Goniometer((1, 0, 0)),
scan = Scan((1, 10), (0, 0.1)))
# Create the datablock
datablock = DataBlockFactory.from_imageset(sweep)
assert(len(datablock) == 1)
datablock = datablock[0]
sweeps = datablock.extract_sweeps()
assert(len(sweeps) == 1)
assert(sweeps[0].get_beam() == sweep.get_beam())
assert(sweeps[0].get_detector() == sweep.get_detector())
assert(sweeps[0].get_goniometer() == sweep.get_goniometer())
assert(sweeps[0].get_scan() == sweep.get_scan())
print 'OK'
def tst_from_sweep(self):
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model import Crystal
from dxtbx.format.Format import Format
filenames = ["filename_%01d.cbf" % (i + 1) for i in range(0, 2)]
imageset = Format.get_imageset(filenames,
beam=Beam(),
detector=Detector(),
goniometer=Goniometer(),
scan=Scan((1, 2), (0, 1)),
as_sweep=True)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1),
space_group_symbol="P1")
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
assert (len(experiments) == 1)
assert (experiments[0].imageset is not None)
assert (experiments[0].beam is not None)
assert (experiments[0].detector is not None)
assert (experiments[0].goniometer is not None)
assert (experiments[0].scan is not None)
assert (experiments[0].crystal is not None)
print 'OK'
def test_experimentlist_to_datablock_imageset(dials_data):
filenames = [
str(f) for f in dials_data("thaumatin_grid_scan").listdir(
"thau_3_2_*.cbf.bz2")
]
imageset = Format.get_imageset(filenames, as_imageset=True)
expts = ExperimentListFactory.from_imageset_and_crystal(imageset,
crystal=None)
datablocks = expts.to_datablocks()
assert len(datablocks) == 1
assert datablocks[0].num_images() == len(expts) == len(imageset)
assert len(datablocks[0].extract_imagesets()) == len(expts)
def test_experimentlist_factory_from_imageset():
imageset = Format.get_imageset(["filename.cbf"], as_imageset=True)
imageset.set_beam(Beam(), 0)
imageset.set_detector(Detector(), 0)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
assert len(experiments) == 1
assert experiments[0].imageset
assert experiments[0].beam
assert experiments[0].detector is not None
assert experiments[0].crystal
def test_experimentlist_factory_from_imageset():
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model import Crystal
from dxtbx.format.Format import Format
imageset = Format.get_imageset(["filename.cbf"], as_imageset=True)
imageset.set_beam(Beam(), 0)
imageset.set_detector(Detector(), 0)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
assert len(experiments) == 1
assert experiments[0].imageset is not None
assert experiments[0].beam is not None
assert experiments[0].detector is not None
assert experiments[0].crystal is not None
def test_from_null_sweep():
filenames = ["template_%2d.cbf" % (i + 1) for i in range(0, 10)]
sweep = Format.get_imageset(filenames,
beam=Beam((0, 0, 1)),
detector=Detector(),
goniometer=Goniometer((1, 0, 0)),
scan=Scan((1, 10), (0, 0.1)))
# Create the datablock
datablock = DataBlockFactory.from_imageset(sweep)
assert len(datablock) == 1
datablock = datablock[0]
sweeps = datablock.extract_sweeps()
assert len(sweeps) == 1
assert sweeps[0].get_beam() == sweep.get_beam()
assert sweeps[0].get_detector() == sweep.get_detector()
assert sweeps[0].get_goniometer() == sweep.get_goniometer()
assert sweeps[0].get_scan() == sweep.get_scan()
def test_from_null_sequence():
filenames = ["template_%2d.cbf" % (i + 1) for i in range(0, 10)]
sequence = Format.get_imageset(
filenames,
beam=Beam((0, 0, 1)),
detector=Detector(),
goniometer=Goniometer((1, 0, 0)),
scan=Scan((1, 10), (0, 0.1)),
)
# Create the experiments
experiments = ExperimentListFactory.from_sequence_and_crystal(sequence,
crystal=None)
assert len(experiments) == 1
imagesets = experiments.imagesets()
assert imagesets[0].get_format_class()
assert len(imagesets) == 1
assert imagesets[0].get_beam() == sequence.get_beam()
assert imagesets[0].get_detector() == sequence.get_detector()
assert imagesets[0].get_goniometer() == sequence.get_goniometer()
assert imagesets[0].get_scan() == sequence.get_scan()
def test_from_null_sequence():
filenames = ["template_%2d.cbf" % (i + 1) for i in range(0, 10)]
sequence = Format.get_imageset(
filenames,
beam=Beam((0, 0, 1)),
detector=Detector(),
goniometer=Goniometer((1, 0, 0)),
scan=Scan((1, 10), (0, 0.1)),
)
# Create the datablock
datablock = DataBlockFactory.from_imageset(sequence)
assert len(datablock) == 1
datablock = datablock[0]
assert datablock.format_class()
sequences = datablock.extract_sequences()
assert len(sequences) == 1
assert sequences[0].get_beam() == sequence.get_beam()
assert sequences[0].get_detector() == sequence.get_detector()
assert sequences[0].get_goniometer() == sequence.get_goniometer()
assert sequences[0].get_scan() == sequence.get_scan()
def test_experimentlist_dumper_dump_empty_sequence(tmp_path):
filenames = [tmp_path / f"filename_{i}.cbf" for i in range(1, 3)]
imageset = Format.get_imageset(
filenames,
beam=Beam((1, 0, 0)),
detector=Detector(),
goniometer=Goniometer(),
scan=Scan((1, 2), (0.0, 1.0)),
as_sequence=True,
)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
filename = tmp_path / "temp.json"
experiments.as_json(filename)
experiments2 = ExperimentListFactory.from_json_file(filename,
check_format=False)
check(experiments, experiments2)
def test_experimentlist_factory_from_sweep():
filenames = ["filename_%01d.cbf" % (i + 1) for i in range(0, 2)]
imageset = Format.get_imageset(
filenames,
beam=Beam(),
detector=Detector(),
goniometer=Goniometer(),
scan=Scan((1, 2), (0, 1)),
as_sweep=True,
)
crystal = Crystal((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol="P1")
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
assert len(experiments) == 1
assert experiments[0].imageset is not None
assert experiments[0].beam is not None
assert experiments[0].detector is not None
assert experiments[0].goniometer is not None
assert experiments[0].scan is not None
assert experiments[0].crystal is not None