def test_single_deprecation(image_test_dir):
"""Test out the ScanFactory."""
with pytest.warns(DeprecationWarning):
ScanFactory.single(
scan_helper_image_files.template_directory_index_to_image(
"image_###.dat", image_test_dir, 2
),
None,
1.0,
18 + 0.5,
0.5,
1,
)
def test_from_phil():
from dxtbx.model.scan import ScanFactory, scan_phil_scope
from libtbx.phil import parse
params = scan_phil_scope.fetch(
parse(
"""
scan {
image_range = 1, 10
oscillation = (-4, 0.1)
}
"""
)
).extract()
s1 = ScanFactory.from_phil(params)
assert s1.get_num_images() == 10
assert s1.get_image_range() == (1, 10)
assert s1.get_oscillation() == (-4, 0.1)
assert s1.get_batch_offset() == 0
assert s1.get_batch_range() == s1.get_image_range()
for i in range(s1.get_image_range()[0], s1.get_image_range()[1] + 1):
assert s1.get_batch_for_image_index(i) == i
assert s1.get_batch_for_array_index(i - 1) == i
params = scan_phil_scope.fetch(
parse(
"""
scan {
image_range = 1, 20
extrapolate_scan = True
oscillation = (20, 0.01)
batch_offset = 10
}
"""
)
).extract()
s2 = ScanFactory.from_phil(params, s1)
assert s2.get_num_images() == 20
assert s2.get_image_range() == (1, 20)
assert s2.get_oscillation() == (20, 0.01)
assert s2.get_batch_offset() == 10
assert s2.get_batch_range() == (11, 30)
ir1, ir2 = s2.get_image_range()
for i in range(ir1, ir2):
assert s2.get_batch_for_image_index(i) == i + s2.get_batch_offset()
assert s2.is_batch_valid(s2.get_batch_for_image_index(i))
def _scan(self):
"""
Create the scan object
"""
from dxtbx.model.scan import ScanFactory
configuration = self.header["configuration"]
# kappa_start = configuration['kappa_start']
# kappa_increment = configuration['kappa_increment']
# phi_start = configuration['phi_start']
# phi_increment = configuration['phi_increment']
# omega_start = configuration['omega_start']
# omega_increment = configuration['omega_increment']
# two_theta_start = configuration['two_theta_start']
# two_theta_increment = configuration['two_theta_increment']
kappa_start = 0
kappa_increment = 0
phi_start = 0
phi_increment = 0
omega_start = 0
omega_increment = 0
two_theta_start = 0
two_theta_increment = 0
# nimages = configuration['nimages']
nimages = 1
return ScanFactory.make_scan(
image_range=(1, nimages),
exposure_times=[0] * nimages,
oscillation=(phi_start, phi_increment),
epochs=[0] * nimages,
)
def work_xScanFactory():
'''Test out the ScanFactory.'''
import dxtbx
directory = os.path.join(os.path.split(dxtbx.__file__)[0], 'tests')
template = 'image_###.dat'
xscans = [
ScanFactory.single(
scan_helper_image_files.template_directory_index_to_image(
template, directory, j + 1),
scan_helper_image_formats.FORMAT_CBF, 1.0, 18 + 0.5 * j, 0.5, j)
for j in range(20)
]
xscans.reverse()
try:
print sum(xscans[1:], xscans[0])
print 'I should not see this message'
except RuntimeError:
pass
xscans.sort()
sum(xscans[1:], xscans[0])
a = ScanFactory.add(xscans[:10])
b = ScanFactory.add(xscans[10:])
a + b
filename = scan_helper_image_files.template_directory_index_to_image(
template, directory, 1)
assert (len(ScanFactory.search(filename)) == 20)
(a + b)[1:5]
(a + b)[:10]
cbf = os.path.join(directory, 'phi_scan_001.cbf')
print 'OK'
def test_xScanFactory():
"""Test out the ScanFactory."""
import dxtbx
directory = os.path.join(os.path.split(dxtbx.__file__)[0], "tests")
template = "image_###.dat"
xscans = [
ScanFactory.single(
scan_helper_image_files.template_directory_index_to_image(
template, directory, j + 1),
scan_helper_image_formats.FORMAT_CBF,
1.0,
18 + 0.5 * j,
0.5,
j,
) for j in range(20)
]
xscans.reverse()
with pytest.raises(RuntimeError):
print(sum(xscans[1:], xscans[0]))
xscans.sort()
sum(xscans[1:], xscans[0])
a = ScanFactory.add(xscans[:10])
b = ScanFactory.add(xscans[10:])
a + b
filename = scan_helper_image_files.template_directory_index_to_image(
template, directory, 1)
assert len(ScanFactory.search(filename)) == 20
(a + b)[1:5]
(a + b)[:10]
def test_xScanFactory(image_test_dir):
"""Test out the ScanFactory."""
template = "image_###.dat"
xscans = [
ScanFactory.single_file(
scan_helper_image_files.template_directory_index_to_image(
template, image_test_dir, j + 1
),
1.0,
18 + 0.5 * j,
0.5,
j,
)
for j in range(20)
]
xscans.reverse()
with pytest.raises(RuntimeError):
print(sum(xscans[1:], xscans[0]))
xscans.sort()
sum(xscans[1:], xscans[0])
a = ScanFactory.add(xscans[:10])
b = ScanFactory.add(xscans[10:])
a + b
filename = scan_helper_image_files.template_directory_index_to_image(
template, image_test_dir, 1
)
assert len(ScanFactory.search(filename)) == 20
(a + b)[1:5]
(a + b)[:10]
def _scan(self):
"""
Create the scan object
"""
phi_start = 0
phi_increment = 0
nimages = 1
return ScanFactory.make_scan(
image_range=(1, nimages),
exposure_times=[0] * nimages,
oscillation=(phi_start, phi_increment),
epochs=[0] * nimages,
)
def work_xScanFactory():
'''Test out the ScanFactory.'''
import dxtbx
directory = os.path.join(os.path.split(dxtbx.__file__)[0], 'tests')
template = 'image_###.dat'
xscans = [ScanFactory.single(
scan_helper_image_files.template_directory_index_to_image(
template, directory, j + 1), scan_helper_image_formats.FORMAT_CBF,
1.0, 18 + 0.5 * j, 0.5, j) for j in range(20)]
xscans.reverse()
try:
print sum(xscans[1:], xscans[0])
print 'I should not see this message'
except RuntimeError, e:
pass
def _scan(self):
'''
Create the scan object
'''
from dxtbx.model.scan import ScanFactory
configuration = self.header['configuration']
kappa_start = configuration['kappa_start']
kappa_increment = configuration['kappa_increment']
phi_start = configuration['phi_start']
phi_increment = configuration['phi_increment']
omega_start = configuration['omega_start']
omega_increment = configuration['omega_increment']
two_theta_start = configuration['two_theta_start']
two_theta_increment = configuration['two_theta_increment']
nimages = configuration['nimages']
return ScanFactory.make_scan(image_range=(1, nimages),
exposure_times=[0] * nimages,
oscillation=(phi_start, phi_increment),
epochs=[0] * nimages)
template, directory, j + 1), scan_helper_image_formats.FORMAT_CBF,
1.0, 18 + 0.5 * j, 0.5, j) for j in range(20)]
xscans.reverse()
try:
print sum(xscans[1:], xscans[0])
print 'I should not see this message'
except RuntimeError, e:
pass
xscans.sort()
sum(xscans[1:], xscans[0])
a = ScanFactory.add(xscans[:10])
b = ScanFactory.add(xscans[10:])
a + b
filename = scan_helper_image_files.template_directory_index_to_image(
template, directory, 1)
assert(len(ScanFactory.search(filename)) == 20)
(a + b)[1:5]
(a + b)[:10]
cbf = os.path.join(directory, 'phi_scan_001.cbf')
print 'OK'
"""
include scope dials.test.algorithms.refinement.geometry_phil
include scope dials.test.algorithms.refinement.minimiser_phil
""",
process_includes=True,
)
models = setup_geometry.Extract(master_phil, cmdline_args=args)
mydetector = models.detector
mygonio = models.goniometer
mycrystal = models.crystal
mybeam = models.beam
# Build a mock scan for a 180 degree sweep
sf = ScanFactory()
myscan = sf.make_scan(
image_range=(1, 1800),
exposure_times=0.1,
oscillation=(0, 0.1),
epochs=range(1800),
deg=True,
)
sweep_range = myscan.get_oscillation_range(deg=False)
temp = myscan.get_oscillation(deg=False)
im_width = temp[1] - temp[0]
assert sweep_range == (0.0, pi)
assert approx_equal(im_width, 0.1 * pi / 180.0)
# Build an experiment list
experiments = ExperimentList()
from dxtbx.datablock import DataBlockFactory, DataBlockDumper
from dxtbx.imageset import ImageSetFactory, ImageSweep, ImageSetData
from dxtbx.model.goniometer import GoniometerFactory
from dxtbx.model.scan import ScanFactory
import glob, os, sys
"""
Modification of AB's prepare_sweep.py.
Usage: libtbx.python prepare_sweep.py img_dir start_img, end_img savefile
"""
root = sys.argv[1]
start, end = int(sys.argv[2]), int(sys.argv[3])
g = GoniometerFactory.single_axis()
s = ScanFactory.make_scan((start, end), 0, (0, 1), [0] * (end - start + 1))
sw = ImageSetFactory.from_template(template=os.path.join(
root, "fft_frame_I_mf_####.cbf"),
scan=s,
goniometer=g,
image_range=(start, end))
dump = DataBlockDumper(DataBlockFactory.from_imageset(sw))
dump.as_file(sys.argv[4])