def test_imagesetfactory(centroid_files, dials_data):
sequence = ImageSetFactory.new(centroid_files)
assert isinstance(sequence[0], ImageSequence)
template = dials_data("centroid_test_data").join(
"centroid_####.cbf").strpath
image_range = (3, 6)
sequence = ImageSetFactory.from_template(template, image_range)
assert isinstance(sequence[0], ImageSequence)
assert len(sequence[0]) == 4
assert sequence[0].paths()[0].endswith("3.cbf")
assert sequence[0].paths()[-1].endswith("6.cbf")
imageset = ImageSetFactory.make_imageset(centroid_files)
assert len(imageset) == 9
imageset = ImageSetFactory.make_imageset(centroid_files,
check_format=False)
assert len(imageset) == 9
sequence = ImageSetFactory.make_sequence(template, list(range(1, 9 + 1)))
assert len(sequence) == 9
sequence = ImageSetFactory.make_sequence(template, list(range(3, 6 + 1)))
assert len(sequence) == 4
def to_imageset(input_filename, extra_filename=None):
'''Get an image set from the xds input filename plus an extra filename
Params:
input_filename The XDS.INP file
extra_filename A (G)XPARM.XDS, INTGRATE.HKL or XDS_ASCII.HKL file
Returns:
The imageset
'''
from iotbx.xds import xds_inp
from dxtbx.imageset import ImageSetFactory
import dxtbx
# Read the input filename
handle = xds_inp.reader()
handle.read_file(input_filename)
# Get the template
template = handle.name_template_of_data_frames[0].replace('?', '#')
image_range = handle.data_range
detector_name = handle.detector
if extra_filename is not None:
# we can get all the extra dxtbx models from extra_filename
check_format = False
else:
# we need the image files present to get the dxtbx models
check_format = True
# Create the imageset
imageset = ImageSetFactory.from_template(
template, image_range=image_range, check_format=False)[0]
# If an extra filename has been specified, try to load models
if extra_filename:
models = dxtbx.load(extra_filename)
detector = models.get_detector()
if detector_name.strip() == 'PILATUS':
from dxtbx.model import ParallaxCorrectedPxMmStrategy
from cctbx.eltbx import attenuation_coefficient
table = attenuation_coefficient.get_table("Si")
wavelength = models.get_beam().get_wavelength()
mu = table.mu_at_angstrom(wavelength) / 10.0
t0 = handle.sensor_thickness
for panel in detector:
panel.set_px_mm_strategy(ParallaxCorrectedPxMmStrategy(mu, t0))
panel.set_trusted_range(
(handle.minimum_valid_pixel_value, handle.overload))
imageset.set_beam(models.get_beam())
imageset.set_detector(detector)
imageset.set_goniometer(models.get_goniometer())
# take the image range from XDS.INP
scan = models.get_scan()
scan.set_image_range(image_range)
imageset.set_scan(scan)
# Return the imageset
return imageset
def test_imagesetfactory(centroid_files, dials_regression):
from dxtbx.imageset import ImageSetFactory, ImageSweep
filenames = centroid_files
sweep = ImageSetFactory.new(filenames)
assert isinstance(sweep[0], ImageSweep)
template = os.path.join(dials_regression, "centroid_test_data",
"centroid_####.cbf")
image_range = (3, 6)
sweep = ImageSetFactory.from_template(template, image_range)
assert isinstance(sweep[0], ImageSweep)
assert len(sweep[0]) == 4
assert sweep[0].paths()[0].endswith("3.cbf")
assert sweep[0].paths()[-1].endswith("6.cbf")
imageset = ImageSetFactory.make_imageset(filenames)
assert len(imageset) == 9
imageset = ImageSetFactory.make_imageset(filenames, check_format=False)
assert len(imageset) == 9
sweep = ImageSetFactory.make_sweep(template, list(range(1, 9 + 1)))
assert len(sweep) == 9
sweep = ImageSetFactory.make_sweep(template, list(range(3, 6 + 1)))
assert len(sweep) == 4
def imagesweep_from_dict(d, check_format=True, directory=None):
"""Construct and image sweep from the dictionary."""
# Get the template (required)
template = load_path(str(d["template"]), directory=directory)
# If the scan isn't set, find all available files
scan_dict = d.get("scan")
if scan_dict is None:
image_range = None
else:
image_range = scan_dict.get("image_range")
# Set the models with the exisiting models as templates
beam = BeamFactory.from_dict(d.get("beam"))
goniometer = GoniometerFactory.from_dict(d.get("goniometer"))
detector = DetectorFactory.from_dict(d.get("detector"))
scan = ScanFactory.from_dict(d.get("scan"))
# Construct the sweep
try:
sweep = ImageSetFactory.from_template(
template,
image_range,
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
check_format=check_format,
)[0]
except Exception:
indices = range(image_range[0], image_range[1] + 1)
sweep = ImageSetFactory.make_sweep(
template,
indices,
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
check_format=check_format,
)
# Set some external lookups
if "mask" in d and d["mask"] is not None and d["mask"] is not "":
path = load_path(d["mask"], directory=directory)
with open(path) as infile:
sweep.external_lookup.mask.filename = path
sweep.external_lookup.mask.data = ImageBool(pickle.load(infile))
if "gain" in d and d["gain"] is not None and d["gain"] is not "":
path = load_path(d["gain"], directory=directory)
with open(path) as infile:
sweep.external_lookup.gain.filename = path
sweep.external_lookup.gain.data = ImageDouble(pickle.load(infile))
if "pedestal" in d and d["pedestal"] is not None and d["pedestal"] is not "":
path = load_path(d["pedestal"], directory=directory)
with open(path) as infile:
sweep.external_lookup.pedestal.filename = path
sweep.external_lookup.pedestal.data = ImageDouble(pickle.load(infile))
# Return the sweep
return sweep
def test_make_sequence_with_percent_character(dials_data, tmp_path):
images = [
dials_data("centroid_test_data").join(f"centroid_{i:04}.cbf")
for i in range(1, 10)
]
directory = tmp_path / "test%"
directory.mkdir()
try:
for image in images:
try:
(directory / image.basename).symlink_to(image)
except OSError:
shutil.copy(image, directory)
template = str(directory / "centroid_####.cbf")
sequence = ImageSetFactory.make_sequence(template, range(1, 10))
assert len(sequence) == 9
sequences = ImageSetFactory.new(
[str(directory / image.basename) for image in images])
assert len(sequences) == 1
assert len(sequences[0]) == 9
sequences = ImageSetFactory.from_template(template)
assert len(sequences) == 1
assert len(sequences[0]) == 9
finally: # clean up potentially copied files after running test
for image in images:
try:
(directory / image.basename).unlink()
except FileNotFoundError:
pass
def imagesweep_from_dict(d, check_format=True):
'''Construct and image sweep from the dictionary.'''
from dxtbx.imageset import ImageSetFactory
from dxtbx.model import BeamFactory, DetectorFactory, GoniometerFactory, ScanFactory
from dxtbx.serialize.filename import load_path
# Get the template (required)
template = load_path(str(d['template']))
# If the scan isn't set, find all available files
scan_dict = d.get('scan')
if scan_dict is None:
image_range = None
else:
image_range = scan_dict.get('image_range')
# Set the models with the exisiting models as templates
beam = BeamFactory.from_dict(d.get('beam'))
goniometer = GoniometerFactory.from_dict(d.get('goniometer'))
detector = DetectorFactory.from_dict(d.get('detector'))
scan = ScanFactory.from_dict(d.get('scan'))
# Construct the sweep
try:
sweep = ImageSetFactory.from_template(template,
image_range,
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
check_format=check_format)[0]
except Exception:
indices = range(image_range[0], image_range[1] + 1)
sweep = ImageSetFactory.make_sweep(template,
indices,
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
check_format=check_format)
# Set some external lookups
if 'mask' in d and d['mask'] is not None and d['mask'] is not "":
with open(d['mask']) as infile:
sweep.external_lookup.mask.filename = d['mask']
sweep.external_lookup.mask.data = ImageBool(pickle.load(infile))
if 'gain' in d and d['gain'] is not None and d['gain'] is not "":
with open(d['gain']) as infile:
sweep.external_lookup.gain.filename = d['gain']
sweep.external_lookup.gain.data = ImageDouble(pickle.load(infile))
if 'pedestal' in d and d['pedestal'] is not None and d[
'pedestal'] is not "":
with open(d['pedestal']) as infile:
sweep.external_lookup.pedestal.filename = d['pedestal']
sweep.external_lookup.pedestal.data = ImageDouble(
pickle.load(infile))
# Return the sweep
return sweep
def imagesweep_from_dict(d, check_format=True):
'''Construct and image sweep from the dictionary.'''
from dxtbx.imageset import ImageSetFactory
from dxtbx.serialize import beam, detector, goniometer, scan
from dxtbx.serialize.filename import load_path
# Get the template (required)
template = load_path(str(d['template']))
# If the scan isn't set, find all available files
scan_dict = d.get('scan')
if scan_dict is None:
image_range = None
else:
image_range = scan_dict.get('image_range')
# Construct the sweep
try:
sweep = ImageSetFactory.from_template(
template, image_range, check_format=check_format)[0]
# Get the existing models as dictionaries
beam_dict = beam.to_dict(sweep.get_beam())
gonio_dict = goniometer.to_dict(sweep.get_goniometer())
detector_dict = detector.to_dict(sweep.get_detector())
scan_dict = scan.to_dict(sweep.get_scan())
except Exception:
indices = range(image_range[0], image_range[1] + 1)
sweep = ImageSetFactory.make_sweep(
template, indices, check_format=False)
beam_dict = None
gonio_dict = None
detector_dict = None
scan_dict = None
# Set some external lookups
if 'mask' in d and d['mask'] is not None:
with open(d['mask']) as infile:
sweep.external_lookup.mask.filename = d['mask']
sweep.external_lookup.mask.data = pickle.load(infile)
if 'gain' in d and d['gain'] is not None:
with open(d['gain']) as infile:
sweep.external_lookup.gain.filename = d['gain']
sweep.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in d and d['pedestal'] is not None:
with open(d['pedestal']) as infile:
sweep.external_lookup.pedestal.filename = d['pedestal']
sweep.external_lookup.pedestal.data = pickle.load(infile)
# Set the models with the exisiting models as templates
sweep.set_beam(beam.from_dict(d.get('beam'), beam_dict))
sweep.set_goniometer(goniometer.from_dict(d.get('goniometer'), gonio_dict))
sweep.set_detector(detector.from_dict(d.get('detector'), detector_dict))
sweep.set_scan(scan.from_dict(d.get('scan'), scan_dict))
# Return the sweep
return sweep
def run(self):
from dxtbx.imageset import ImageSetFactory, ImageSweep
from os.path import join
filenames = self.get_file_list()
sweep = ImageSetFactory.new(filenames)
assert(isinstance(sweep[0], ImageSweep) == True)
print 'OK'
template = join(dials_regression, "centroid_test_data", "centroid_####.cbf")
image_range = (3, 6)
sweep = ImageSetFactory.from_template(template, image_range)
assert(isinstance(sweep[0], ImageSweep) == True)
assert len(sweep[0]) == 4
assert sweep[0].paths()[0].endswith("3.cbf")
assert sweep[0].paths()[-1].endswith("6.cbf")
print 'OK'
imageset = ImageSetFactory.make_imageset(filenames)
assert len(imageset) == 9
print 'OK'
imageset = ImageSetFactory.make_imageset(
filenames,
check_format=False)
assert len(imageset) == 9
print 'OK'
sweep = ImageSetFactory.make_sweep(
template,
list(range(1, 9+1)))
assert len(sweep) == 9
print 'OK'
sweep = ImageSetFactory.make_sweep(
template,
list(range(3, 6+1)))
assert len(sweep) == 4
print 'OK'
def test_make_sequence_with_percent_character(dials_data, tmp_path):
images = [
dials_data("centroid_test_data").join(f"centroid_{i:04}.cbf")
for i in range(1, 10)
]
directory = tmp_path / "test%"
directory.mkdir()
for image in images:
(directory / image.basename).symlink_to(image)
template = str(directory / "centroid_####.cbf")
sequence = ImageSetFactory.make_sequence(template, range(1, 10))
assert len(sequence) == 9
sequences = ImageSetFactory.new(
[str(directory / image.basename) for image in images]
)
assert len(sequences) == 1
assert len(sequences[0]) == 9
sequences = ImageSetFactory.from_template(template)
assert len(sequences) == 1
assert len(sequences[0]) == 9
def to_imageset(input_filename, extra_filename=None):
"""Get an image set from the xds input filename plus an extra filename
Params:
input_filename The XDS.INP file
extra_filename A (G)XPARM.XDS, INTGRATE.HKL or XDS_ASCII.HKL file
Returns:
The imageset
"""
from iotbx.xds import xds_inp
from dxtbx.imageset import ImageSetFactory
import dxtbx
# Read the input filename
handle = xds_inp.reader()
handle.read_file(input_filename)
# Get the template
template = handle.name_template_of_data_frames[0].replace("?", "#")
if template.endswith("h5"):
template = template.replace("######", "master")
image_range = handle.data_range
detector_name = handle.detector
if extra_filename is not None:
# we can get all the extra dxtbx models from extra_filename
check_format = False
else:
# we need the image files present to get the dxtbx models
check_format = True
# If an extra filename has been specified, try to load models
if extra_filename:
models = dxtbx.load(extra_filename)
detector = models.get_detector()
if detector_name.strip() in ("PILATUS",
"EIGER") or handle.silicon is not None:
from dxtbx.model import ParallaxCorrectedPxMmStrategy
from cctbx.eltbx import attenuation_coefficient
if handle.silicon is None:
table = attenuation_coefficient.get_table("Si")
wavelength = models.get_beam().get_wavelength()
mu = table.mu_at_angstrom(wavelength) / 10.0
else:
mu = handle.silicon
t0 = handle.sensor_thickness
for panel in detector:
panel.set_px_mm_strategy(ParallaxCorrectedPxMmStrategy(mu, t0))
panel.set_trusted_range(
(handle.minimum_valid_pixel_value, handle.overload))
beam = models.get_beam()
detector = models.get_detector()
goniometer = models.get_goniometer()
scan = models.get_scan()
scan.set_image_range(image_range)
else:
beam = None
detector = None
goniometer = None
scan = None
# Create the imageset
imageset = ImageSetFactory.from_template(
template,
image_range=image_range,
check_format=check_format,
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
)[0]
# Return the imageset
return imageset
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])
def to_imageset(input_filename, extra_filename=None):
'''Get an image set from the xds input filename plus an extra filename
Params:
input_filename The XDS.INP file
extra_filename A (G)XPARM.XDS, INTGRATE.HKL or XDS_ASCII.HKL file
Returns:
The imageset
'''
from iotbx.xds import xds_inp
from dxtbx.imageset import ImageSetFactory
import dxtbx
# Read the input filename
handle = xds_inp.reader()
handle.read_file(input_filename)
# Get the template
template = handle.name_template_of_data_frames[0].replace('?', '#')
image_range = handle.data_range
detector_name = handle.detector
if extra_filename is not None:
# we can get all the extra dxtbx models from extra_filename
check_format = False
else:
# we need the image files present to get the dxtbx models
check_format = True
# Create the imageset
imageset = ImageSetFactory.from_template(template,
image_range=image_range,
check_format=False)[0]
# If an extra filename has been specified, try to load models
if extra_filename:
models = dxtbx.load(extra_filename)
detector = models.get_detector()
if detector_name.strip() == 'PILATUS':
from dxtbx.model import ParallaxCorrectedPxMmStrategy
from cctbx.eltbx import attenuation_coefficient
table = attenuation_coefficient.get_table("Si")
wavelength = models.get_beam().get_wavelength()
mu = table.mu_at_angstrom(wavelength) / 10.0
t0 = handle.sensor_thickness
for panel in detector:
panel.set_px_mm_strategy(ParallaxCorrectedPxMmStrategy(mu, t0))
panel.set_trusted_range(
(handle.minimum_valid_pixel_value, handle.overload))
imageset.set_beam(models.get_beam())
imageset.set_detector(detector)
imageset.set_goniometer(models.get_goniometer())
# take the image range from XDS.INP
scan = models.get_scan()
scan.set_image_range(image_range)
imageset.set_scan(scan)
# Return the imageset
return imageset
