def tst_dump_empty_sweep(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
from uuid import uuid4
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 3))))
imageset.set_beam(Beam((1, 0, 0)))
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 3), (0.0, 1.0)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=1)
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
dump = ExperimentListDumper(experiments)
filename = 'temp%s.json' % uuid4().hex
dump.as_json(filename)
experiments2 = ExperimentListFactory.from_json_file(filename,
check_format=False)
self.check(experiments, experiments2)
print 'OK'
def tst_from_datablock(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.datablock import DataBlockFactory
from dxtbx.model.crystal import crystal_model
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 2))))
imageset.set_beam(Beam())
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 2), (0, 1)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)
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)
print 'OK'
def tst_dump_empty_sweep(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
from uuid import uuid4
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 3))))
imageset.set_beam(Beam((1, 0, 0)))
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 3), (0.0, 1.0)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=1)
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
dump = ExperimentListDumper(experiments)
filename = 'temp%s.json' % uuid4().hex
dump.as_json(filename)
experiments2 = ExperimentListFactory.from_json_file(filename,
check_format=False)
self.check(experiments, experiments2)
print 'OK'
def tst_from_datablock(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.datablock import DataBlockFactory
from dxtbx.model.crystal import crystal_model
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 2))))
imageset.set_beam(Beam())
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 2), (0, 1)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)
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)
print 'OK'
pass
def generate_spots(crystal_model,
detector,
beam,
goniometer=None,
scan=None,
sel_fraction=1.0):
import math
experiment = Experiment(beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
crystal=crystal_model)
# if we don't set the imageset then from_predictions uses the StillsReflectionPredictor :-(
from dxtbx.imageset import NullReader, ImageSweep
imageset = ImageSweep(NullReader,
indices=range(len(scan.get_epochs())),
beam=beam,
goniometer=goniometer,
detector=detector,
scan=scan)
experiment.imageset = imageset
predicted = flex.reflection_table.from_predictions(experiment)
sel = flex.random_selection(len(predicted),
int(math.floor(sel_fraction * len(predicted))))
predicted = predicted.select(sel)
predicted['imageset_id'] = flex.size_t(len(predicted), 0)
predicted['xyzobs.px.value'] = predicted['xyzcal.px']
predicted['xyzobs.px.variance'] = flex.vec3_double(len(predicted),
(0.5, 0.5, 0.5))
return predicted
def run(self):
from dxtbx.imageset import MultiFileReader, ImageSweep
from dxtbx.format.Registry import Registry
# Get the filenames
filenames = self.get_file_list()
# Create the format class
format_class = Registry.find(filenames[0])
# Create the reader
reader = MultiFileReader(format_class, filenames)
# Create the sweep
sweep = ImageSweep(reader)
# Run a load of tests
self.tst_get_item(sweep)
self.tst_len(sweep, len(filenames))
self.tst_iter(sweep)
self.tst_indices(sweep, range(0, 9))
self.tst_paths(sweep, filenames)
self.tst_is_valid(sweep)
self.tst_get_detectorbase(sweep, range(len(filenames)), 9)
self.tst_get_models(sweep, range(len(filenames)), 9)
self.tst_get_array_range(sweep, (0, 9))
self.tst_to_array(sweep, (3, 7), (3, 7, 50, 100, 100, 200))
self.tst_set_models(sweep)
def generate_spots(crystal_model,
detector,
beam,
goniometer=None,
scan=None,
sel_fraction=1.0):
experiment = Experiment(beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
crystal=crystal_model)
# if we don't set the imageset then from_predictions uses the StillsReflectionPredictor :-(
filenames = [""] * len(scan)
reader = Reader(filenames)
masker = Masker(filenames)
data = ImageSetData(reader, masker)
imageset = ImageSweep(data, beam, detector, goniometer, scan)
experiment.imageset = imageset
predicted = flex.reflection_table.from_predictions(experiment)
sel = flex.random_selection(len(predicted),
int(math.floor(sel_fraction * len(predicted))))
predicted = predicted.select(sel)
predicted['imageset_id'] = flex.size_t(len(predicted), 0)
predicted['xyzobs.px.value'] = predicted['xyzcal.px']
predicted['xyzobs.px.variance'] = flex.vec3_double(len(predicted),
(0.5, 0.5, 0.5))
return predicted
def as_imageset(self, filename):
'''
Return as an imageset
'''
from dxtbx.format.FormatEigerStream import FormatEigerStream
from dxtbx.imageset import MultiFileReader, ImageSweep
# Create the reader
reader = MultiFileReader(FormatEigerStream, [filename])
# Create the sweep
return ImageSweep(reader)
def _create_single_file_imageset(self, format_class, filename,
format_kwargs=None):
''' Create an imageset from a multi image file. '''
from dxtbx.imageset import SingleFileReader, ImageSet, ImageSweep
from os.path import abspath
if format_kwargs is None:
format_kwargs = {}
format_instance = format_class(abspath(filename), **format_kwargs)
try:
scan = format_instance.get_scan()
if abs(scan.get_oscillation()[1]) > 0.0:
return ImageSweep(SingleFileReader(format_instance),
format_kwargs=format_kwargs)
except Exception:
pass
return ImageSet(SingleFileReader(format_instance),
format_kwargs=format_kwargs)
def get_imageset(
Class,
filenames,
beam=None,
detector=None,
goniometer=None,
scan=None,
as_sweep=False,
as_imageset=False,
single_file_indices=None,
format_kwargs=None,
template=None,
check_format=True,
lazy=False,
):
"""
Factory method to create an imageset
"""
from dxtbx.imageset import ImageSetData
from dxtbx.imageset import ImageSweep
from os.path import abspath
from scitbx.array_family import flex
if isinstance(filenames, str):
filenames = [filenames]
elif len(filenames) > 1:
assert len(set(filenames)) == 1
filenames = filenames[0:1]
# Make filenames absolute
filenames = map(abspath, filenames)
# Make it a dictionary
if format_kwargs is None:
format_kwargs = {}
# If get_num_images hasn't been implemented, we need indices for number of images
if Class.get_num_images == FormatMultiImage.get_num_images:
assert single_file_indices is not None
assert min(single_file_indices) >= 0
num_images = max(single_file_indices) + 1
else:
num_images = None
# Get some information from the format class
reader = Class.get_reader()(filenames, num_images=num_images, **format_kwargs)
masker = Class.get_masker()(filenames, num_images=num_images, **format_kwargs)
# Get the format instance
assert len(filenames) == 1
if check_format is True:
format_instance = Class(filenames[0], **format_kwargs)
else:
format_instance = None
if not as_sweep:
lazy = True
# Read the vendor type
if check_format is True:
vendor = format_instance.get_vendortype()
else:
vendor = ""
# Get the format kwargs
params = format_kwargs
# Check if we have a sweep
# Make sure only 1 or none is set
assert [as_imageset, as_sweep].count(True) < 2
if as_imageset:
is_sweep = False
elif as_sweep:
is_sweep = True
else:
if scan is None and format_instance is None:
raise RuntimeError(
"""
One of the following needs to be set
- as_imageset=True
- as_sweep=True
- scan
- check_format=True
"""
)
if scan is None:
test_scan = format_instance.get_scan()
else:
test_scan = scan
if test_scan is not None and test_scan.get_oscillation()[1] != 0:
is_sweep = True
else:
is_sweep = False
assert not (as_sweep and lazy), "No lazy support for sweeps"
if single_file_indices is not None:
single_file_indices = flex.size_t(single_file_indices)
# Create an imageset or sweep
if not is_sweep:
# Use imagesetlazy
# Setup ImageSetLazy and just return it. No models are set.
if lazy:
from dxtbx.imageset import ImageSetLazy
iset = ImageSetLazy(
ImageSetData(
reader=reader,
masker=masker,
vendor=vendor,
params=params,
format=Class,
),
indices=single_file_indices,
)
return iset
# Create the imageset
from dxtbx.imageset import ImageSet
iset = ImageSet(
ImageSetData(
reader=reader,
masker=masker,
vendor=vendor,
params=params,
format=Class,
),
indices=single_file_indices,
)
# If any are None then read from format
if [beam, detector, goniometer, scan].count(None) != 0:
# Get list of models
beam = []
detector = []
goniometer = []
scan = []
for i in range(format_instance.get_num_images()):
beam.append(format_instance.get_beam(i))
detector.append(format_instance.get_detector(i))
goniometer.append(format_instance.get_goniometer(i))
scan.append(format_instance.get_scan(i))
if single_file_indices is None:
single_file_indices = list(range(format_instance.get_num_images()))
# Set the list of models
for i in range(len(single_file_indices)):
iset.set_beam(beam[single_file_indices[i]], i)
iset.set_detector(detector[single_file_indices[i]], i)
iset.set_goniometer(goniometer[single_file_indices[i]], i)
iset.set_scan(scan[single_file_indices[i]], i)
else:
# Get the template
template = filenames[0]
# Check indices are sequential
if single_file_indices is not None:
assert all(
i + 1 == j
for i, j in zip(single_file_indices[:-1], single_file_indices[1:])
)
num_images = len(single_file_indices)
else:
num_images = format_instance.get_num_images()
# Check the scan makes sense - we must want to use <= total images
if scan is not None:
assert scan.get_num_images() <= num_images
# If any are None then read from format
if beam is None:
beam = format_instance.get_beam()
if detector is None:
detector = format_instance.get_detector()
if goniometer is None:
goniometer = format_instance.get_goniometer()
if scan is None:
scan = format_instance.get_scan()
if scan is not None:
for f in filenames[1:]:
format_instance = Class(f, **format_kwargs)
scan += format_instance.get_scan()
isetdata = ImageSetData(
reader=reader,
masker=masker,
vendor=vendor,
params=params,
format=Class,
template=template,
)
# Create the sweep
iset = ImageSweep(
isetdata,
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
indices=single_file_indices,
)
# Return the imageset
return iset
def get_imageset(
Class,
filenames,
beam=None,
detector=None,
goniometer=None,
scan=None,
as_imageset=False,
as_sweep=False,
single_file_indices=None,
format_kwargs=None,
template=None,
check_format=True,
):
"""
Factory method to create an imageset
"""
from dxtbx.imageset import ImageSetData
from dxtbx.imageset import ImageSet
from dxtbx.imageset import ImageSweep
from dxtbx.sweep_filenames import template_regex
from os.path import abspath
# Get filename absolute paths
filenames = map(abspath, filenames)
# Make it a dict
if format_kwargs is None:
format_kwargs = {}
# Get some information from the format class
reader = Class.get_reader()(filenames, **format_kwargs)
masker = Class.get_masker()(filenames, **format_kwargs)
# Get the format instance
if check_format is True:
format_instance = Class(filenames[0], **format_kwargs)
else:
format_instance = None
# Read the vendor type
if check_format is True:
vendor = format_instance.get_vendortype()
else:
vendor = ""
# Get the format kwargs
params = format_kwargs
# Make sure only 1 or none is set
assert [as_imageset, as_sweep].count(True) < 2
if as_imageset:
is_sweep = False
elif as_sweep:
is_sweep = True
else:
if scan is None and format_instance is None:
raise RuntimeError("""
One of the following needs to be set
- as_imageset=True
- as_sweep=True
- scan
- check_format=True
""")
if scan is None:
test_scan = format_instance.get_scan()
else:
test_scan = scan
if test_scan is not None and test_scan.get_oscillation()[1] != 0:
is_sweep = True
else:
is_sweep = False
# Create an imageset or sweep
if not is_sweep:
# Create the imageset
iset = ImageSet(
ImageSetData(
reader=reader,
masker=masker,
vendor=vendor,
params=params,
format=Class,
))
# If any are None then read from format
if [beam, detector, goniometer, scan].count(None) != 0:
# Get list of models
beam = []
detector = []
goniometer = []
scan = []
for f in filenames:
format_instance = Class(f, **format_kwargs)
beam.append(format_instance.get_beam())
detector.append(format_instance.get_detector())
goniometer.append(format_instance.get_goniometer())
scan.append(format_instance.get_scan())
# Set the list of models
for i in range(len(filenames)):
iset.set_beam(beam[i], i)
iset.set_detector(detector[i], i)
iset.set_goniometer(goniometer[i], i)
iset.set_scan(scan[i], i)
else:
# Get the template
if template is None:
template = template_regex(filenames[0])[0]
else:
template = str(template)
# Check scan makes sense
if scan:
if check_format is True:
assert scan.get_num_images() == len(filenames)
# If any are None then read from format
if beam is None and format_instance is not None:
beam = format_instance.get_beam()
if detector is None and format_instance is not None:
detector = format_instance.get_detector()
if goniometer is None and format_instance is not None:
goniometer = format_instance.get_goniometer()
if scan is None and format_instance is not None:
scan = format_instance.get_scan()
if scan is not None:
for f in filenames[1:]:
format_instance = Class(f, **format_kwargs)
scan += format_instance.get_scan()
assert beam is not None, "Can't create Sweep without beam"
assert detector is not None, "Can't create Sweep without detector"
assert goniometer is not None, "Can't create Sweep without goniometer"
assert scan is not None, "Can't create Sweep without scan"
# Create the sweep
iset = ImageSweep(
ImageSetData(
reader=reader,
masker=masker,
vendor=vendor,
params=params,
format=Class,
template=template,
),
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
)
# Return the imageset
return iset
def tst_from_null_sweep(self):
from dxtbx.imageset import NullReader, ImageSweep, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
sweep = ImageSweep(NullReader(SweepFileList("template_%2d.cbf", (0, 10))))
sweep.set_beam(Beam((0, 0, 1)))
sweep.set_detector(Detector())
sweep.set_goniometer(Goniometer((1, 0, 0)))
sweep.set_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_null_reader_sweep(self):
from dxtbx.imageset import NullReader, ImageSweep, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
template = 'hello_world_%d.cbf'
paths = [template % 1]
# Create the null reader
reader = NullReader(SweepFileList(template, (0, 1)))
# Create the imageset
imageset = ImageSweep(reader)
# Try to get an item
try:
imageset[0]
assert(False)
except Exception:
print 'OK'
# Try to slice the imageset
imageset2 = imageset[0:1]
print 'OK'
# Try some functions which should work
assert(len(imageset) == 1)
assert(imageset == imageset)
assert(imageset.indices() == [0])
assert(imageset.is_valid())
assert(imageset.get_template() == template)
print 'OK'
# Get the image paths
assert(imageset.paths() == paths)
assert(imageset.get_path(0) == paths[0])
print 'OK'
imageset.set_beam(Beam())
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1,1), (0, 1)))
assert(isinstance(imageset.get_beam(), Beam))
assert(isinstance(imageset.get_detector(), Detector))
assert(isinstance(imageset.get_goniometer(), Goniometer))
assert(isinstance(imageset.get_scan(), Scan))
print 'OK'
def tst_from_null_sweep(self):
from dxtbx.datablock import DataBlockFactory
from dxtbx.imageset import NullReader, ImageSweep, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
sweep = ImageSweep(NullReader(SweepFileList("template_%2d.cbf", (0, 10))))
sweep.set_beam(Beam((0, 0, 1)))
sweep.set_detector(Detector())
sweep.set_goniometer(Goniometer((1, 0, 0)))
sweep.set_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'
