def exercise_multi_axis_goniometer():
import libtbx.load_env
from libtbx.test_utils import approx_equal
import os
if not libtbx.env.has_module("dials_regression"):
print "Skipping tstFormatCBFFull.py: dials_regression not present"
return
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/image_examples/dials-190",
test=os.path.isdir)
from dxtbx.imageset import ImageSetFactory
imgset = ImageSetFactory.new(os.path.join(data_dir, "whatev1_01_00001.cbf"))[0]
gonio = imgset.get_goniometer()
assert approx_equal(gonio.get_fixed_rotation(), (1,0,0,0,1,0,0,0,1))
assert approx_equal(gonio.get_setting_rotation(), (1,0,0,0,1,0,0,0,1))
from dxtbx.imageset import ImageSetFactory
imgset = ImageSetFactory.new(os.path.join(data_dir, "whatev1_02_00001.cbf"))[0]
gonio = imgset.get_goniometer()
assert approx_equal(gonio.get_fixed_rotation(), (1,0,0,0,1,0,0,0,1))
assert approx_equal(
gonio.get_setting_rotation(),
(1, 0, 0, 0, -0.5, 0.866, 0.0, -0.866, -0.5), eps=1e-4)
from dxtbx.imageset import ImageSetFactory
imgset = ImageSetFactory.new(os.path.join(data_dir, "whatev1_03_00001.cbf"))[0]
gonio = imgset.get_goniometer()
assert approx_equal(gonio.get_fixed_rotation(), (1,0,0,0,1,0,0,0,1))
assert approx_equal(
gonio.get_setting_rotation(),
(1, 0, 0, 0, 0.5, 0.866, 0.0, -0.866, 0.5), eps=1e-4)
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 print_sweep(list_of_images):
from dxtbx.imageset import ImageSetFactory
sweeps = ImageSetFactory.new(list_of_images)
for s in sweeps:
print s.get_detector()
print s.get_beam()
print s.get_goniometer()
print s.get_scan()
# compute the beam centre... in mm... w.r.t. fast, slow axis
print 'Derived quantities:'
from scitbx import matrix
d = s.get_detector()[0]
b = s.get_beam()
o = matrix.col(d.get_origin())
f = matrix.col(d.get_fast_axis())
s = matrix.col(d.get_slow_axis())
s0 = matrix.col(b.get_direction())
n = f.cross(s)
beam_offset = o - o.dot(s0) * s0
print ' beam centre (mm, fast, slow): %.2f %.2f' % (- beam_offset.dot(f),
- beam_offset.dot(s))
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 _make_stills(self, imageset):
''' Make a still imageset. '''
from dxtbx.imageset import ImageSetFactory
from dxtbx.serialize.filename import load_path
filenames = [load_path(p) for p in imageset['images']]
return ImageSetFactory.make_imageset(
filenames, None, check_format=self._check_format)
def tst_consistent(self):
from dxtbx.imageset import ImageSetFactory
from glob import glob
from os.path import join
from dxtbx.model import Scan
# Create a sweep
sweep_filenames = join(self.path, 'centroid_test_data', 'centroid*.cbf')
sweep = ImageSetFactory.new(sorted(glob(sweep_filenames)))[0]
# Create experiment with sweep and good scan
e = Experiment(imageset=sweep, scan=sweep.get_scan())
assert(e.is_consistent())
# Create experiment with sweep and defective scan
scan = sweep.get_scan()
scan.set_image_range((1, 1))
e = Experiment(imageset=sweep, scan=scan)
#assert(not e.is_consistent()) # FIXME
## Create experiment with imageset and good scan
#assert(e.is_consistent())
## Create experiment with imageset and non-still scan
#assert(not e.is_consistent())
## Create experiment with imageset and scan with more than 1 image
#assert(not e.is_consistent())
## Create experiment with imageset and defective scan
#assert(not e.is_consistent())
# Test passed
print 'OK'
def basic_imageset_from_dict(d):
''' Construct an ImageSet class from the dictionary.'''
from dxtbx.imageset import ImageSetFactory
from dxtbx.serialize import beam, detector
from dxtbx.serialize.filename import load_path
# Get the filename list and create the imageset
filenames = map(lambda p: load_path(p), map(str, d['filenames']))
imageset = ImageSetFactory.new(filenames)[0]
# Set some external lookups
if 'mask' in d and d['mask'] is not None:
with open(d['mask']) as infile:
imageset.external_lookup.mask.filename = d['mask']
imageset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in d and d['gain'] is not None:
with open(d['gain']) as infile:
imageset.external_lookup.gain.filename = d['gain']
imageset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in d and d['pedestal'] is not None:
with open(d['pedestal']) as infile:
imageset.external_lookup.pedestal.filename = d['pedestal']
imageset.external_lookup.pedestal.data = pickle.load(infile)
# Get the existing models as dictionaries
beam_dict = beam.to_dict(imageset.get_beam())
detector_dict = detector.to_dict(imageset.get_detector())
# Set models
imageset.set_beam(beam.from_dict(d.get('beam'), beam_dict))
imageset.set_detector(detector.from_dict(d.get('detector'), detector_dict))
# Return the imageset
return imageset
def convert_stills_to_sweep(self, imageset):
from dxtbx.model import Scan
assert self.params.geometry.scan.oscillation is not None
for i in range(len(imageset)):
self.override_beam(
imageset.get_beam(index=i),
self.params.geometry.beam)
self.override_detector(
imageset.get_detector(index=i),
self.params.geometry.detector)
self.override_goniometer(
imageset.get_goniometer(index=i),
self.params.geometry.goniometer)
beam = imageset.get_beam(index=0)
detector = imageset.get_detector(index=0)
goniometer = imageset.get_goniometer(index=0)
for i in range(1, len(imageset)):
assert beam.is_similar_to(
imageset.get_beam(index=i),
wavelength_tolerance = self.params.input.tolerance.beam.wavelength,
direction_tolerance = self.params.input.tolerance.beam.direction,
polarization_normal_tolerance = self.params.input.tolerance.beam.polarization_normal,
polarization_fraction_tolerance = self.params.input.tolerance.beam.polarization_fraction)
assert detector.is_similar_to(
imageset.get_detector(index=i),
fast_axis_tolerance = self.params.input.tolerance.detector.fast_axis,
slow_axis_tolerance = self.params.input.tolerance.detector.slow_axis,
origin_tolerance = self.params.input.tolerance.detector.origin)
assert goniometer.is_similar_to(
imageset.get_goniometer(index=i),
rotation_axis_tolerance = self.params.input.tolerance.goniometer.rotation_axis,
fixed_rotation_tolerance = self.params.input.tolerance.goniometer.fixed_rotation,
setting_rotation_tolerance = self.params.input.tolerance.goniometer.setting_rotation)
assert beam is not None
assert detector is not None
assert goniometer is not None
if self.params.geometry.scan.image_range is not None:
image_range = self.params.geometry.scan.image_range
else:
image_range = (1, len(imageset))
oscillation = self.params.geometry.scan.oscillation
scan = Scan(image_range=image_range, oscillation=oscillation)
from dxtbx.sweep_filenames import template_regex
from dxtbx.imageset import ImageSetFactory
indices = list(range(image_range[0], image_range[1]+1))
template = template_regex(imageset.get_path(0))[0]
if template is None:
paths = [imageset.get_path(i) for i in range(len(imageset))]
assert len(set(paths)) == 1
template = paths[0]
new_sweep = ImageSetFactory.make_sweep(
template = template,
indices = indices,
format_class = imageset.reader().get_format_class(),
beam = beam,
detector = detector,
goniometer = goniometer,
scan = scan)
return new_sweep
def run(self):
from dxtbx.imageset import ImageSetFactory, ImageSweep
filenames = self.get_file_list()
sweep = ImageSetFactory.new(filenames)
assert(isinstance(sweep[0], ImageSweep) == True)
print 'OK'
def _create_multi_file_imageset(self, format_class, records,
format_kwargs=None):
''' Create a multi file sweep or imageset. '''
from dxtbx.imageset import ImageSetFactory
from os.path import abspath
# Make either an imageset or sweep
if len(records) == 1 and records[0].template is not None:
# Get the image range
image_range = records[0].scan.get_image_range()
image_range = (image_range[0], image_range[1]+1)
# Create the sweep
imageset = ImageSetFactory.make_sweep(
abspath(records[0].template), range(*image_range),
format_class,
records[0].beam, records[0].detector,
records[0].goniometer, records[0].scan,
format_kwargs=format_kwargs)
else:
# Get the filenames
filenames = []
for r in records:
assert(r.template is None)
filenames.append(r.filename)
# make an imageset
imageset = ImageSetFactory.make_imageset(
map(abspath, filenames),
format_class,
format_kwargs=format_kwargs)
for i, r in enumerate(records):
imageset.set_beam(r.beam, i)
imageset.set_detector(r.detector, i)
imageset.set_goniometer(r.goniometer, i)
imageset.set_scan(r.scan, i)
# Return the imageset
return imageset
def run(file_names):
if len(file_names) == 1 and file_names[0].endswith('json'):
from dxtbx.serialize import load
datablock = load.datablock(file_names[0])
assert(len(datablock) == 1)
sweep = datablock[0].extract_sweeps()[0]
else:
from dxtbx.imageset import ImageSetFactory
sweep = ImageSetFactory.new(file_names)[0]
xsx = xds.to_xds(sweep)
xsx.XDS_INP()
def run(file_names):
if len(file_names) == 1 and file_names[0].endswith('json'):
from dxtbx.serialize import load
datablock = load.datablock(file_names[0])
assert(len(datablock) == 1)
sweep = datablock[0].extract_sweeps()[0]
else:
from dxtbx.imageset import ImageSetFactory
sweep = ImageSetFactory.new(file_names)[0]
detector = sweep.get_detector()
beam = sweep.get_beam()
print detector.get_ray_intersection(beam.get_s0())[1]
def _make_stills(self, imageset, format_kwargs=None):
''' Make a still imageset. '''
from dxtbx.imageset import ImageSetFactory
from dxtbx.serialize.filename import load_path
filenames = [load_path(p) for p in imageset['images']]
indices = None
if "single_file_indices" in imageset:
indices = imageset['single_file_indices']
assert len(indices) == len(filenames)
return ImageSetFactory.make_imageset(
filenames, None, check_format=self._check_format,
single_file_indices=indices, format_kwargs=format_kwargs)
def set_frame_wedge(self, start, end, apply_offset = True):
'''Set the allowed range of images for processing.'''
# XXX RJG Better to pass slice of imageset here?
if apply_offset:
start = start - self._fp_offset
end = end - self._fp_offset
self._fp_wedge = start, end
if self._fp_matching_images:
images = []
for j in self._fp_matching_images:
if j < start or j > end:
continue
images.append(j)
self._fp_matching_images = images
## reload the header information as well - this will be
## for the old wedge...# read the image header
## XXX this shouldn't be needed
from dxtbx.imageset import ImageSetFactory
imageset = ImageSetFactory.new(self.get_image_name(start))[0]
# print this to the debug channel
Debug.write('Latest header information for image %d:' % start)
print >> Debug, imageset.get_detector()
print >> Debug, imageset.get_scan()
print >> Debug, imageset.get_beam()
print >> Debug, imageset.get_goniometer()
# populate wavelength, beam etc from this
if self._fp_wavelength_prov is None or \
self._fp_wavelength_prov == 'header':
self._fp_wavelength_prov = 'header'
if self._fp_distance_prov is None or \
self._fp_distance_prov == 'header':
self._fp_distance_prov = 'header'
if self._fp_beam_prov is None or \
self._fp_beam_prov == 'header':
self._fp_beam_prov = 'header'
return
def _make_sweep(self, imageset, scan):
''' Make an image sweep. '''
from dxtbx.sweep_filenames import template_image_range
from dxtbx.imageset import ImageSetFactory
from dxtbx.serialize.filename import load_path
# Get the template format
template = load_path(imageset['template'])
# Get the number of images (if no scan is given we'll try
# to find all the images matching the template
if scan is None:
i0, i1 = template_image_range(template)
else:
i0, i1 = scan.get_image_range()
# Make a sweep from the input data
return ImageSetFactory.make_sweep(template,
list(range(i0, i1+1)), None, check_format=self._check_format)
def exercise_to_xds():
if not libtbx.env.has_module("dials_regression"):
print "Skipping exercise_to_xds(): dials_regression not present"
return
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/centroid_test_data",
test=os.path.isdir)
template = os.path.join(data_dir, "centroid_00*.cbf")
file_names = glob.glob(template)
sweep = ImageSetFactory.new(file_names)[0]
to_xds = xds.to_xds(sweep)
s1 = StringIO()
to_xds.XDS_INP(out=s1)
s2 = StringIO()
real_space_a = (-5.327642, -39.034747, -4.988286)
real_space_b = (-35.253495, 7.596265, -22.127661)
real_space_c = (-22.673623, -1.486119, 35.793463)
to_xds.xparm_xds(real_space_a, real_space_b, real_space_c, space_group=1, out=s2)
# run coordinate frame converter on xparm.xds as a sanity check
f = open_tmp_file(suffix="XPARM.XDS", mode="wb")
s2.seek(0)
f.writelines(s2.readlines())
f.close()
from rstbx.cftbx import coordinate_frame_helpers
converter = coordinate_frame_helpers.import_xds_xparm(f.name)
scan = sweep.get_scan()
detector = sweep.get_detector()
goniometer = sweep.get_goniometer()
beam = sweep.get_beam()
assert approx_equal(real_space_a, converter.get_real_space_a())
assert approx_equal(real_space_b, converter.get_real_space_b())
assert approx_equal(real_space_c, converter.get_real_space_c())
assert approx_equal(goniometer.get_rotation_axis(),
converter.get_rotation_axis())
assert approx_equal(
beam.get_direction(), converter.get_sample_to_source().elems)
assert approx_equal(detector[0].get_fast_axis(), converter.get_detector_fast())
assert approx_equal(detector[0].get_slow_axis(), converter.get_detector_slow())
assert approx_equal(detector[0].get_origin(), converter.get_detector_origin())
def _create_imageset(self, format_class, template, filenames):
''' Create a multi file sweep or imageset. '''
from dxtbx.imageset import ImageSetFactory
from dxtbx.sweep_filenames import template_string_number_index
# Get the image range
index = slice(*template_string_number_index(template))
first = int(filenames[0][index])
last = int(filenames[-1][index])
# Check all images in range are present
numbers = [int(f[index]) for f in filenames]
assert(all([x+1==y for x, y in zip(numbers, numbers[1:])]))
# Read the image
fmt = format_class(filenames[0])
# Get the meta data from the format
b = fmt.get_beam()
d = fmt.get_detector()
g = fmt.get_goniometer()
s = fmt.get_scan()
# Update the image range
s.set_image_range((first, last))
# Get the image range
image_range = s.get_image_range()
image_range = (image_range[0], image_range[1]+1)
# Create the sweep
imageset = ImageSetFactory.make_sweep(
template, range(*image_range),
format_class,
b, d, g, s)
# Return the imageset
return imageset
def _make_sequence(
self,
imageset,
beam=None,
detector=None,
goniometer=None,
scan=None,
format_kwargs=None,
):
"""Make an image sequence."""
# Get the template format
template = resolve_path(imageset["template"], directory=self._directory)
# Get the number of images (if no scan is given we'll try
# to find all the images matching the template
if scan is None:
i0, i1 = template_image_range(template)
else:
i0, i1 = scan.get_image_range()
format_class = None
if self._check_format is False:
if "single_file_indices" in imageset:
format_class = FormatMultiImage
# Make a sequence from the input data
return ImageSetFactory.make_sequence(
template,
list(range(i0, i1 + 1)),
format_class=format_class,
check_format=self._check_format,
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
format_kwargs=format_kwargs,
)
def run(self, experiments, reflections):
from dials.util import log
self.logger.log_step_time("INTEGRATE")
logfile = os.path.splitext(self.logger.rank_log_file_path)[0] + "_integrate.log"
log.config(logfile=logfile)
processor = integrate_only_processor(self.params)
# Re-generate the image sets using their format classes so we can read the raw data
# Integrate the experiments one at a time to not use up memory
all_integrated = flex.reflection_table()
current_imageset = None
current_imageset_path = None
for expt_id, expt in enumerate(experiments):
assert len(expt.imageset.paths()) == 1 and len(expt.imageset) == 1
self.logger.log("Starting integration experiment %d"%expt_id)
refls = reflections.select(reflections['exp_id'] == expt.identifier)
if expt.imageset.paths()[0] != current_imageset_path:
current_imageset_path = expt.imageset.paths()[0]
current_imageset = ImageSetFactory.make_imageset(expt.imageset.paths())
idx = expt.imageset.indices()[0]
expt.imageset = current_imageset[idx:idx+1]
idents = refls.experiment_identifiers()
del idents[expt_id]
idents[0] = expt.identifier
refls['id'] = flex.int(len(refls), 0)
integrated = processor.integrate(experiments[expt_id:expt_id+1], refls)
idents = integrated.experiment_identifiers()
del idents[0]
idents[expt_id] = expt.identifier
integrated['id'] = flex.int(len(integrated), expt_id)
all_integrated.extend(integrated)
self.logger.log("Integration done, %d experiments, %d reflections"%(len(experiments), len(all_integrated)))
return experiments, all_integrated
def basic_imageset_from_dict(d, directory=None):
"""Construct an ImageSet class from the dictionary."""
# Get the filename list and create the imageset
filenames = [
resolve_path(str(p), directory=directory) for p in d["filenames"]
]
imageset = ImageSetFactory.new(filenames)[0]
# Set some external lookups
if "mask" in d and d["mask"] is not None and d["mask"] != "":
path = resolve_path(d["mask"], directory=directory)
with open(path) as infile:
imageset.external_lookup.mask.filename = path
imageset.external_lookup.mask.data = ImageBool(pickle.load(infile))
if "gain" in d and d["gain"] is not None and d["gain"] != "":
path = resolve_path(d["gain"], directory=directory)
with open(path) as infile:
imageset.external_lookup.gain.filename = path
imageset.external_lookup.gain.data = ImageDouble(
pickle.load(infile))
if "pedestal" in d and d["pedestal"] is not None and d["pedestal"] != "":
path = resolve_path(d["pedestal"], directory=directory)
with open(path) as infile:
imageset.external_lookup.pedestal.filename = path
imageset.external_lookup.pedestal.data = ImageDouble(
pickle.load(infile))
# Get the existing models as dictionaries
beam_dict = imageset.get_beam(0).to_dict()
detector_dict = imageset.get_detector(0).to_dict()
# Set models
imageset.set_beam(BeamFactory.from_dict(d.get("beam"), beam_dict))
imageset.set_detector(
DetectorFactory.from_dict(d.get("detector"), detector_dict))
return imageset
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_pickle_imageset(centroid_files):
from dxtbx.imageset import ImageSetFactory, ImageSweep
sweep = ImageSetFactory.new(centroid_files)[0]
# Read the 5th image
image = sweep[4]
# Pickle, then unpickle
sweep2 = pickle.loads(pickle.dumps(sweep))
assert sweep.get_template() == sweep2.get_template()
assert sweep.get_array_range() == sweep2.get_array_range()
assert sweep.get_beam() == sweep2.get_beam()
assert sweep.get_goniometer() == sweep2.get_goniometer()
assert sweep.get_scan() == sweep2.get_scan()
assert sweep.paths() == sweep2.paths()
assert sweep == sweep2
# Check auxiliary methods after pickling
sweep3 = sweep2[0:4]
sweep4 = sweep3[0:2]
sweep4.get_detectorbase(0)
sweep4[0]
def tst_consistent(self):
from dxtbx.imageset import ImageSetFactory
from glob import glob
from os.path import join
from dxtbx.model import Scan
# Create a sweep
sweep_filenames = join(self.path, 'centroid_test_data',
'centroid*.cbf')
sweep = ImageSetFactory.new(sorted(glob(sweep_filenames)))[0]
# Create experiment with sweep and good scan
e = Experiment(imageset=sweep, scan=sweep.get_scan())
assert (e.is_consistent())
# Create experiment with sweep and defective scan
scan = sweep.get_scan()
scan.set_image_range((1, 1))
e = Experiment(imageset=sweep, scan=scan)
#assert(not e.is_consistent()) # FIXME
## Create experiment with imageset and good scan
#assert(e.is_consistent())
## Create experiment with imageset and non-still scan
#assert(not e.is_consistent())
## Create experiment with imageset and scan with more than 1 image
#assert(not e.is_consistent())
## Create experiment with imageset and defective scan
#assert(not e.is_consistent())
# Test passed
print 'OK'
def tst_cspad_hierarchy(self):
from dxtbx.serialize import dump, load
from dxtbx.imageset import ImageSetFactory
import libtbx.load_env
import os
from glob import glob
try:
path = libtbx.env.dist_path('dials_regression')
except Exception:
print "No dials_regression directory found"
return
# Get the imageset
filename = os.path.join(path, "spotfinding_test_data", "idx*.cbf")
imageset = ImageSetFactory.new(glob(filename))
assert(len(imageset) == 1)
imageset = imageset[0]
# Dump and reload
from uuid import uuid4
filename = '%s.json' % uuid4().hex
dump.imageset(imageset, filename)
imageset2 = load.imageset(filename)
# Check they're are the same
assert(imageset2.get_beam() == imageset.get_beam())
d1 = imageset.get_detector()
d2 = imageset2.get_detector()
assert(len(d1) == len(d2))
for i, (p1, p2) in enumerate(zip(d1, d2)):
assert(p1 == p2)
assert(imageset2.get_detector() == imageset.get_detector())
assert(imageset2 == imageset)
# Test passed
print 'OK'
def _make_sweep(self, imageset, scan, format_kwargs=None):
''' Make an image sweep. '''
from dxtbx.sweep_filenames import template_image_range
from dxtbx.imageset import ImageSetFactory
from dxtbx.serialize.filename import load_path
# Get the template format
template = load_path(imageset['template'])
# Get the number of images (if no scan is given we'll try
# to find all the images matching the template
if scan is None:
i0, i1 = template_image_range(template)
else:
i0, i1 = scan.get_image_range()
# Make a sweep from the input data
return ImageSetFactory.make_sweep(
template,
list(range(i0, i1+1)),
None,
check_format=self._check_format,
scan=scan,
format_kwargs=format_kwargs)
def tst_cspad_hierarchy(self):
from dxtbx.serialize import dump, load
from dxtbx.imageset import ImageSetFactory
import libtbx.load_env
import os
from glob import glob
try:
path = libtbx.env.dist_path('dials_regression')
except Exception:
print "No dials_regression directory found"
return
# Get the imageset
filename = os.path.join(path, "spotfinding_test_data", "idx*.cbf")
imageset = ImageSetFactory.new(glob(filename))
assert (len(imageset) == 1)
imageset = imageset[0]
# Dump and reload
from uuid import uuid4
filename = '%s.json' % uuid4().hex
dump.imageset(imageset, filename)
imageset2 = load.imageset(filename)
# Check they're are the same
assert (imageset2.get_beam() == imageset.get_beam())
d1 = imageset.get_detector()
d2 = imageset2.get_detector()
assert (len(d1) == len(d2))
for i, (p1, p2) in enumerate(zip(d1, d2)):
assert (p1 == p2)
assert (imageset2.get_detector() == imageset.get_detector())
assert (imageset2 == imageset)
# Test passed
print 'OK'
def do_import(filename):
datablocks = DataBlockFactory.from_filenames([filename])
if len(datablocks) == 0:
try:
datablocks = DataBlockFactory.from_json_file(filename)
except ValueError:
raise Abort("Could not load %s" % filename)
if len(datablocks) == 0:
raise Abort("Could not load %s" % filename)
if len(datablocks) > 1:
raise Abort("Got multiple datablocks from file %s" % filename)
# Ensure the indexer and downstream applications treat this as set of stills
reset_sets = []
from dxtbx.imageset import ImageSetFactory
for imageset in datablocks[0].extract_imagesets():
image = ImageSetFactory.imageset_from_anyset(imageset)
image.set_scan(None)
image.set_goniometer(None)
reset_sets.append(image)
return DataBlockFactory.from_imageset(reset_sets)[0]
def imagesequence_from_dict(d, check_format=True, directory=None):
"""Construct and image sequence from the dictionary."""
# Get the template (required)
template = resolve_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 sequence
try:
sequence = ImageSetFactory.from_template(
template,
image_range,
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
check_format=check_format,
)[0]
except Exception:
indices = list(range(image_range[0], image_range[1] + 1))
sequence = ImageSetFactory.make_sequence(
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"] != "":
path = resolve_path(d["mask"], directory=directory)
with open(path) as infile:
sequence.external_lookup.mask.filename = path
sequence.external_lookup.mask.data = ImageBool(pickle.load(infile))
if "gain" in d and d["gain"] is not None and d["gain"] != "":
path = resolve_path(d["gain"], directory=directory)
with open(path) as infile:
sequence.external_lookup.gain.filename = path
sequence.external_lookup.gain.data = ImageDouble(
pickle.load(infile))
if "pedestal" in d and d["pedestal"] is not None and d["pedestal"] != "":
path = resolve_path(d["pedestal"], directory=directory)
with open(path) as infile:
sequence.external_lookup.pedestal.filename = path
sequence.external_lookup.pedestal.data = ImageDouble(
pickle.load(infile))
return sequence
def import_xds_as_still(xdsinp, xparm_in):
#from dxtbx.serialize import xds
from dxtbx.datablock import DataBlockFactory
# Get the sweep from the XDS files
#sweep = xds.to_imageset(xds_inp, xds_other)
from iotbx.xds import xds_inp
from dxtbx.imageset import ImageSetFactory
import dxtbx
# Read the input filename
handle = xds_inp.reader()
handle.read_file(xdsinp)
# Get the template
template = handle.name_template_of_data_frames[0]
image_range = handle.data_range
detector_name = handle.detector
#assert image_range[0] == image_range[1]
im_nr = int((image_range[1] - image_range[0] + 1) / 2)
from yamtbx.dataproc.dataset import template_to_filenames
# Create the imageset
#imageset = ImageSetFactory.from_template(template, image_range=image_range, check_format=False)[0]
imageset = ImageSetFactory.make_imageset(
[os.path.realpath(template_to_filenames(template, im_nr, im_nr)[0])])
models = dxtbx.load(xparm_in)
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))
imageset.set_beam(models.get_beam())
imageset.set_detector(detector)
imageset.set_goniometer(None)
imageset.set_scan(None)
#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)
from dxtbx.serialize import xds
# Get the crystal from the XDS files
crystal = xds.to_crystal(xparm_in)
# Create the experiment list
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
# Set the crystal in the experiment list
assert (len(experiments) == 1)
# Return the experiment list
return experiments
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 run(argv=None):
if (argv is None):
argv = sys.argv
# XXX Could/should handle effective metrology the same way, except
# it does not have a single scope.
work_phil = phil.process_command_line(args=argv[1:],
master_string=master_str + phil_str +
additional_spotfinder_phil_defs)
work_params = work_phil.work.extract()
app = wx.App(0)
wx.SystemOptions.SetOptionInt("osx.openfiledialog.always-show-types", 1)
frame = XrayFrame(None, -1, "X-ray image display", size=(800, 720))
frame.Show()
# show settings panel
frame.OnShowSettings(None)
frame.settings_frame.panel.center_ctrl.SetValue(work_params.beam_center)
frame.settings_frame.panel.integ_ctrl.SetValue(
work_params.show_integration_results)
frame.settings_frame.panel.spots_ctrl.SetValue(
work_params.show_spotfinder_results)
frame.settings.show_effective_tiling = work_params.show_effective_tiling
frame.settings_frame.panel.collect_values()
if (work_params.effective_metrology is not None):
from xfel.cftbx.detector.metrology import \
master_phil, metrology_as_transformation_matrices
stream = open(work_params.effective_metrology)
metrology_phil = master_phil.fetch(sources=[phil.parse(stream.read())])
stream.close()
frame.metrology_matrices = metrology_as_transformation_matrices(
metrology_phil.extract())
# Update initial settings with values from the command line. Needs
# to be done before image is loaded (but after the frame is
# instantiated).
frame.params = work_params
frame.init_pyslip()
frame.pyslip.tiles.user_requests_antialiasing = work_params.anti_aliasing
frame.pyslip.tiles.show_untrusted = frame.params.show_untrusted
paths = work_phil.remaining_args
if (len(paths) == 1 and os.path.basename(paths[0]) == "DISTL_pickle"):
assert os.path.isfile(paths[0])
frame.load_distl_output(paths[0])
elif (len(paths) > 0):
frame.CHOOSER_SIZE = 1500
from dxtbx.imageset import ImageSetFactory
from rstbx.slip_viewer.frame import chooser_wrapper
sets = ImageSetFactory.new(paths)
for imgset in sets:
for idx in imgset.indices():
frame.add_file_name_or_data(chooser_wrapper(imgset, idx))
idx = sets[0].indices()[0]
frame.load_image(chooser_wrapper(sets[0], idx))
app.MainLoop()
return 0
def __call__(self, imageset):
"""
Override the parameters
"""
from copy import deepcopy
from dxtbx.imageset import ImageSequence, ImageSetFactory
from dxtbx.model import (
BeamFactory,
DetectorFactory,
GoniometerFactory,
ScanFactory,
)
if self.params.geometry.convert_sequences_to_stills:
imageset = ImageSetFactory.imageset_from_anyset(imageset)
for j in imageset.indices():
imageset.set_scan(None, j)
imageset.set_goniometer(None, j)
if not isinstance(imageset, ImageSequence):
if self.params.geometry.convert_stills_to_sequences:
imageset = self.convert_stills_to_sequence(imageset)
if isinstance(imageset, ImageSequence):
beam = BeamFactory.from_phil(self.params.geometry, imageset.get_beam())
detector = DetectorFactory.from_phil(
self.params.geometry, imageset.get_detector(), beam
)
goniometer = GoniometerFactory.from_phil(
self.params.geometry, imageset.get_goniometer()
)
scan = ScanFactory.from_phil(
self.params.geometry, deepcopy(imageset.get_scan())
)
i0, i1 = scan.get_array_range()
j0, j1 = imageset.get_scan().get_array_range()
if i0 < j0 or i1 > j1:
imageset = self.extrapolate_imageset(
imageset=imageset,
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
)
else:
imageset.set_beam(beam)
imageset.set_detector(detector)
imageset.set_goniometer(goniometer)
imageset.set_scan(scan)
else:
for i in range(len(imageset)):
beam = BeamFactory.from_phil(self.params.geometry, imageset.get_beam(i))
detector = DetectorFactory.from_phil(
self.params.geometry, imageset.get_detector(i), beam
)
goniometer = GoniometerFactory.from_phil(
self.params.geometry, imageset.get_goniometer(i)
)
scan = ScanFactory.from_phil(self.params.geometry, imageset.get_scan(i))
imageset.set_beam(beam, i)
imageset.set_detector(detector, i)
imageset.set_goniometer(goniometer, i)
imageset.set_scan(scan, i)
return imageset
def factory(list_of_images):
from dxtbx.imageset import ImageSetFactory
sweeps = ImageSetFactory.new(list_of_images)
assert len(sweeps) == 1
return sweeps[0]
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 optparse import OptionParser
from dxtbx.serialize import dump
from dxtbx.imageset import ImageSetFactory
# Specify the command line options
usage = "usage: %prog [options] /path/to/image/files.ext"
parser = OptionParser(usage)
# Add a verbose option (False by default)
parser.add_option('-o', '--output-file',
dest='output_file', type="string",
default="imageset.json",
help='Enter a destination filename for serialization')
# Parse the arguments
(options, args) = parser.parse_args()
# Print help if no arguments specified, otherwise call spot prediction
if len(args) == 0:
print parser.print_help()
else:
imagesets = ImageSetFactory.new(args)
if len(imagesets) == 0:
print "Error: no imagesets to serialize."
elif len(imagesets) > 1:
print "Error: more than 1 imageset has been specified"
else:
dump.imageset(imagesets[0], options.output_file)
print "Serialized imageset to {0}".format(options.output_file)
def test_to_xds(dials_regression, tmpdir):
tmpdir.chdir()
template = os.path.join(dials_regression, "centroid_test_data", "centroid_00*.cbf")
file_names = glob.glob(template)
sweep = ImageSetFactory.new(file_names)[0]
to_xds = xds.to_xds(sweep)
s1 = to_xds.XDS_INP()
expected = """\
DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=495976
SENSOR_THICKNESS= 0.320
!SENSOR_MATERIAL / THICKNESS Si 0.320
!SILICON= 3.960382
DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
NX=2463 NY=2527 QX=0.1720 QY=0.1720
DETECTOR_DISTANCE= 190.180000
ORGX= 1235.84 ORGY= 1279.58
ROTATION_AXIS= 1.00000 0.00000 0.00000
STARTING_ANGLE= 0.000
OSCILLATION_RANGE= 0.200
X-RAY_WAVELENGTH= 0.97950
INCIDENT_BEAM_DIRECTION= -0.000 -0.000 1.021
FRACTION_OF_POLARIZATION= 0.999
POLARIZATION_PLANE_NORMAL= 0.000 1.000 0.000
NAME_TEMPLATE_OF_DATA_FRAMES= %s
TRUSTED_REGION= 0.0 1.41
UNTRUSTED_RECTANGLE= 487 495 0 2528
UNTRUSTED_RECTANGLE= 981 989 0 2528
UNTRUSTED_RECTANGLE= 1475 1483 0 2528
UNTRUSTED_RECTANGLE= 1969 1977 0 2528
UNTRUSTED_RECTANGLE= 0 2464 195 213
UNTRUSTED_RECTANGLE= 0 2464 407 425
UNTRUSTED_RECTANGLE= 0 2464 619 637
UNTRUSTED_RECTANGLE= 0 2464 831 849
UNTRUSTED_RECTANGLE= 0 2464 1043 1061
UNTRUSTED_RECTANGLE= 0 2464 1255 1273
UNTRUSTED_RECTANGLE= 0 2464 1467 1485
UNTRUSTED_RECTANGLE= 0 2464 1679 1697
UNTRUSTED_RECTANGLE= 0 2464 1891 1909
UNTRUSTED_RECTANGLE= 0 2464 2103 2121
UNTRUSTED_RECTANGLE= 0 2464 2315 2333
DATA_RANGE= 1 9
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT\
""" % os.path.join(
dials_regression, "centroid_test_data", "centroid_????.cbf"
)
assert s1 == expected
real_space_a = (-5.327642, -39.034747, -4.988286)
real_space_b = (-35.253495, 7.596265, -22.127661)
real_space_c = (-22.673623, -1.486119, 35.793463)
s2 = to_xds.xparm_xds(real_space_a, real_space_b, real_space_c, space_group=1)
# run coordinate frame converter on xparm.xds as a sanity check
with open("xparm.xds", mode="wb") as fh:
fh.write(s2.encode("ASCII"))
from rstbx.cftbx import coordinate_frame_helpers
converter = coordinate_frame_helpers.import_xds_xparm("xparm.xds")
detector = sweep.get_detector()
goniometer = sweep.get_goniometer()
beam = sweep.get_beam()
assert approx_equal(real_space_a, converter.get_real_space_a())
assert approx_equal(real_space_b, converter.get_real_space_b())
assert approx_equal(real_space_c, converter.get_real_space_c())
assert approx_equal(goniometer.get_rotation_axis(), converter.get_rotation_axis())
assert approx_equal(beam.get_direction(), converter.get_sample_to_source().elems)
assert approx_equal(detector[0].get_fast_axis(), converter.get_detector_fast())
assert approx_equal(detector[0].get_slow_axis(), converter.get_detector_slow())
assert approx_equal(detector[0].get_origin(), converter.get_detector_origin())
def _load_datablocks(self, obj, check_format=True):
''' Create the datablock from a dictionary. '''
from libtbx.containers import OrderedDict
from dxtbx.format.Registry import Registry
from dxtbx.model import Beam, Detector, Scan
from dxtbx.model import Detector
from dxtbx.serialize.filename import load_path
from dxtbx.imageset import ImageSetFactory, ImageGrid
# If we have a list, extract for each dictionary in the list
if isinstance(obj, list):
return [self._load_datablocks(dd, check_format) for dd in obj]
elif not isinstance(obj, dict):
raise RuntimeError('unknown datablock dictionary type')
assert(obj['__id__'] == 'DataBlock')
# Get the list of models
blist = obj.get('beam', [])
dlist = obj.get('detector', [])
glist = obj.get('goniometer', [])
slist = obj.get('scan', [])
def load_models(obj):
try:
beam = Beam.from_dict(blist[obj['beam']])
except Exception:
beam = None
try:
dobj = dlist[obj['detector']]
detector = Detector.from_dict(dobj)
except Exception:
detector = None
try:
from dxtbx.serialize import goniometer
gonio = goniometer.from_dict(glist[obj['goniometer']])
except Exception:
gonio = None
try:
scan = Scan.from_dict(slist[obj['scan']])
except Exception:
scan = None
return beam, detector, gonio, scan
# Loop through all the imagesets
imagesets = []
for imageset in obj['imageset']:
ident = imageset['__id__']
if "params" in imageset:
format_kwargs = imageset['params']
else:
format_kwargs = {}
if ident == 'ImageSweep':
beam, detector, gonio, scan = load_models(imageset)
if "template" in imageset:
template = load_path(imageset['template'])
i0, i1 = scan.get_image_range()
iset = ImageSetFactory.make_sweep(
template, range(i0, i1+1), None,
beam, detector, gonio, scan, check_format,
format_kwargs=format_kwargs)
if 'mask' in imageset and imageset['mask'] is not None:
imageset['mask'] = load_path(imageset['mask'])
iset.external_lookup.mask.filename = imageset['mask']
if check_format:
with open(imageset['mask']) as infile:
iset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in imageset and imageset['gain'] is not None:
imageset['gain'] = load_path(imageset['gain'])
iset.external_lookup.gain.filename = imageset['gain']
if check_format:
with open(imageset['gain']) as infile:
iset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in imageset and imageset['pedestal'] is not None:
imageset['pedestal'] = load_path(imageset['pedestal'])
iset.external_lookup.pedestal.filename = imageset['pedestal']
if check_format:
with open(imageset['pedestal']) as infile:
iset.external_lookup.pedestal.data = pickle.load(infile)
elif "master" in imageset:
template = load_path(imageset['master'])
i0, i1 = scan.get_image_range()
indices = imageset['images']
assert min(indices) == i0-1 and max(indices) == i1-1
iset = ImageSetFactory.make_sweep(
template, range(i0, i1+1), None,
beam, detector, gonio, scan, check_format,
format_kwargs=format_kwargs)
if 'mask' in imageset and imageset['mask'] is not None:
imageset['mask'] = load_path(imageset['mask'])
iset.external_lookup.mask.filename = imageset['mask']
if check_format:
with open(imageset['mask']) as infile:
iset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in imageset and imageset['gain'] is not None:
imageset['gain'] = load_path(imageset['gain'])
iset.external_lookup.gain.filename = imageset['gain']
if check_format:
with open(imageset['gain']) as infile:
iset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in imageset and imageset['pedestal'] is not None:
imageset['pedestal'] = load_path(imageset['pedestal'])
iset.external_lookup.pedestal.filename = imageset['pedestal']
if check_format:
with open(imageset['pedestal']) as infile:
iset.external_lookup.pedestal.data = pickle.load(infile)
imagesets.append(iset)
elif ident == 'ImageSet' or ident == "ImageGrid":
filenames = [image['filename'] for image in imageset['images']]
indices = [image['image'] for image in imageset['images'] if 'image' in image]
assert len(indices) == 0 or len(indices) == len(filenames)
iset = ImageSetFactory.make_imageset(
filenames, None, check_format, indices, format_kwargs=format_kwargs)
if ident == "ImageGrid":
grid_size = imageset['grid_size']
iset = ImageGrid.from_imageset(iset, grid_size)
for i, image in enumerate(imageset['images']):
beam, detector, gonio, scan = load_models(image)
iset.set_beam(beam, i)
iset.set_detector(detector, i)
iset.set_goniometer(gonio, i)
iset.set_scan(scan, i)
if 'mask' in imageset and imageset['mask'] is not None:
imageset['mask'] = load_path(imageset['mask'])
iset.external_lookup.mask.filename = imageset['mask']
if check_format:
with open(imageset['mask']) as infile:
iset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in imageset and imageset['gain'] is not None:
imageset['gain'] = load_path(imageset['gain'])
iset.external_lookup.gain.filename = imageset['gain']
if check_format:
with open(imageset['gain']) as infile:
iset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in imageset and imageset['pedestal'] is not None:
imageset['pedestal'] = load_path(imageset['pedestal'])
iset.external_lookup.pedestal.filename = imageset['pedestal']
if check_format:
with open(imageset['pedestal']) as infile:
iset.external_lookup.pedestal.data = pickle.load(infile)
imagesets.append(iset)
else:
raise RuntimeError('expected ImageSet/ImageSweep, got %s' % ident)
# Return the datablock
return DataBlock(imagesets)
def factory(list_of_images): from dxtbx.imageset import ImageSetFactory sweeps = ImageSetFactory.new(list_of_images) assert(len(sweeps) == 1) return sweeps[0]
img = dxtbx.load(imgname)
detector = img.get_detector()
beam = img.get_beam()
scan = img.get_scan()
gonio = img.get_goniometer()
print "s0 from ",imgname,": ",beam.get_s0()
print "wavelength from ",imgname,": ",beam.get_wavelength()
crystal = copy.deepcopy(experiments.crystals()[0])
axis = gonio.get_rotation_axis()
start_angle, delta_angle = scan.get_oscillation()
crystal.rotate_around_origin(axis, start_angle + (delta_angle/2), deg=True)
if (output_format == "json"):
exp_list = ExperimentList()
exp_list.append(Experiment(imageset=ImageSetFactory.make_imageset(list([imgname])),
beam=beam,
detector=detector,
goniometer=gonio,
scan=scan,
crystal=crystal))
if (add_background_images==True):
if (len(bkglist) != 1):
bkgname=bkglist[i]
exp_list[0].imageset.external_lookup.pedestal.filename=os.path.abspath(bkgname)
dump.experiment_list(exp_list,json_dir+"/experiments_for_lunus_{0:05d}.json".format(imnum))
else:
from scitbx import matrix
A_matrix = matrix.sqr(crystal.get_A()).inverse()
At = np.asarray(A_matrix.transpose()).reshape((3,3))
print At
def combine(datablock_list, reflections_list, params):
'''
Combine the found spots.
'''
from dxtbx.datablock import BeamComparison
from dxtbx.datablock import DetectorComparison
from dxtbx.datablock import GoniometerComparison
from dxtbx.datablock import DataBlock
from dxtbx.imageset import ImageSetFactory
from dials.algorithms.spot_finding import StrongSpotCombiner
from logging import info
from dials.array_family import flex
assert len(datablock_list) == len(reflections_list)
# Get a list of imagesets
imageset_list = []
for db in datablock_list:
iset = db.extract_imagesets()
assert len(iset) == 1
imageset_list.append(iset[0])
compare_beam = BeamComparison(
wavelength_tolerance=params.input.tolerance.beam.wavelength,
direction_tolerance=params.input.tolerance.beam.direction,
polarization_normal_tolerance=params.input.tolerance.beam.polarization_normal,
polarization_fraction_tolerance=params.input.tolerance.beam.polarization_fraction)
compare_detector = DetectorComparison(
fast_axis_tolerance=params.input.tolerance.detector.fast_axis,
slow_axis_tolerance=params.input.tolerance.detector.slow_axis,
origin_tolerance=params.input.tolerance.detector.origin)
compare_goniometer = GoniometerComparison(
rotation_axis_tolerance=params.input.tolerance.goniometer.rotation_axis,
fixed_rotation_tolerance=params.input.tolerance.goniometer.fixed_rotation,
setting_rotation_tolerance=params.input.tolerance.goniometer.setting_rotation)
scan_tolerance = params.input.tolerance.scan.oscillation
# The initial models
format_class = imageset_list[0].reader().get_format_class()
beam = imageset_list[0].get_beam()
detector = imageset_list[0].get_detector()
goniometer = imageset_list[0].get_goniometer()
scan = imageset_list[0].get_scan()
template = imageset_list[0].get_template()
# Check all the models
for imageset in imageset_list[1:]:
b = imageset.get_beam()
d = imageset.get_detector()
g = imageset.get_goniometer()
s = imageset.get_scan()
if not imageset.reader().get_format_class() == format_class:
raise RuntimeError('Format classes do not match')
if not imageset.get_template() == template:
raise RuntimeError('Templates do not match')
if not compare_beam(beam, b):
raise RuntimeError('Beam models are too dissimilar')
if not compare_detector(detector, d):
raise RuntimeError('Detector models are too dissimilar')
if not compare_goniometer(goniometer, g):
raise RuntimeError('Goniometer models are too dissimilar')
try:
scan.append(s, scan_tolerance=scan_tolerance)
except Exception:
raise RuntimeError('Scans do not match')
# Get the image range
image_range = scan.get_image_range()
image_range = (image_range[0], image_range[1]+1)
# Create the sweep
imageset = ImageSetFactory.make_sweep(
template, range(*image_range),
format_class,
beam, detector,
goniometer, scan)
# Combine spots
combiner = StrongSpotCombiner()
for index, rlist in enumerate(reflections_list, start=1):
assert rlist['id'].all_eq(0)
info("Combining %d reflections from reflection list %d" % (
len(rlist),
index))
combiner.add(rlist['shoebox'])
shoeboxes = combiner.shoeboxes()
# Calculate the spot centroids and intensities
info('Combined into %d reflections' % len(shoeboxes))
centroid = shoeboxes.centroid_valid()
info('Calculated {0} spot centroids'.format(len(shoeboxes)))
intensity = shoeboxes.summed_intensity()
info('Calculated {0} spot intensities'.format(len(shoeboxes)))
# Construct the reflection table
reflections = flex.reflection_table(
flex.observation(
shoeboxes.panels(),
centroid,
intensity),
shoeboxes)
reflections['id'] = flex.int(len(reflections), 0)
reflections.set_flags(
flex.size_t_range(len(reflections)),
reflections.flags.strong)
# Return the datablock and reflections
return DataBlock([imageset]), reflections
img = dxtbx.load(imgname)
# detector = img.get_detector()
# beam = img.get_beam()
scan = img.get_scan()
gonio = img.get_goniometer()
print "s0 from ",imgname,": ",beam.get_s0()
print "wavelength from ",imgname,": ",beam.get_wavelength()
crystal = copy.deepcopy(experiments.crystals()[0])
axis = gonio.get_rotation_axis()
start_angle, delta_angle = scan.get_oscillation()
crystal.rotate_around_origin(axis, start_angle + (delta_angle/2), deg=True)
if (output_format == "json"):
exp_list = ExperimentList()
exp_list.append(Experiment(imageset=ImageSetFactory.make_imageset(list([imgname])),
beam=beam,
detector=detector,
goniometer=gonio,
scan=scan,
crystal=crystal))
if (add_background_images==True):
if (len(bkglist) != 1):
bkgname=bkglist[i]
else:
bkgname=bkglist[0]
exp_list[0].imageset.external_lookup.pedestal.filename=os.path.abspath(bkgname)
dump.experiment_list(exp_list,json_dir+"/experiments_for_lunus_{0:05d}.json".format(imnum))
else:
from scitbx import matrix
A_matrix = matrix.sqr(crystal.get_A()).inverse()
def factory(list_of_images):
sequences = ImageSetFactory.new(list_of_images)
assert len(sequences) == 1
return sequences[0]
def index(experiments, reflections, params):
"""
Index the input experiments and reflections.
Args:
experiments: The experiments to index
reflections (list): A list of reflection tables containing strong spots
params: An instance of the indexing phil scope
Returns:
(tuple): tuple containing:
experiments: The indexed experiment list
reflections (dials.array_family.flex.reflection_table):
The indexed reflections
"""
if experiments.crystals()[0] is not None:
known_crystal_models = experiments.crystals()
else:
known_crystal_models = None
if len(reflections) == 0:
raise ValueError("No reflection lists found in input")
elif len(reflections) == 1:
reflections[0]["imageset_id"] = reflections[0]["id"]
elif len(reflections) > 1:
assert len(reflections) == len(experiments)
for i in range(len(reflections)):
reflections[i]["imageset_id"] = flex.int(len(reflections[i]), i)
if i > 0:
reflections[0].extend(reflections[i])
reflections = reflections[0]
# If there are scan and goniometer objects present but the oscillation angle is zero
# then expt.scan and expt.goniometer to None, as the behaviour of some downstream
# algorithms depend on the presence/absence of these objects
for expt in experiments:
if (expt.goniometer is not None and expt.scan is not None
and expt.scan.is_still()):
expt.imageset = ImageSetFactory.imageset_from_anyset(expt.imageset)
expt.goniometer = None
expt.scan = None
if params.indexing.image_range:
reflections = slice_reflections(reflections,
params.indexing.image_range)
if len(experiments) == 1 or params.indexing.joint_indexing:
indexed_experiments, indexed_reflections = _index_experiments(
experiments,
reflections,
copy.deepcopy(params),
known_crystal_models=known_crystal_models,
)
else:
indexed_experiments = ExperimentList()
indexed_reflections = flex.reflection_table()
with concurrent.futures.ProcessPoolExecutor(
max_workers=params.indexing.nproc) as pool:
futures = []
for i_expt, expt in enumerate(experiments):
refl = reflections.select(reflections["imageset_id"] == i_expt)
refl["imageset_id"] = flex.size_t(len(refl), 0)
futures.append(
pool.submit(
_index_experiments,
ExperimentList([expt]),
refl,
copy.deepcopy(params),
known_crystal_models=known_crystal_models,
))
for future in concurrent.futures.as_completed(futures):
try:
idx_expts, idx_refl = future.result()
except Exception as e:
print(e)
else:
if idx_expts is None:
continue
for j_expt, _ in enumerate(idx_expts):
sel = idx_refl["id"] == j_expt
idx_refl["id"].set_selected(
sel,
len(indexed_experiments) + j_expt)
idx_refl["imageset_id"] = flex.size_t(
len(idx_refl), i_expt)
indexed_reflections.extend(idx_refl)
indexed_experiments.extend(idx_expts)
return indexed_experiments, indexed_reflections
def exercise_to_xds():
if not libtbx.env.has_module("dials"):
print "Skipping test: dials not present"
return
if not libtbx.env.has_module("dials_regression"):
print "Skipping exercise_to_xds(): dials_regression not present"
return
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/centroid_test_data",
test=os.path.isdir)
template = os.path.join(data_dir, "centroid_*.cbf")
file_names = glob.glob(template)
expected_output = """\
DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=495976
SENSOR_THICKNESS= 0.320
DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
NX=2463 NY=2527 QX=0.1720 QY=0.1720
DETECTOR_DISTANCE= 190.180
ORGX= 1235.84 ORGY= 1279.58
ROTATION_AXIS= 1.00000 0.00000 0.00000
STARTING_ANGLE= 0.000
OSCILLATION_RANGE= 0.200
X-RAY_WAVELENGTH= 0.97950
INCIDENT_BEAM_DIRECTION= -0.000 -0.000 1.021
FRACTION_OF_POLARIZATION= 0.999
POLARIZATION_PLANE_NORMAL= 0.000 1.000 0.000
NAME_TEMPLATE_OF_DATA_FRAMES= %s
TRUSTED_REGION= 0.0 1.41
UNTRUSTED_RECTANGLE= 487 495 0 2528
UNTRUSTED_RECTANGLE= 981 989 0 2528
UNTRUSTED_RECTANGLE= 1475 1483 0 2528
UNTRUSTED_RECTANGLE= 1969 1977 0 2528
UNTRUSTED_RECTANGLE= 0 2464 195 213
UNTRUSTED_RECTANGLE= 0 2464 407 425
UNTRUSTED_RECTANGLE= 0 2464 619 637
UNTRUSTED_RECTANGLE= 0 2464 831 849
UNTRUSTED_RECTANGLE= 0 2464 1043 1061
UNTRUSTED_RECTANGLE= 0 2464 1255 1273
UNTRUSTED_RECTANGLE= 0 2464 1467 1485
UNTRUSTED_RECTANGLE= 0 2464 1679 1697
UNTRUSTED_RECTANGLE= 0 2464 1891 1909
UNTRUSTED_RECTANGLE= 0 2464 2103 2121
UNTRUSTED_RECTANGLE= 0 2464 2315 2333
DATA_RANGE= 1 9
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT\
""" % (template.replace("*", "????"))
cmd = " ".join(["dxtbx.to_xds"] + file_names)
result = easy_run.fully_buffered(cmd)
# allow extra lines to have been added (these may be comments)
for record in expected_output.split('\n'):
assert record.strip() in "\n".join(result.stdout_lines), record
# now test reading from a json file
sweep = ImageSetFactory.new(file_names)[0]
f = open_tmp_file(suffix="sweep.json", mode="wb")
dump.imageset(sweep, f)
f.close()
cmd = " ".join(["dxtbx.to_xds", f.name])
print cmd
result = easy_run.fully_buffered(cmd)
# allow extra lines to have been added (these may be comments)
for record in expected_output.split('\n'):
assert record.strip() in "\n".join(result.stdout_lines), record
def imagesweep_from_dict(d, check_format=True, directory=None):
'''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']), 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 combine(datablock_list, reflections_list, params):
'''
Combine the found spots.
'''
from dxtbx.datablock import BeamComparison
from dxtbx.datablock import DetectorComparison
from dxtbx.datablock import GoniometerComparison
from dxtbx.datablock import DataBlock
from dxtbx.imageset import ImageSetFactory
from dials.algorithms.spot_finding import StrongSpotCombiner
from dials.array_family import flex
assert len(datablock_list) == len(reflections_list)
# Get a list of imagesets
imageset_list = []
for db in datablock_list:
iset = db.extract_imagesets()
assert len(iset) == 1
imageset_list.append(iset[0])
compare_beam = BeamComparison(
wavelength_tolerance=params.input.tolerance.beam.wavelength,
direction_tolerance=params.input.tolerance.beam.direction,
polarization_normal_tolerance=params.input.tolerance.beam.polarization_normal,
polarization_fraction_tolerance=params.input.tolerance.beam.polarization_fraction)
compare_detector = DetectorComparison(
fast_axis_tolerance=params.input.tolerance.detector.fast_axis,
slow_axis_tolerance=params.input.tolerance.detector.slow_axis,
origin_tolerance=params.input.tolerance.detector.origin)
compare_goniometer = GoniometerComparison(
rotation_axis_tolerance=params.input.tolerance.goniometer.rotation_axis,
fixed_rotation_tolerance=params.input.tolerance.goniometer.fixed_rotation,
setting_rotation_tolerance=params.input.tolerance.goniometer.setting_rotation)
scan_tolerance = params.input.tolerance.scan.oscillation
# The initial models
format_class = imageset_list[0].get_format_class()
beam = imageset_list[0].get_beam()
detector = imageset_list[0].get_detector()
goniometer = imageset_list[0].get_goniometer()
scan = imageset_list[0].get_scan()
template = imageset_list[0].get_template()
# Check all the models
for imageset in imageset_list[1:]:
b = imageset.get_beam()
d = imageset.get_detector()
g = imageset.get_goniometer()
s = imageset.get_scan()
if not imageset.get_format_class() == format_class:
raise RuntimeError('Format classes do not match')
if not imageset.get_template() == template:
raise RuntimeError('Templates do not match')
if not compare_beam(beam, b):
raise RuntimeError('Beam models are too dissimilar')
if not compare_detector(detector, d):
raise RuntimeError('Detector models are too dissimilar')
if not compare_goniometer(goniometer, g):
raise RuntimeError('Goniometer models are too dissimilar')
try:
scan.append(s, scan_tolerance=scan_tolerance)
except Exception:
raise RuntimeError('Scans do not match')
# Get the image range
image_range = scan.get_image_range()
image_range = (image_range[0], image_range[1]+1)
# Create the sweep
imageset = ImageSetFactory.make_sweep(
template, range(*image_range),
format_class,
beam, detector,
goniometer, scan)
# Combine spots
combiner = StrongSpotCombiner()
for index, rlist in enumerate(reflections_list, start=1):
assert rlist['id'].all_eq(0)
logger.info("Combining %d reflections from reflection list %d" % (
len(rlist),
index))
combiner.add(rlist['shoebox'])
shoeboxes = combiner.shoeboxes()
# Calculate the spot centroids and intensities
logger.info('Combined into %d reflections' % len(shoeboxes))
centroid = shoeboxes.centroid_valid()
logger.info('Calculated {0} spot centroids'.format(len(shoeboxes)))
intensity = shoeboxes.summed_intensity()
logger.info('Calculated {0} spot intensities'.format(len(shoeboxes)))
# Construct the reflection table
reflections = flex.reflection_table(
flex.observation(
shoeboxes.panels(),
centroid,
intensity),
shoeboxes)
reflections['id'] = flex.int(len(reflections), 0)
reflections.set_flags(
flex.size_t_range(len(reflections)),
reflections.flags.strong)
# Return the datablock and reflections
return DataBlock([imageset]), reflections
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')
# Construct the sweep
try:
sweep = ImageSetFactory.from_template(template,
image_range,
check_format=check_format)[0]
# Get the existing models as dictionaries
beam_dict = sweep.get_beam().to_dict()
gonio_dict = sweep.get_goniometer().to_dict()
detector_dict = sweep.get_detector().to_dict()
scan_dict = sweep.get_scan().to_dict()
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(BeamFactory.from_dict(d.get('beam'), beam_dict))
sweep.set_goniometer(
GoniometerFactory.from_dict(d.get('goniometer'), gonio_dict))
sweep.set_detector(
DetectorFactory.from_dict(d.get('detector'), detector_dict))
sweep.set_scan(ScanFactory.from_dict(d.get('scan'), scan_dict))
# Return the sweep
return sweep
def run(argv=None):
if (argv is None):
argv = sys.argv
# XXX Could/should handle effective metrology the same way, except
# it does not have a single scope.
work_phil = phil.process_command_line(
args=argv[1:],
master_string=master_str + phil_str + additional_spotfinder_phil_defs)
work_params = work_phil.work.extract()
app = wx.App(0)
wx.SystemOptions.SetOptionInt("osx.openfiledialog.always-show-types", 1)
frame = XrayFrame(None, -1, "X-ray image display", size=(800,720))
frame.Show()
# show settings panel
frame.OnShowSettings(None)
frame.settings_frame.panel.center_ctrl.SetValue(
work_params.beam_center)
frame.settings_frame.panel.integ_ctrl.SetValue(
work_params.show_integration_results)
frame.settings_frame.panel.spots_ctrl.SetValue(
work_params.show_spotfinder_results)
frame.settings.show_effective_tiling = work_params.show_effective_tiling
frame.settings_frame.panel.collect_values()
if (work_params.effective_metrology is not None):
from xfel.cftbx.detector.metrology import \
master_phil, metrology_as_transformation_matrices
stream = open(work_params.effective_metrology)
metrology_phil = master_phil.fetch(sources=[phil.parse(stream.read())])
stream.close()
frame.metrology_matrices = metrology_as_transformation_matrices(
metrology_phil.extract())
# Update initial settings with values from the command line. Needs
# to be done before image is loaded (but after the frame is
# instantiated).
frame.params = work_params
frame.init_pyslip()
frame.pyslip.tiles.user_requests_antialiasing = work_params.anti_aliasing
frame.pyslip.tiles.show_untrusted = frame.params.show_untrusted
paths = work_phil.remaining_args
if (len(paths) == 1 and os.path.basename(paths[0]) == "DISTL_pickle"):
assert os.path.isfile(paths[0])
frame.load_distl_output(paths[0])
elif (len(paths) > 0):
frame.CHOOSER_SIZE = 1500
from dxtbx.imageset import ImageSetFactory
from rstbx.slip_viewer.frame import chooser_wrapper
sets = ImageSetFactory.new(paths)
for imgset in sets:
for idx in imgset.indices():
frame.add_file_name_or_data(chooser_wrapper(imgset, idx))
idx = sets[0].indices()[0]
frame.load_image(chooser_wrapper(sets[0],idx))
app.MainLoop()
return 0
from glob import glob
from dxtbx.imageset import ImageSetFactory
# Check dials_regression is configured
try:
path = libtbx.env.dist_path('dials_regression')
except KeyError, e:
print 'FAIL: dials_regression not configured'
raise
# Find the filenames
template = os.path.join(path, 'centroid_test_data', 'centroid_*.cbf')
filenames = glob(template)
# Create the sweep
sweep = ImageSetFactory.new(filenames)
assert(len(sweep) == 1)
sweep = sweep[0]
# Get the models
beam = sweep.get_beam()
detector = sweep.get_detector()
gonio = sweep.get_goniometer()
scan = sweep.get_scan()
print beam
print detector
print gonio
print scan
print "sweep: ", sweep
print "sweep indices: ", sweep.indices()
def _load_datablocks(self, obj, check_format=True):
''' Create the datablock from a dictionary. '''
from libtbx.containers import OrderedDict
from dxtbx.format.Registry import Registry
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model import HierarchicalDetector
from dxtbx.serialize.filename import load_path
from dxtbx.imageset import ImageSetFactory
import pickle
# If we have a list, extract for each dictionary in the list
if isinstance(obj, list):
return [self._load_datablocks(dd, check_format) for dd in obj]
elif not isinstance(obj, dict):
raise RuntimeError('unknown datablock dictionary type')
assert(obj['__id__'] == 'DataBlock')
# Get the list of models
blist = obj.get('beam', [])
dlist = obj.get('detector', [])
glist = obj.get('goniometer', [])
slist = obj.get('scan', [])
def load_models(obj):
try:
beam = Beam.from_dict(blist[obj['beam']])
except Exception:
beam = None
try:
dobj = dlist[obj['detector']]
if 'hierarchy' in dobj:
detector = HierarchicalDetector.from_dict(dobj)
else:
detector = Detector.from_dict(dobj)
except Exception:
detector = None
try:
gonio = Goniometer.from_dict(glist[obj['goniometer']])
except Exception:
gonio = None
try:
scan = Scan.from_dict(slist[obj['scan']])
except Exception:
scan = None
return beam, detector, gonio, scan
# Loop through all the imagesets
imagesets = []
for imageset in obj['imageset']:
ident = imageset['__id__']
if ident == 'ImageSweep':
beam, detector, gonio, scan = load_models(imageset)
template = load_path(imageset['template'])
i0, i1 = scan.get_image_range()
iset = ImageSetFactory.make_sweep(
template, range(i0, i1+1), None,
beam, detector, gonio, scan, check_format)
if 'mask' in imageset and imageset['mask'] is not None:
imageset['mask'] = load_path(imageset['mask'])
iset.external_lookup.mask.filename = imageset['mask']
if check_format:
with open(imageset['mask']) as infile:
iset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in imageset and imageset['gain'] is not None:
imageset['gain'] = load_path(imageset['gain'])
iset.external_lookup.gain.filename = imageset['gain']
if check_format:
with open(imageset['gain']) as infile:
iset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in imageset and imageset['pedestal'] is not None:
imageset['pedestal'] = load_path(imageset['pedestal'])
iset.external_lookup.pedestal.filename = imageset['pedestal']
if check_format:
with open(imageset['pedestal']) as infile:
iset.external_lookup.pedestal.data = pickle.load(infile)
imagesets.append(iset)
elif ident == 'ImageSet':
filenames = [image['filename'] for image in imageset['images']]
iset = ImageSetFactory.make_imageset(
filenames, None, check_format)
for i, image in enumerate(imageset['images']):
beam, detector, gonio, scan = load_models(image)
iset.set_beam(beam, i)
iset.set_detector(detector, i)
if gonio:
iset.set_goniometer(gonio, i)
if scan:
iset.set_scan(scan, i)
if 'mask' in imageset and imageset['mask'] is not None:
imageset['mask'] = load_path(imageset['mask'])
iset.external_lookup.mask.filename = imageset['mask']
if check_format:
with open(imageset['mask']) as infile:
iset.external_lookup.mask.data = pickle.load(infile)
if 'gain' in imageset and imageset['gain'] is not None:
imageset['gain'] = load_path(imageset['gain'])
iset.external_lookup.gain.filename = imageset['gain']
if check_format:
with open(imageset['gain']) as infile:
iset.external_lookup.gain.data = pickle.load(infile)
if 'pedestal' in imageset and imageset['pedestal'] is not None:
imageset['pedestal'] = load_path(imageset['pedestal'])
iset.external_lookup.pedestal.filename = imageset['pedestal']
if check_format:
with open(imageset['pedestal']) as infile:
iset.external_lookup.pedestal.data = pickle.load(infile)
imagesets.append(iset)
else:
raise RuntimeError('expected ImageSet/ImageSweep, got %s' % ident)
# Return the datablock
return DataBlock(imagesets)
def convert_stills_to_sweep(self, imageset):
from dxtbx.model import Scan
assert self.params.geometry.scan.oscillation is not None
beam = imageset.get_beam(index=0)
detector = imageset.get_detector(index=0)
goniometer = imageset.get_goniometer(index=0)
for i in range(1, len(imageset)):
b_i = imageset.get_beam(i)
d_i = imageset.get_detector(i)
g_i = imageset.get_goniometer(i)
assert (beam is None and b_i is None) or beam.is_similar_to(
imageset.get_beam(index=i),
wavelength_tolerance=self.params.input.tolerance.beam.
wavelength,
direction_tolerance=self.params.input.tolerance.beam.direction,
polarization_normal_tolerance=self.params.input.tolerance.beam.
polarization_normal,
polarization_fraction_tolerance=self.params.input.tolerance.
beam.polarization_fraction,
)
assert (detector is None
and d_i is None) or detector.is_similar_to(
imageset.get_detector(index=i),
fast_axis_tolerance=self.params.input.tolerance.
detector.fast_axis,
slow_axis_tolerance=self.params.input.tolerance.
detector.slow_axis,
origin_tolerance=self.params.input.tolerance.detector.
origin,
)
assert (goniometer is None
and g_i is None) or goniometer.is_similar_to(
imageset.get_goniometer(index=i),
rotation_axis_tolerance=self.params.input.tolerance.
goniometer.rotation_axis,
fixed_rotation_tolerance=self.params.input.tolerance.
goniometer.fixed_rotation,
setting_rotation_tolerance=self.params.input.tolerance.
goniometer.setting_rotation,
)
oscillation = self.params.geometry.scan.oscillation
from dxtbx.sweep_filenames import template_regex_from_list
from dxtbx.imageset import ImageSetFactory
template, indices = template_regex_from_list(imageset.paths())
image_range = (min(indices), max(indices))
assert (image_range[1] + 1 - image_range[0]) == len(indices)
scan = Scan(image_range=image_range, oscillation=oscillation)
if template is None:
paths = [imageset.get_path(i) for i in range(len(imageset))]
assert len(set(paths)) == 1
template = paths[0]
new_sweep = ImageSetFactory.make_sweep(
template=template,
indices=indices,
format_class=imageset.reader().get_format_class(),
beam=beam,
detector=detector,
goniometer=goniometer,
scan=scan,
)
return new_sweep
def exercise_to_xds():
if not libtbx.env.has_module("dials_regression"):
print "Skipping exercise_to_xds(): dials_regression not present"
return
data_dir = libtbx.env.find_in_repositories(
relative_path="dials_regression/centroid_test_data",
test=os.path.isdir)
template = os.path.join(data_dir, "centroid_*.cbf")
file_names = glob.glob(template)
expected_output = """\
DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=495976
SENSOR_THICKNESS= 0.320
DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
NX=2463 NY=2527 QX=0.1720 QY=0.1720
DETECTOR_DISTANCE= 190.180
ORGX= 1235.84 ORGY= 1279.58
ROTATION_AXIS= 1.00000 0.00000 0.00000
STARTING_ANGLE= 0.000
OSCILLATION_RANGE= 0.200
X-RAY_WAVELENGTH= 0.97950
INCIDENT_BEAM_DIRECTION= -0.000 -0.000 1.021
FRACTION_OF_POLARIZATION= 0.999
POLARIZATION_PLANE_NORMAL= 0.000 1.000 0.000
NAME_TEMPLATE_OF_DATA_FRAMES= %s
TRUSTED_REGION= 0.0 1.41
UNTRUSTED_RECTANGLE= 487 495 0 2528
UNTRUSTED_RECTANGLE= 981 989 0 2528
UNTRUSTED_RECTANGLE= 1475 1483 0 2528
UNTRUSTED_RECTANGLE= 1969 1977 0 2528
UNTRUSTED_RECTANGLE= 0 2464 195 213
UNTRUSTED_RECTANGLE= 0 2464 407 425
UNTRUSTED_RECTANGLE= 0 2464 619 637
UNTRUSTED_RECTANGLE= 0 2464 831 849
UNTRUSTED_RECTANGLE= 0 2464 1043 1061
UNTRUSTED_RECTANGLE= 0 2464 1255 1273
UNTRUSTED_RECTANGLE= 0 2464 1467 1485
UNTRUSTED_RECTANGLE= 0 2464 1679 1697
UNTRUSTED_RECTANGLE= 0 2464 1891 1909
UNTRUSTED_RECTANGLE= 0 2464 2103 2121
UNTRUSTED_RECTANGLE= 0 2464 2315 2333
DATA_RANGE= 1 9
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT\
""" %(template.replace("*", "????"))
cmd = " ".join(["dxtbx.to_xds"] + file_names)
result = easy_run.fully_buffered(cmd)
# allow extra lines to have been added (these may be comments)
for record in expected_output.split('\n'):
assert record.strip() in "\n".join(result.stdout_lines), record
# now test reading from a json file
sweep = ImageSetFactory.new(file_names)[0]
f = open_tmp_file(suffix="sweep.json", mode="wb")
dump.imageset(sweep, f)
f.close()
cmd = " ".join(["dxtbx.to_xds", f.name])
result = easy_run.fully_buffered(cmd)
# allow extra lines to have been added (these may be comments)
for record in expected_output.split('\n'):
assert record.strip() in "\n".join(result.stdout_lines), record
# Print out the contents of the dxtbx understanding of a bunch of images to
# an example XDS.INP file. This should illustrate the usage of the dxtbx
# classes.
import sys
from dxtbx.serialize import xds
def run(file_names):
if len(file_names) == 1 and file_names[0].endswith('json'):
from dxtbx.serialize import load
try:
datablock = load.datablock(file_names[0])
assert len(datablock) == 1
sweep = datablock[0].extract_sweeps()[0]
except ValueError, e:
if str(e) == '"__id__" does not equal "imageset"':
experiments = load.experiment_list(file_names[0])
assert len(experiments) == 1
sweep = experiments[0].imageset
else:
raise
else:
from dxtbx.imageset import ImageSetFactory
sweep = ImageSetFactory.new(file_names)[0]
xsx = xds.to_xds(sweep)
xsx.XDS_INP()
if __name__ == '__main__':
run(sys.argv[1:])
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
