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 = []):
'''Create a new sweep named name, belonging to XWavelength object
wavelength, representing the images in directory starting with image,
with beam centre optionally defined.'''
# + 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)
# bug # 2274 - maybe migrate the data to a local disk (this
# will depend if the user has added -migrate_data to the cl)
directory = FileHandler.migrate(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
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=(Flags.get_reversephi() 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
from xia2.Handlers.Phil import PhilIndex
params = PhilIndex.get_python_object()
if params.general.check_image_files_readable:
for j in range(start, end + 1):
if not j in self._images:
Debug.write('image %s missing' % \
self.get_image_name(j))
error = True
continue
if not os.access(self.get_image_name(j), os.R_OK):
Debug.write('image %s unreadable' % \
self.get_image_name(j))
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 not wavelength == 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)
