import os
import pickle
from dxtbx.format.image import ImageBool, ImageDouble
from dxtbx.imageset import ImageSequence, ImageSet, ImageSetFactory
from dxtbx.model import BeamFactory, DetectorFactory, GoniometerFactory, ScanFactory
from dxtbx.serialize.filename import resolve_path
[docs]def filename_to_absolute(filename):
"""Convert filenames to absolute form."""
if isinstance(filename, list):
return [os.path.abspath(f) for f in filename]
return os.path.abspath(filename)
[docs]def filename_or_none(filename):
if filename is None or filename == "":
return None
return filename_to_absolute(filename)
[docs]def basic_imageset_to_dict(imageset):
"""Convert an imageset to a dictionary
Params:
imageset The imageset
Returns:
A dictionary of the parameters
"""
return {
"__id__": "imageset",
"filenames": filename_to_absolute(imageset.paths()),
"mask": filename_or_none(imageset.external_lookup.mask.filename),
"gain": filename_or_none(imageset.external_lookup.gain.filename),
"pedestal": filename_or_none(imageset.external_lookup.pedestal.filename),
"beam": imageset.get_beam(0).to_dict(),
"detector": imageset.get_detector(0).to_dict(),
}
[docs]def imagesequence_to_dict(sequence):
"""Convert a sequence to a dictionary
Params:
sequence The sequence
Returns:
A dictionary of the parameters
"""
return {
"__id__": "imageset",
"template": filename_to_absolute(sequence.get_template()),
"mask": filename_or_none(sequence.external_lookup.mask.filename),
"gain": filename_or_none(sequence.external_lookup.gain.filename),
"pedestal": filename_or_none(sequence.external_lookup.pedestal.filename),
"beam": sequence.get_beam().to_dict(),
"detector": sequence.get_detector().to_dict(),
"goniometer": sequence.get_goniometer().to_dict(),
"scan": sequence.get_scan().to_dict(),
}
[docs]def imageset_to_dict(imageset):
"""Convert the imageset to a dictionary
Params:
imageset The imageset
Returns:
A dictionary of the parameters
"""
# If this is an imageset then return a list of filenames
if isinstance(imageset, ImageSequence):
return imagesequence_to_dict(imageset)
elif isinstance(imageset, ImageSet):
return basic_imageset_to_dict(imageset)
else:
raise TypeError("Unknown ImageSet Type")
[docs]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
[docs]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 existing 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
[docs]def imageset_from_dict(d, check_format=True, directory=None):
"""Convert the dictionary to a sequence
Params:
d The dictionary of parameters
Returns:
The sequence
"""
# Check the input
if d is None:
return None
# Check the version and id
if str(d["__id__"]) != "imageset":
raise ValueError('"__id__" does not equal "imageset"')
if "filenames" in d:
return basic_imageset_from_dict(d, directory=directory)
elif "template" in d:
return imagesequence_from_dict(
d, check_format=check_format, directory=directory
)
else:
raise TypeError("Unable to deserialize given imageset")
