def get_maxima(self, threshold = 5.0):
'''Run diffdump, printpeaks to get a list of diffraction maxima
at their image positions, to allow for further analysis.'''
if not self._image:
raise RuntimeError, 'image not set'
if not os.path.exists(self._image):
raise RuntimeError, 'image %s does not exist' % \
self._image
dd = Diffdump()
dd.set_image(self._image)
header = dd.readheader()
beam = header['raw_beam']
pixel = header['pixel']
template, directory = image2template_directory(self._image)
image_number = image2image(os.path.split(self._image)[-1])
spot_file = '%s.spt' % template_number2image(
template, image_number)
self.start()
self.input('template "%s"' % template)
self.input('directory "%s"' % directory)
self.input('findspots local find %d file %s' % \
(image_number, spot_file))
self.input('go')
self.close_wait()
self.check_for_errors()
output = open(os.path.join(self.get_working_directory(),
spot_file)).readlines()
os.remove(os.path.join(self.get_working_directory(),
spot_file))
peaks = []
for record in output[3:-2]:
lst = record.split()
x = float(lst[0])
y = float(lst[1])
i = float(lst[4]) / float(lst[5])
x /= pixel[0]
y /= pixel[1]
if i < threshold:
continue
# this is Mosflm right? Swap X & Y!!
peaks.append((y, x, i))
return peaks
def get_template(f):
global target_template
if not is_image_name(f):
return
if is_xds_file(f):
return
# in here, check the permissions on the file...
template = None
directory = None
if not os.access(f, os.R_OK):
Debug.write('No read permission for %s' % f)
try:
template, directory = image2template_directory(f)
template = os.path.join(directory, template)
if target_template:
if template not in target_template:
return
except Exception as e:
Debug.write('Exception A: %s (%s)' % (str(e), f))
Debug.write(traceback.format_exc())
if template is None or directory is None:
raise RuntimeError('template not recognised for %s' % f)
return template
def _setup_from_image(self, image):
"""Configure myself from an image name."""
template, directory = image2template_directory(image)
self._fp_matching_images = find_matching_images(template, directory)
# trim this down to only allowed images...
if self._fp_wedge:
start, end = self._fp_wedge
images = []
for j in self._fp_matching_images:
if j < start or j > end:
continue
images.append(j)
self._fp_matching_images = images
from xia2.Schema import load_imagesets
imagesets = load_imagesets(
template,
directory,
image_range=(self._fp_matching_images[0],
self._fp_matching_images[-1]),
)
assert len(imagesets) == 1, "multiple imagesets match %s" % template
imageset = imagesets[0]
self._setup_from_imageset(imageset)
def get_maxima(self, threshold=5.0):
'''Run diffdump, printpeaks to get a list of diffraction maxima
at their image positions, to allow for further analysis.'''
if not self._image:
raise RuntimeError('image not set')
if not os.path.exists(self._image):
raise RuntimeError('image %s does not exist' % \
self._image)
dd = Diffdump()
dd.set_image(self._image)
header = dd.readheader()
beam = header['raw_beam']
pixel = header['pixel']
template, directory = image2template_directory(self._image)
image_number = image2image(os.path.split(self._image)[-1])
spot_file = '%s.spt' % template_number2image(
template, image_number)
self.start()
self.input('template "%s"' % template)
self.input('directory "%s"' % directory)
self.input('findspots local find %d file %s' % \
(image_number, spot_file))
self.input('go')
self.close_wait()
self.check_for_errors()
output = open(os.path.join(self.get_working_directory(),
spot_file)).readlines()
os.remove(os.path.join(self.get_working_directory(), spot_file))
peaks = []
for record in output[3:-2]:
lst = record.split()
x = float(lst[0])
y = float(lst[1])
i = float(lst[4]) / float(lst[5])
x /= pixel[0]
y /= pixel[1]
if i < threshold:
continue
# this is Mosflm right? Swap X & Y!!
peaks.append((y, x, i))
return peaks
def _setup_from_image(self, image):
'''Configure myself from an image name.'''
template, directory = image2template_directory(image)
self._fp_matching_images = find_matching_images(template, directory)
# trim this down to only allowed images...
if self._fp_wedge:
start, end = self._fp_wedge
images = []
for j in self._fp_matching_images:
if j < start or j > end:
continue
images.append(j)
self._fp_matching_images = images
from xia2.Schema import load_imagesets
imagesets = load_imagesets(
template, directory,
image_range=(self._fp_matching_images[0], self._fp_matching_images[-1]))
assert len(imagesets) == 1, 'multiple imagesets match %s' % template
imageset = imagesets[0]
self._setup_from_imageset(imageset)
return
if scan is None: continue
if imageset.get_scan().get_num_images() > max_images:
best_sweep = imageset
self._imageset = best_sweep
return
if __name__ == '__main__':
if len(sys.argv) < 2:
image = os.path.join(os.environ['XIA2_ROOT'],
'Data', 'Test', 'Images', '12287_1_E1_001.img')
else:
image = sys.argv[1]
template, directory = image2template_directory(image)
sl = SweepFactory(template, directory)
for s in sl:
t = s.get_collect()
print 'Data collection took %s seconds' % (t[1] - t[0])
print 'For a total of %s seconds of exposure' % \
(s.get_exposure_time() * \
len(s.get_images()))
print 'Images: %d to %d' % (min(s.get_images()), max(s.get_images()))
print 'Template: %s' % s.get_template()
print ''
def setup(self):
"""Set everything up..."""
# check arguments are all ascii
Debug.write("Start parsing command line: " + str(sys.argv))
for token in sys.argv:
try:
token.encode("ascii")
except UnicodeDecodeError:
raise RuntimeError("non-ascii characters in input")
self._argv = copy.deepcopy(sys.argv)
replacements = {
"-2d": "pipeline=2d",
"-2di": "pipeline=2di",
"-3d": "pipeline=3d",
"-3di": "pipeline=3di",
"-3dii": "pipeline=3dii",
"-3dd": "pipeline=3dd",
"-dials": "pipeline=dials",
"-quick": "dials.fast_mode=true",
"-failover": "failover=true",
"-small_molecule": "small_molecule=true",
}
for k, v in replacements.iteritems():
if k in self._argv:
print(
"***\nCommand line option %s is deprecated.\nPlease use %s instead\n***"
% (k, v))
self._argv[self._argv.index(k)] = v
if "-atom" in self._argv:
idx = self._argv.index("-atom")
element = self._argv[idx + 1]
self._argv[idx:idx + 2] = ["atom=%s" % element]
print(
"***\nCommand line option -atom %s is deprecated.\nPlease use atom=%s instead\n***"
% (element, element))
# first of all try to interpret arguments as phil parameters/files
from xia2.Handlers.Phil import master_phil
from libtbx.phil import command_line
cmd_line = command_line.argument_interpreter(master_phil=master_phil)
working_phil, self._argv = cmd_line.process_and_fetch(
args=self._argv, custom_processor="collect_remaining")
PhilIndex.merge_phil(working_phil)
try:
params = PhilIndex.get_python_object()
except RuntimeError as e:
raise Sorry(e)
# sanity check / interpret Auto in input
from libtbx import Auto
if params.xia2.settings.input.atom is None:
if params.xia2.settings.input.anomalous is Auto:
PhilIndex.update("xia2.settings.input.anomalous=false")
else:
if params.xia2.settings.input.anomalous is False:
raise Sorry(
"Setting anomalous=false and atom type inconsistent")
params.xia2.settings.input.anomalous = True
PhilIndex.update("xia2.settings.input.anomalous=true")
if params.xia2.settings.resolution.keep_all_reflections is Auto:
if (params.xia2.settings.small_molecule is True
and params.xia2.settings.resolution.d_min is None
and params.xia2.settings.resolution.d_max is None):
PhilIndex.update(
"xia2.settings.resolution.keep_all_reflections=true")
else:
PhilIndex.update(
"xia2.settings.resolution.keep_all_reflections=false")
if params.xia2.settings.small_molecule is True:
Debug.write("Small molecule selected")
if params.xia2.settings.symmetry.chirality is None:
PhilIndex.update("xia2.settings.symmetry.chirality=nonchiral")
params = PhilIndex.get_python_object()
# pipeline options
self._read_pipeline()
for (parameter, value) in (
("project", params.xia2.settings.project),
("crystal", params.xia2.settings.crystal),
):
validate_project_crystal_name(parameter, value)
Debug.write("Project: %s" % params.xia2.settings.project)
Debug.write("Crystal: %s" % params.xia2.settings.crystal)
# FIXME add some consistency checks in here e.g. that there are
# images assigned, there is a lattice assigned if cell constants
# are given and so on
params = PhilIndex.get_python_object()
mp_params = params.xia2.settings.multiprocessing
from xia2.Handlers.Environment import get_number_cpus
if mp_params.mode == "parallel":
if mp_params.type == "qsub":
if which("qsub") is None:
raise Sorry("qsub not available")
if mp_params.njob is Auto:
mp_params.njob = get_number_cpus()
if mp_params.nproc is Auto:
mp_params.nproc = 1
elif mp_params.nproc is Auto:
mp_params.nproc = get_number_cpus()
elif mp_params.mode == "serial":
if mp_params.type == "qsub":
if which("qsub") is None:
raise Sorry("qsub not available")
if mp_params.njob is Auto:
mp_params.njob = 1
if mp_params.nproc is Auto:
mp_params.nproc = get_number_cpus()
PhilIndex.update("xia2.settings.multiprocessing.njob=%d" %
mp_params.njob)
PhilIndex.update("xia2.settings.multiprocessing.nproc=%d" %
mp_params.nproc)
params = PhilIndex.get_python_object()
mp_params = params.xia2.settings.multiprocessing
if mp_params.nproc > 1 and os.name == "nt":
raise Sorry("nproc > 1 is not supported on Windows.") # #191
if params.xia2.settings.indexer is not None:
add_preference("indexer", params.xia2.settings.indexer)
if params.xia2.settings.refiner is not None:
add_preference("refiner", params.xia2.settings.refiner)
if params.xia2.settings.integrater is not None:
add_preference("integrater", params.xia2.settings.integrater)
if params.xia2.settings.scaler is not None:
add_preference("scaler", params.xia2.settings.scaler)
if params.xia2.settings.multi_sweep_indexing is Auto:
if (params.xia2.settings.small_molecule is True
and "dials" == params.xia2.settings.indexer):
PhilIndex.update("xia2.settings.multi_sweep_indexing=True")
else:
PhilIndex.update("xia2.settings.multi_sweep_indexing=False")
if (params.xia2.settings.multi_sweep_indexing is True
and params.xia2.settings.multiprocessing.mode == "parallel"):
Chatter.write(
"Multi sweep indexing disabled:\nMSI is not available for parallel processing."
)
PhilIndex.update("xia2.settings.multi_sweep_indexing=False")
input_json = params.xia2.settings.input.json
if input_json is not None and len(input_json):
for json_file in input_json:
assert os.path.isfile(json_file)
load_experiments(json_file)
reference_geometry = params.xia2.settings.input.reference_geometry
if reference_geometry is not None and len(reference_geometry) > 0:
reference_geometries = "\n".join([
"xia2.settings.input.reference_geometry=%s" %
os.path.abspath(g)
for g in params.xia2.settings.input.reference_geometry
])
Debug.write(reference_geometries)
PhilIndex.update(reference_geometries)
Debug.write("xia2.settings.trust_beam_centre=true")
PhilIndex.update("xia2.settings.trust_beam_centre=true")
params = PhilIndex.get_python_object()
params = PhilIndex.get_python_object()
if params.xia2.settings.input.xinfo is not None:
xinfo_file = os.path.abspath(params.xia2.settings.input.xinfo)
PhilIndex.update("xia2.settings.input.xinfo=%s" % xinfo_file)
params = PhilIndex.get_python_object()
self.set_xinfo(xinfo_file)
# issue #55 if not set ATOM in xinfo but anomalous=true or atom= set
# on commandline, set here, should be idempotent
if params.xia2.settings.input.anomalous is True:
crystals = self._xinfo.get_crystals()
for xname in crystals:
xtal = crystals[xname]
Debug.write("Setting anomalous for crystal %s" % xname)
xtal.set_anomalous(True)
else:
xinfo_file = "%s/automatic.xinfo" % os.path.abspath(os.curdir)
PhilIndex.update("xia2.settings.input.xinfo=%s" % xinfo_file)
params = PhilIndex.get_python_object()
if params.dials.find_spots.phil_file is not None:
PhilIndex.update(
"dials.find_spots.phil_file=%s" %
os.path.abspath(params.dials.find_spots.phil_file))
if params.dials.index.phil_file is not None:
PhilIndex.update("dials.index.phil_file=%s" %
os.path.abspath(params.dials.index.phil_file))
if params.dials.refine.phil_file is not None:
PhilIndex.update("dials.refine.phil_file=%s" %
os.path.abspath(params.dials.refine.phil_file))
if params.dials.integrate.phil_file is not None:
PhilIndex.update("dials.integrate.phil_file=%s" %
os.path.abspath(params.dials.integrate.phil_file))
if params.xds.index.xparm is not None:
Flags.set_xparm(params.xds.index.xparm)
if params.xds.index.xparm_ub is not None:
Flags.set_xparm_ub(params.xds.index.xparm_ub)
if params.xia2.settings.scale.freer_file is not None:
freer_file = os.path.abspath(params.xia2.settings.scale.freer_file)
if not os.path.exists(freer_file):
raise RuntimeError("%s does not exist" % freer_file)
from xia2.Modules.FindFreeFlag import FindFreeFlag
column = FindFreeFlag(freer_file)
Debug.write("FreeR_flag column in %s found: %s" %
(freer_file, column))
PhilIndex.update("xia2.settings.scale.freer_file=%s" % freer_file)
if params.xia2.settings.scale.reference_reflection_file is not None:
reference_reflection_file = os.path.abspath(
params.xia2.settings.scale.reference_reflection_file)
if not os.path.exists(reference_reflection_file):
raise RuntimeError("%s does not exist" %
reference_reflection_file)
PhilIndex.update(
"xia2.settings.scale.reference_reflection_file=%s" %
reference_reflection_file)
params = PhilIndex.get_python_object()
datasets = unroll_datasets(PhilIndex.params.xia2.settings.input.image)
for dataset in datasets:
start_end = None
# here we only care about ':' which are later than C:\
if ":" in dataset[3:]:
tokens = dataset.split(":")
# cope with windows drives i.e. C:\data\blah\thing_0001.cbf:1:100
if len(tokens[0]) == 1:
tokens = ["%s:%s" % (tokens[0], tokens[1])] + tokens[2:]
if len(tokens) != 3:
raise RuntimeError("/path/to/image_0001.cbf:start:end")
dataset = tokens[0]
start_end = int(tokens[1]), int(tokens[2])
from xia2.Applications.xia2setup import is_hd5f_name
if os.path.exists(os.path.abspath(dataset)):
dataset = os.path.abspath(dataset)
else:
directories = [os.getcwd()] + self._argv[1:]
found = False
for d in directories:
if os.path.exists(os.path.join(d, dataset)):
dataset = os.path.join(d, dataset)
found = True
break
if not found:
raise Sorry("Could not find %s in %s" %
(dataset, " ".join(directories)))
if is_hd5f_name(dataset):
self._hdf5_master_files.append(dataset)
if start_end:
Debug.write("Image range: %d %d" % start_end)
if dataset not in self._default_start_end:
self._default_start_end[dataset] = []
self._default_start_end[dataset].append(start_end)
else:
Debug.write("No image range specified")
else:
template, directory = image2template_directory(
os.path.abspath(dataset))
self._default_template.append(os.path.join(
directory, template))
self._default_directory.append(directory)
Debug.write("Interpreted from image %s:" % dataset)
Debug.write("Template %s" % template)
Debug.write("Directory %s" % directory)
if start_end:
Debug.write("Image range: %d %d" % start_end)
key = os.path.join(directory, template)
if key not in self._default_start_end:
self._default_start_end[key] = []
self._default_start_end[key].append(start_end)
else:
Debug.write("No image range specified")
# finally, check that all arguments were read and raise an exception
# if any of them were nonsense.
with open("xia2-working.phil", "wb") as f:
f.write(PhilIndex.working_phil.as_str())
f.write(
os.linesep
) # temporarily required for https://github.com/dials/dials/issues/522
with open("xia2-diff.phil", "wb") as f:
f.write(PhilIndex.get_diff().as_str())
f.write(
os.linesep
) # temporarily required for https://github.com/dials/dials/issues/522
Debug.write("\nDifference PHIL:")
Debug.write(PhilIndex.get_diff().as_str(), strip=False)
Debug.write("Working PHIL:")
Debug.write(PhilIndex.working_phil.as_str(), strip=False)
nonsense = "Unknown command-line options:"
was_nonsense = False
for j, argv in enumerate(self._argv):
if j == 0:
continue
if argv[0] != "-" and "=" not in argv:
continue
if j not in self._understood:
nonsense += " %s" % argv
was_nonsense = True
if was_nonsense:
raise RuntimeError(nonsense)
if imageset.get_scan().get_num_images() > max_images:
best_sweep = imageset
self._imageset = best_sweep
return
if __name__ == '__main__':
if len(sys.argv) < 2:
image = os.path.join(os.environ['XIA2_ROOT'], 'Data', 'Test', 'Images',
'12287_1_E1_001.img')
else:
image = sys.argv[1]
template, directory = image2template_directory(image)
sl = SweepFactory(template, directory)
for s in sl:
t = s.get_collect()
print 'Data collection took %s seconds' % (t[1] - t[0])
print 'For a total of %s seconds of exposure' % \
(s.get_exposure_time() * \
len(s.get_images()))
print 'Images: %d to %d' % (min(s.get_images()), max(s.get_images()))
print 'Template: %s' % s.get_template()
print ''
def __init__(self, name,
wavelength,
sample,
directory = None,
image = None,
beam = None,
reversephi = False,
distance = None,
gain = 0.0,
dmin = 0.0,
dmax = 0.0,
polarization = 0.0,
frames_to_process = None,
user_lattice = None,
user_cell = None,
epoch = 0,
ice = False,
excluded_regions = None):
'''Create a new sweep named name, belonging to XWavelength object
wavelength, representing the images in directory starting with image,
with beam centre optionally defined.'''
if excluded_regions is None:
excluded_regions = []
# + check the wavelength is an XWavelength object
# raise an exception if not... or not...
if not wavelength.__class__.__name__ == 'XWavelength':
pass
# FIXME bug 2221 if DIRECTORY starts with ~/ or ~graeme (say) need to
# interpret this properly - e.g. map it to a full PATH.
directory = expand_path(directory)
self._name = name
self._wavelength = wavelength
self._sample = sample
self._directory = directory
self._image = image
self._reversephi = reversephi
self._epoch = epoch
self._user_lattice = user_lattice
self._user_cell = user_cell
self._header = { }
self._resolution_high = dmin
self._resolution_low = dmax
self._ice = ice
self._excluded_regions = excluded_regions
self._imageset = None
# FIXME in here also need to be able to accumulate the total
# dose from all experimental measurements (complex) and provide
# a _epoch_to_dose dictionary or some such... may be fiddly as
# this will need to parse across multiple templates. c/f Bug # 2798
self._epoch_to_image = { }
self._image_to_epoch = { }
# to allow first, last image for processing to be
# set... c/f integrater interface
self._frames_to_process = frames_to_process
# + derive template, list of images
params = PhilIndex.get_python_object()
if directory and image:
self._template, self._directory = \
image2template_directory(os.path.join(directory,
image))
from xia2.Schema import load_imagesets
imagesets = load_imagesets(
self._template, self._directory, image_range=self._frames_to_process,
reversephi=(params.xia2.settings.input.reverse_phi or self._reversephi))
assert len(imagesets) == 1, "one imageset expected, %d found" % \
len(imagesets)
self._imageset = copy.deepcopy(imagesets[0])
start, end = self._imageset.get_array_range()
self._images = list(range(start+1, end+1))
# FIXME in here check that (1) the list of images is continuous
# and (2) that all of the images are readable. This should also
# take into account frames_to_process if set.
if self._frames_to_process is None:
self._frames_to_process = min(self._images), max(self._images)
start, end = self._frames_to_process
error = False
if params.general.check_image_files_readable:
for j in range(start, end + 1):
image_name = self.get_imageset().get_path(j-start)
if not j in self._images:
Debug.write('image %s missing' %image_name)
error = True
continue
if not os.access(image_name, os.R_OK):
Debug.write('image %s unreadable' %image_name)
error = True
continue
if error:
raise RuntimeError, 'problem with sweep %s' % self._name
# + read the image header information into here?
# or don't I need it? it would be useful for checking
# against wavelength.getWavelength() I guess to make
# sure that the plumbing is all sound.
# check that they match by closer than 0.0001A, if wavelength
# is not None
beam_ = self._imageset.get_beam()
scan = self._imageset.get_scan()
if wavelength is not None:
# FIXME 29/NOV/06 if the wavelength wavelength value
# is 0.0 then first set it to the header value - note
# that this assumes that the header value is correct
# (a reasonable assumption)
if wavelength.get_wavelength() == 0.0:
wavelength.set_wavelength(beam_.get_wavelength())
# FIXME 08/DEC/06 in here need to allow for the fact
# that the wavelength in the image header could be wrong and
# in fact it should be replaced with the input value -
# through the user will need to be warned of this and
# also everything using the FrameProcessor interface
# will also have to respect this!
if math.fabs(beam_.get_wavelength() -
wavelength.get_wavelength()) > 0.0001:
# format = 'wavelength for sweep %s does not ' + \
# 'match wavelength %s'
# raise RuntimeError, format % \
# (name, wavelength.get_name())
format = 'Header wavelength for sweep %s different' + \
' to assigned value (%4.2f vs. %4.2f)'
Chatter.write(format % (name, beam_.get_wavelength(),
wavelength.get_wavelength()))
# also in here look at the image headers to see if we can
# construct a mapping between exposure epoch and image ...
images = []
if self._frames_to_process:
start, end = self._frames_to_process
for j in self._images:
if j >= start and j <= end:
images.append(j)
else:
images = self._images
for j in images:
epoch = scan.get_image_epoch(j)
if epoch == 0.0:
epoch = float(os.stat(self._imageset.get_path(j-images[0])).st_mtime)
self._epoch_to_image[epoch] = j
self._image_to_epoch[j] = epoch
epochs = self._epoch_to_image.keys()
Debug.write('Exposure epoch for sweep %s: %d %d' % \
(self._template, min(epochs), max(epochs)))
self._input_imageset = copy.deepcopy(self._imageset)
# + get the lattice - can this be a pointer, so that when
# this object updates lattice it is globally-for-this-crystal
# updated? The lattice included directly in here includes an
# exact unit cell for data reduction, the crystal lattice
# contains an approximate unit cell which should be
# from the unit cells from all sweeps contained in the
# XCrystal. FIXME should I be using a LatticeInfo object
# in here? See what the Indexer interface produces. ALT:
# just provide an Indexer implementation "hook".
# See Headnote 001 above. See also _get_indexer,
# _get_integrater below.
self._indexer = None
self._refiner = None
self._integrater = None
# I don't need this - it is equivalent to self.getWavelength(
# ).getCrystal().getLattice()
# self._crystal_lattice = None
# this means that this module will have to present largely the
# same interface as Indexer and Integrater so that the calls
# can be appropriately forwarded.
# finally configure the beam if set
if beam is not None:
from dxtbx.model.detector_helpers import set_mosflm_beam_centre
try:
set_mosflm_beam_centre(self.get_imageset().get_detector(),
self.get_imageset().get_beam(),
beam)
except AssertionError, e:
Debug.write('Error setting mosflm beam centre: %s' % e)
def setup(self):
'''Set everything up...'''
# check arguments are all ascii
Debug.write('Start parsing command line: ' + str(sys.argv))
for token in sys.argv:
try:
token.encode('ascii')
except UnicodeDecodeError:
raise RuntimeError('non-ascii characters in input')
self._argv = copy.deepcopy(sys.argv)
replacements = {
'-2d': 'pipeline=2d',
'-2di': 'pipeline=2di',
'-3d': 'pipeline=3d',
'-3di': 'pipeline=3di',
'-3dii': 'pipeline=3dii',
'-3dd': 'pipeline=3dd',
'-dials': 'pipeline=dials',
'-quick': 'dials.fast_mode=true',
'-failover': 'failover=true',
'-small_molecule': 'small_molecule=true'
}
for k, v in replacements.iteritems():
if k in self._argv:
print "***\nCommand line option %s is deprecated.\nPlease use %s instead\n***" % (
k, v)
self._argv[self._argv.index(k)] = v
if '-atom' in self._argv:
idx = self._argv.index('-atom')
element = self._argv[idx + 1]
self._argv[idx:idx + 2] = ['atom=%s' % element]
print "***\nCommand line option -atom %s is deprecated.\nPlease use atom=%s instead\n***" % (
element, element)
# first of all try to interpret arguments as phil parameters/files
from xia2.Handlers.Phil import master_phil
from libtbx.phil import command_line
cmd_line = command_line.argument_interpreter(master_phil=master_phil)
working_phil, self._argv = cmd_line.process_and_fetch(
args=self._argv, custom_processor="collect_remaining")
PhilIndex.merge_phil(working_phil)
try:
params = PhilIndex.get_python_object()
except RuntimeError as e:
raise Sorry(e)
# sanity check / interpret Auto in input
from libtbx import Auto
if params.xia2.settings.input.atom is None:
if params.xia2.settings.input.anomalous is Auto:
PhilIndex.update("xia2.settings.input.anomalous=false")
else:
if params.xia2.settings.input.anomalous == False:
raise Sorry(
'Setting anomalous=false and atom type inconsistent')
params.xia2.settings.input.anomalous = True
PhilIndex.update("xia2.settings.input.anomalous=true")
if params.xia2.settings.resolution.keep_all_reflections is Auto:
if params.xia2.settings.small_molecule == True and \
params.xia2.settings.resolution.d_min is None and \
params.xia2.settings.resolution.d_max is None:
PhilIndex.update(
"xia2.settings.resolution.keep_all_reflections=true")
else:
PhilIndex.update(
"xia2.settings.resolution.keep_all_reflections=false")
if params.xia2.settings.small_molecule == True:
Debug.write('Small molecule selected')
if params.ccp4.pointless.chirality is None:
PhilIndex.update("ccp4.pointless.chirality=nonchiral")
params = PhilIndex.get_python_object()
# pipeline options
self._read_pipeline()
Debug.write('Project: %s' % params.xia2.settings.project)
Debug.write('Crystal: %s' % params.xia2.settings.crystal)
# FIXME add some consistency checks in here e.g. that there are
# images assigned, there is a lattice assigned if cell constants
# are given and so on
params = PhilIndex.get_python_object()
mp_params = params.xia2.settings.multiprocessing
from xia2.Handlers.Environment import get_number_cpus
if mp_params.mode == 'parallel':
if mp_params.type == 'qsub':
if which('qsub') is None:
raise Sorry('qsub not available')
if mp_params.njob is Auto:
mp_params.njob = get_number_cpus()
if mp_params.nproc is Auto:
mp_params.nproc = 1
elif mp_params.nproc is Auto:
mp_params.nproc = get_number_cpus()
elif mp_params.mode == 'serial':
if mp_params.type == 'qsub':
if which('qsub') is None:
raise Sorry('qsub not available')
if mp_params.njob is Auto:
mp_params.njob = 1
if mp_params.nproc is Auto:
mp_params.nproc = get_number_cpus()
PhilIndex.update("xia2.settings.multiprocessing.njob=%d" %
mp_params.njob)
PhilIndex.update("xia2.settings.multiprocessing.nproc=%d" %
mp_params.nproc)
params = PhilIndex.get_python_object()
mp_params = params.xia2.settings.multiprocessing
if params.xia2.settings.indexer is not None:
add_preference("indexer", params.xia2.settings.indexer)
if params.xia2.settings.refiner is not None:
add_preference("refiner", params.xia2.settings.refiner)
if params.xia2.settings.integrater is not None:
add_preference("integrater", params.xia2.settings.integrater)
if params.xia2.settings.scaler is not None:
add_preference("scaler", params.xia2.settings.scaler)
if params.xia2.settings.multi_sweep_indexing is Auto:
if params.xia2.settings.small_molecule == True and 'dials' == params.xia2.settings.indexer:
PhilIndex.update("xia2.settings.multi_sweep_indexing=True")
else:
PhilIndex.update("xia2.settings.multi_sweep_indexing=False")
if params.xia2.settings.multi_sweep_indexing == True and \
params.xia2.settings.multiprocessing.mode == 'parallel':
Chatter.write(
'Multi sweep indexing disabled:\nMSI is not available for parallel processing.'
)
PhilIndex.update("xia2.settings.multi_sweep_indexing=False")
input_json = params.xia2.settings.input.json
if (input_json is not None and len(input_json)):
for json_file in input_json:
assert os.path.isfile(json_file)
load_datablock(json_file)
reference_geometry = params.xia2.settings.input.reference_geometry
if reference_geometry is not None and len(reference_geometry) > 0:
reference_geometries = "\n".join([
"xia2.settings.input.reference_geometry=%s" %
os.path.abspath(g)
for g in params.xia2.settings.input.reference_geometry
])
Debug.write(reference_geometries)
PhilIndex.update(reference_geometries)
Debug.write("xia2.settings.trust_beam_centre=true")
PhilIndex.update("xia2.settings.trust_beam_centre=true")
params = PhilIndex.get_python_object()
params = PhilIndex.get_python_object()
if params.xia2.settings.input.xinfo is not None:
xinfo_file = os.path.abspath(params.xia2.settings.input.xinfo)
PhilIndex.update("xia2.settings.input.xinfo=%s" % xinfo_file)
params = PhilIndex.get_python_object()
self.set_xinfo(xinfo_file)
# issue #55 if not set ATOM in xinfo but anomalous=true or atom= set
# on commandline, set here, should be idempotent
if params.xia2.settings.input.anomalous is True:
crystals = self._xinfo.get_crystals()
for xname in crystals:
xtal = crystals[xname]
Debug.write("Setting anomalous for crystal %s" % xname)
xtal.set_anomalous(True)
else:
xinfo_file = '%s/automatic.xinfo' % os.path.abspath(os.curdir)
PhilIndex.update("xia2.settings.input.xinfo=%s" % xinfo_file)
params = PhilIndex.get_python_object()
if params.dials.find_spots.phil_file is not None:
PhilIndex.update(
"dials.find_spots.phil_file=%s" %
os.path.abspath(params.dials.find_spots.phil_file))
if params.dials.index.phil_file is not None:
PhilIndex.update("dials.index.phil_file=%s" %
os.path.abspath(params.dials.index.phil_file))
if params.dials.refine.phil_file is not None:
PhilIndex.update("dials.refine.phil_file=%s" %
os.path.abspath(params.dials.refine.phil_file))
if params.dials.integrate.phil_file is not None:
PhilIndex.update("dials.integrate.phil_file=%s" %
os.path.abspath(params.dials.integrate.phil_file))
if params.xds.index.xparm is not None:
Flags.set_xparm(params.xds.index.xparm)
if params.xds.index.xparm_ub is not None:
Flags.set_xparm_ub(params.xds.index.xparm_ub)
if params.xia2.settings.scale.freer_file is not None:
freer_file = os.path.abspath(params.xia2.settings.scale.freer_file)
if not os.path.exists(freer_file):
raise RuntimeError('%s does not exist' % freer_file)
from xia2.Modules.FindFreeFlag import FindFreeFlag
column = FindFreeFlag(freer_file)
Debug.write('FreeR_flag column in %s found: %s' % \
(freer_file, column))
PhilIndex.update("xia2.settings.scale.freer_file=%s" % freer_file)
if params.xia2.settings.scale.reference_reflection_file is not None:
reference_reflection_file = os.path.abspath(
params.xia2.settings.scale.reference_reflection_file)
if not os.path.exists(reference_reflection_file):
raise RuntimeError('%s does not exist' %
reference_reflection_file)
PhilIndex.update(
"xia2.settings.scale.reference_reflection_file=%s" %
reference_reflection_file)
params = PhilIndex.get_python_object()
datasets = unroll_datasets(PhilIndex.params.xia2.settings.input.image)
for dataset in datasets:
start_end = None
if ':' in dataset:
tokens = dataset.split(':')
# cope with windows drives i.e. C:\data\blah\thing_0001.cbf:1:100
if len(tokens[0]) == 1:
tokens = ['%s:%s' % (tokens[0], tokens[1])] + tokens[2:]
if len(tokens) != 3:
raise RuntimeError('/path/to/image_0001.cbf:start:end')
dataset = tokens[0]
start_end = int(tokens[1]), int(tokens[2])
from xia2.Applications.xia2setup import is_hd5f_name
if os.path.exists(os.path.abspath(dataset)):
dataset = os.path.abspath(dataset)
else:
directories = [os.getcwd()] + self._argv[1:]
found = False
for d in directories:
if os.path.exists(os.path.join(d, dataset)):
dataset = os.path.join(d, dataset)
found = True
break
if not found:
raise Sorry('Cound not find %s in %s' % \
(dataset, ' '.join(directories)))
if is_hd5f_name(dataset):
self._hdf5_master_files.append(dataset)
if start_end:
Debug.write('Image range: %d %d' % start_end)
if not dataset in self._default_start_end:
self._default_start_end[dataset] = []
self._default_start_end[dataset].append(start_end)
else:
Debug.write('No image range specified')
else:
template, directory = image2template_directory(
os.path.abspath(dataset))
self._default_template.append(os.path.join(
directory, template))
self._default_directory.append(directory)
Debug.write('Interpreted from image %s:' % dataset)
Debug.write('Template %s' % template)
Debug.write('Directory %s' % directory)
if start_end:
Debug.write('Image range: %d %d' % start_end)
key = os.path.join(directory, template)
if not key in self._default_start_end:
self._default_start_end[key] = []
self._default_start_end[key].append(start_end)
else:
Debug.write('No image range specified')
# finally, check that all arguments were read and raise an exception
# if any of them were nonsense.
with open('xia2-working.phil', 'wb') as f:
print >> f, PhilIndex.working_phil.as_str()
with open('xia2-diff.phil', 'wb') as f:
print >> f, PhilIndex.get_diff().as_str()
Debug.write('\nDifference PHIL:')
Debug.write(PhilIndex.get_diff().as_str(), strip=False)
Debug.write('Working PHIL:')
Debug.write(PhilIndex.working_phil.as_str(), strip=False)
nonsense = 'Unknown command-line options:'
was_nonsense = False
for j, argv in enumerate(self._argv):
if j == 0:
continue
if argv[0] != '-' and '=' not in argv:
continue
if not j in self._understood:
nonsense += ' %s' % argv
was_nonsense = True
if was_nonsense:
raise RuntimeError(nonsense)
def exercise_mosflm_index():
if not have_dials_regression:
print "Skipping exercise_mosflm_index(): dials_regression not configured"
return
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Wrappers.Mosflm.MosflmIndex import MosflmIndex
# exercise basic indexing from two images
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
indexer = MosflmIndex()
indexer.set_images((1,45))
from xia2.Experts.FindImages import image2template_directory
templ, directory = image2template_directory(template %1)
indexer.set_directory(directory)
indexer.set_template(templ)
indexer.run()
output = ''.join(indexer.get_all_output())
print output
assert approx_equal(indexer.get_refined_beam_centre(), (94.33, 94.58))
assert approx_equal(indexer.get_refined_unit_cell(),
(78.655, 78.655, 78.655, 90.0, 90.0, 90.0), 1e-3)
assert approx_equal(indexer.get_refined_distance(), 160.0)
assert approx_equal(indexer.get_resolution_estimate(), 2.12)
assert approx_equal(indexer.get_separation(), [0.57, 0.57])
assert approx_equal(indexer.get_raster(), [17, 17, 10, 5, 5])
assert approx_equal(indexer.get_mosaic_spreads(), [0.4, 0.4])
assert indexer.get_lattice() == 'cI'
# now exercise indexing off multiple images and test more settings
os.chdir(cwd)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
indexer = MosflmIndex()
indexer.set_images((5,15,25,35,45))
indexer.set_directory(directory)
indexer.set_template(templ)
indexer.set_unit_cell((78,78,78,90,90,90))
indexer.set_distance(159)
indexer.set_space_group_number(197)
indexer.run()
output = ''.join(indexer.get_all_output())
print output
assert approx_equal(indexer.get_refined_beam_centre(), (94.33, 94.57))
assert approx_equal(indexer.get_refined_unit_cell(),
(78.2082, 78.2082, 78.2082, 90.0, 90.0, 90.0))
assert approx_equal(indexer.get_refined_distance(), 159.0)
assert approx_equal(indexer.get_resolution_estimate(), 2.12)
assert approx_equal(indexer.get_separation(), [0.48, 0.57])
assert approx_equal(indexer.get_raster(), [15, 17, 9, 5, 5])
assert approx_equal(
indexer.get_mosaic_spreads(), [0.5, 0.35, 0.45, 0.65, 0.4], eps=1e-1)
assert indexer.get_lattice() == 'cI'
def exercise_mosflm_refine_cell():
if not have_dials_regression:
print "Skipping exercise_mosflm_refine_cell(): dials_regression not configured"
return
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Wrappers.Mosflm.MosflmIndex import MosflmIndex
from xia2.Wrappers.Mosflm.MosflmRefineCell import MosflmRefineCell
# exercise basic indexing from two images
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
from xia2.Experts.FindImages import image2template_directory
templ, directory = image2template_directory(template %1)
indexer = MosflmIndex()
indexer.set_images((1,45))
indexer.set_directory(directory)
indexer.set_template(templ)
indexer.run()
refiner = MosflmRefineCell()
refiner.set_images(((1,3),(21,23), (43,45)))
refiner.set_input_mat_file("xiaindex.mat")
refiner.set_output_mat_file("xiarefine.mat")
refiner.set_directory(directory)
refiner.set_template(templ)
refiner.set_beam_centre(indexer.get_refined_beam_centre())
refiner.set_mosaic(
sum(indexer.get_mosaic_spreads())/len(indexer.get_mosaic_spreads()))
refiner.run()
output = ''.join(refiner.get_all_output())
print output
background_residual = refiner.get_background_residual()
rms_values = refiner.get_rms_values()
ref_residual = {
1: {1: 0.1, 2: 0.1, 3: 0.1, 43: 0.1, 44: 0.2, 45: 0.1, 21: 0.1, 22: 0.1, 23: 0.1},
2: {1: 0.1, 2: 0.1, 3: 0.1, 43: 0.1, 44: 0.2, 45: 0.1, 21: 0.1, 22: 0.1, 23: 0.1},
3: {1: 0.1, 2: 0.1, 3: 0.1, 43: 0.1, 44: 0.2, 45: 0.1, 21: 0.1, 22: 0.1, 23: 0.1}
}
for cycle in background_residual:
for frame in background_residual[cycle]:
assert abs(background_residual[cycle][frame] -
ref_residual[cycle][frame]) <= 0.1, (cycle, frame)
ref_values = {
1: [0.027, 0.029, 0.027, 0.025, 0.027, 0.025, 0.024, 0.022, 0.025],
2: [0.02, 0.021, 0.023, 0.021, 0.02, 0.017, 0.018, 0.019, 0.022],
3: [0.02, 0.021, 0.025, 0.022, 0.021, 0.019, 0.018, 0.019, 0.021]
}
for cycle in rms_values:
for frame in range(len(rms_values[cycle])):
assert abs(rms_values[cycle][frame] - ref_values[cycle][frame]) <= 0.05
def exercise_mosflm_integrate():
if not have_dials_regression:
print "Skipping exercise_mosflm_integrate(): dials_regression not configured"
return
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Wrappers.Mosflm.MosflmIndex import MosflmIndex
from xia2.Wrappers.Mosflm.MosflmRefineCell import MosflmRefineCell
from xia2.Wrappers.Mosflm.MosflmIntegrate import MosflmIntegrate
# exercise basic indexing from two images
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
from xia2.Experts.FindImages import image2template_directory
templ, directory = image2template_directory(template %1)
indexer = MosflmIndex()
indexer.set_images((1,45))
indexer.set_directory(directory)
indexer.set_template(templ)
indexer.run()
refiner = MosflmRefineCell()
refiner.set_images(((1,3),(21,23), (43,45)))
refiner.set_input_mat_file("xiaindex.mat")
refiner.set_output_mat_file("xiarefine.mat")
refiner.set_directory(directory)
refiner.set_template(templ)
refiner.set_beam_centre(indexer.get_refined_beam_centre())
refiner.set_mosaic(
sum(indexer.get_mosaic_spreads())/len(indexer.get_mosaic_spreads()))
refiner.run()
#output = ''.join(refiner.get_all_output())
#print output
integrater = MosflmIntegrate()
integrater.set_image_range((1,45))
integrater.set_input_mat_file("xiaindex.mat")
#integrater.set_output_mat_file("xiarefine.mat")
integrater.set_directory(directory)
integrater.set_template(templ)
integrater.set_beam_centre(
tuple(float(x) for x in refiner.get_refined_beam_centre()))
integrater.set_distance(refiner.get_refined_distance())
integrater.set_mosaic(refiner.get_refined_mosaic())
integrater.set_space_group_number(197)
integrater.set_unit_cell(refiner.get_refined_unit_cell())
integrater.run()
hklout = integrater.get_hklout()
assert os.path.exists(hklout)
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(hklout).as_miller_arrays(
merge_equivalents=False)
for ma in miller_arrays:
assert ma.size() == 81011, ma.size()
assert len(miller_arrays) == 13, len(miller_arrays)
assert not integrater.get_bgsig_too_large()
assert not integrater.get_getprof_error()
assert integrater.get_batches_out() == (1, 45)
assert integrater.get_mosaic_spreads() == [
0.43, 0.42, 0.42, 0.41, 0.41, 0.41, 0.42, 0.42, 0.42, 0.42, 0.42, 0.42,
0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.39, 0.39, 0.39, 0.39, 0.39]
assert integrater.get_nref() == 81011
assert len(integrater.get_postref_result()) == 45
assert integrater.get_postref_result()[1] == {
'ovrl': 0.0, 'full': 507.0, 'dist': 158.6, 'ccx': -0.01, 'yscale': 1.0,
'sdrat': 7.5, 'tilt': 25.0, 'rsym': 0.027, 'bad': 0.0, 'i/sigi': 18.1,
'i/sigi_out': 1.6, 'twist': 13.0, 'resid': 0.021, 'wresid': 1.1,
'part': 1309.0, 'nsym': 18.0, 'neg': 158.0, 'ccy': -0.01, 'ccom': -0.01,
'toff': 0.0, 'roff': 0.0}
assert integrater.get_residuals() == [
1.1, 0.9, 1.0, 1.0, 0.8, 0.9, 1.0, 0.8, 0.9, 0.9, 0.9, 0.9, 1.0, 1.0, 1.0,
0.9, 0.9, 0.9, 0.9, 0.8, 1.0, 0.9, 0.8, 0.9, 1.0, 0.8, 1.0, 0.9, 0.8, 0.8,
0.9, 0.9, 0.9, 0.9, 0.9, 1.0, 0.8, 0.9, 1.0, 0.7, 0.8, 0.9, 0.8, 0.9, 1.0]
assert integrater.get_spot_status() \
== 'ooooooooooooooooooooooooooooooooooooooooooooo'
def get_template_and_directory(dials_data):
xia2_demo_data = dials_data("insulin")
template = xia2_demo_data.join("insulin_1_%03i.img").strpath
with mock.patch.object(sys, "argv", []):
return image2template_directory(template % 1)
def get_template_and_directory(xia2_regression_build):
xia2_demo_data = os.path.join(xia2_regression_build, "test_data",
"insulin")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
with mock.patch.object(sys, 'argv', []):
return image2template_directory(template % 1)
def __init__(
self,
name,
wavelength,
sample,
directory=None,
image=None,
beam=None,
reversephi=False,
distance=None,
gain=0.0,
dmin=0.0,
dmax=0.0,
polarization=0.0,
frames_to_process=None,
user_lattice=None,
user_cell=None,
epoch=0,
ice=False,
excluded_regions=None,
):
"""Create a new sweep named name, belonging to XWavelength object
wavelength, representing the images in directory starting with image,
with beam centre optionally defined."""
if excluded_regions is None:
excluded_regions = []
# FIXME bug 2221 if DIRECTORY starts with ~/ or ~graeme (say) need to
# interpret this properly - e.g. map it to a full PATH.
directory = expand_path(directory)
self._name = name
self._wavelength = wavelength
self.sample = sample
self._directory = directory
self._image = image
self._reversephi = reversephi
self._epoch = epoch
self._user_lattice = user_lattice
self._user_cell = user_cell
self._header = {}
self._resolution_high = dmin
self._resolution_low = dmax
self._ice = ice
self._excluded_regions = excluded_regions
self._imageset = None
# FIXME in here also need to be able to accumulate the total
# dose from all experimental measurements (complex) and provide
# a _epoch_to_dose dictionary or some such... may be fiddly as
# this will need to parse across multiple templates. c/f Bug # 2798
self._epoch_to_image = {}
self._image_to_epoch = {}
# to allow first, last image for processing to be
# set... c/f integrater interface
self._frames_to_process = frames_to_process
# + derive template, list of images
params = PhilIndex.get_python_object()
if directory and image:
self._template, self._directory = image2template_directory(
os.path.join(directory, image))
from xia2.Schema import load_imagesets
imagesets = load_imagesets(
self._template,
self._directory,
image_range=self._frames_to_process,
reversephi=(params.xia2.settings.input.reverse_phi
or self._reversephi),
)
assert len(
imagesets
) == 1, "one imageset expected, %d found" % len(imagesets)
self._imageset = copy.deepcopy(imagesets[0])
start, end = self._imageset.get_array_range()
self._images = list(range(start + 1, end + 1))
# FIXME in here check that (1) the list of images is continuous
# and (2) that all of the images are readable. This should also
# take into account frames_to_process if set.
if self._frames_to_process is None:
self._frames_to_process = min(self._images), max(self._images)
start, end = self._frames_to_process
error = False
if params.general.check_image_files_readable:
for j in range(start, end + 1):
if j not in self._images:
logger.debug("image %i missing for %s" %
(j, self.get_imageset().get_template()))
error = True
continue
image_name = self.get_imageset().get_path(j - start)
if not os.access(image_name, os.R_OK):
logger.debug("image %s unreadable" % image_name)
error = True
continue
if error:
raise RuntimeError("problem with sweep %s" % self._name)
beam_ = self._imageset.get_beam()
scan = self._imageset.get_scan()
if wavelength is not None:
# If the wavelength value is 0.0 then first set it to the header
# value - note that this assumes that the header value is correct
# (a reasonable assumption)
if wavelength.get_wavelength() == 0.0:
wavelength.set_wavelength(beam_.get_wavelength())
# FIXME 08/DEC/06 in here need to allow for the fact
# that the wavelength in the image header could be wrong and
# in fact it should be replaced with the input value -
# through the user will need to be warned of this and
# also everything using the FrameProcessor interface
# will also have to respect this!
if (math.fabs(beam_.get_wavelength() -
wavelength.get_wavelength()) > 0.0001):
logger.info(
"Header wavelength for sweep %s different"
" to assigned value (%4.2f vs. %4.2f)",
name,
beam_.get_wavelength(),
wavelength.get_wavelength(),
)
# also in here look at the image headers to see if we can
# construct a mapping between exposure epoch and image ...
images = []
if self._frames_to_process:
start, end = self._frames_to_process
for j in self._images:
if j >= start and j <= end:
images.append(j)
else:
images = self._images
for j in images:
epoch = scan.get_image_epoch(j)
if epoch == 0.0:
epoch = float(
os.stat(self._imageset.get_path(j -
images[0])).st_mtime)
self._epoch_to_image[epoch] = j
self._image_to_epoch[j] = epoch
epochs = self._epoch_to_image
logger.debug("Exposure epoch for sweep %s: %d %d" %
(self._template, min(epochs), max(epochs)))
self._input_imageset = copy.deepcopy(self._imageset)
# + get the lattice - can this be a pointer, so that when
# this object updates lattice it is globally-for-this-crystal
# updated? The lattice included directly in here includes an
# exact unit cell for data reduction, the crystal lattice
# contains an approximate unit cell which should be
# from the unit cells from all sweeps contained in the
# XCrystal. FIXME should I be using a LatticeInfo object
# in here? See what the Indexer interface produces. ALT:
# just provide an Indexer implementation "hook".
# See Headnote 001 above. See also _get_indexer,
# _get_integrater below.
self._indexer = None
self._refiner = None
self._integrater = None
# I don't need this - it is equivalent to self.getWavelength(
# ).getCrystal().getLattice()
# self._crystal_lattice = None
# this means that this module will have to present largely the
# same interface as Indexer and Integrater so that the calls
# can be appropriately forwarded.
# finally configure the beam if set
if beam is not None:
from dxtbx.model.detector_helpers import set_mosflm_beam_centre
try:
set_mosflm_beam_centre(
self.get_imageset().get_detector(),
self.get_imageset().get_beam(),
beam,
)
except AssertionError as e:
logger.debug("Error setting mosflm beam centre: %s" % e)
self._beam_centre = beam
self._distance = distance
self._gain = gain
self._polarization = polarization
self._add_detector_identification_to_cif()
def exercise_mosflm_integrate():
if not have_dials_regression:
print "Skipping exercise_mosflm_integrate(): dials_regression not configured"
return
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Wrappers.Mosflm.MosflmIndex import MosflmIndex
from xia2.Wrappers.Mosflm.MosflmRefineCell import MosflmRefineCell
from xia2.Wrappers.Mosflm.MosflmIntegrate import MosflmIntegrate
# exercise basic indexing from two images
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
from xia2.Experts.FindImages import image2template_directory
templ, directory = image2template_directory(template %1)
indexer = MosflmIndex()
indexer.set_images((1,45))
indexer.set_directory(directory)
indexer.set_template(templ)
indexer.run()
refiner = MosflmRefineCell()
refiner.set_images(((1,3),(21,23), (43,45)))
refiner.set_input_mat_file("xiaindex.mat")
refiner.set_output_mat_file("xiarefine.mat")
refiner.set_directory(directory)
refiner.set_template(templ)
refiner.set_beam_centre(indexer.get_refined_beam_centre())
refiner.set_mosaic(
sum(indexer.get_mosaic_spreads())/len(indexer.get_mosaic_spreads()))
refiner.run()
#output = ''.join(refiner.get_all_output())
#print output
integrater = MosflmIntegrate()
integrater.set_image_range((1,45))
integrater.set_input_mat_file("xiaindex.mat")
#integrater.set_output_mat_file("xiarefine.mat")
integrater.set_directory(directory)
integrater.set_template(templ)
integrater.set_beam_centre(
tuple(float(x) for x in refiner.get_refined_beam_centre()))
integrater.set_distance(refiner.get_refined_distance())
integrater.set_mosaic(refiner.get_refined_mosaic())
integrater.set_space_group_number(197)
integrater.set_unit_cell(refiner.get_refined_unit_cell())
integrater.run()
hklout = integrater.get_hklout()
assert os.path.exists(hklout)
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(hklout).as_miller_arrays(
merge_equivalents=False)
for ma in miller_arrays:
assert ma.size() == 81011, ma.size()
assert len(miller_arrays) == 13, len(miller_arrays)
assert not integrater.get_bgsig_too_large()
assert not integrater.get_getprof_error()
assert integrater.get_batches_out() == (1, 45)
assert integrater.get_mosaic_spreads() == [
0.43, 0.42, 0.42, 0.41, 0.41, 0.41, 0.42, 0.42, 0.42, 0.42, 0.42, 0.42,
0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.41, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
0.4, 0.39, 0.39, 0.39, 0.39, 0.39]
assert integrater.get_nref() == 81011
assert len(integrater.get_postref_result()) == 45
assert integrater.get_postref_result()[1] == {
'ovrl': 0.0, 'full': 507.0, 'dist': 158.6, 'ccx': -0.01, 'yscale': 1.0,
'sdrat': 7.5, 'tilt': 25.0, 'rsym': 0.027, 'bad': 0.0, 'i/sigi': 18.1,
'i/sigi_out': 1.6, 'twist': 13.0, 'resid': 0.021, 'wresid': 1.1,
'part': 1309.0, 'nsym': 18.0, 'neg': 158.0, 'ccy': -0.01, 'ccom': -0.01,
'toff': 0.0, 'roff': 0.0}
assert integrater.get_residuals() == [
1.1, 0.9, 1.0, 1.0, 0.8, 0.9, 1.0, 0.8, 0.9, 0.9, 0.9, 0.9, 1.0, 1.0, 1.0,
0.9, 0.9, 0.9, 0.9, 0.8, 1.0, 0.9, 0.8, 0.9, 1.0, 0.8, 1.0, 0.9, 0.8, 0.8,
0.9, 0.9, 0.9, 0.9, 0.9, 1.0, 0.8, 0.9, 1.0, 0.7, 0.8, 0.9, 0.8, 0.9, 1.0]
assert integrater.get_spot_status() \
== 'ooooooooooooooooooooooooooooooooooooooooooooo'
