def to_datablocks(self):
"""Return the experiment list as a datablock list.
This assumes that the experiment contains 1 datablock."""
from dxtbx.datablock import DataBlockFactory
# Convert the experiment list to dict
obj = self.to_dict()
# Convert the dictionary to a datablock dictionary
obj["__id__"] = "DataBlock"
for e in obj["experiment"]:
iid = e["imageset"]
imageset = obj["imageset"][iid]
if "beam" in e:
imageset["beam"] = e["beam"]
if "detector" in e:
imageset["detector"] = e["detector"]
if "goniometer" in e:
imageset["goniometer"] = e["goniometer"]
if "scan" in e:
imageset["scan"] = e["scan"]
# Remove the experiments
del obj["experiment"]
# Create the datablock
return DataBlockFactory.from_dict([obj])
def to_datablocks(self):
''' Return the experiment list as a datablock list.
This assumes that the experiment contains 1 datablock.'''
from dxtbx.datablock import DataBlockFactory
# Convert the experiment list to dict
obj = self.to_dict()
# Convert the dictionary to a datablock dictionary
obj['__id__'] = 'DataBlock'
for e in obj['experiment']:
iid = e['imageset']
imageset = obj['imageset'][iid]
if 'beam' in e:
imageset['beam'] = e['beam']
if 'detector' in e:
imageset['detector'] = e['detector']
if 'goniometer' in e:
imageset['goniometer'] = e['goniometer']
if 'scan' in e:
imageset['scan'] = e['scan']
# Remove the experiments
del obj['experiment']
# Create the datablock
return DataBlockFactory.from_dict([obj])
def test_json(dials_regression, tmpdir):
tmpdir.chdir()
# Call dials.export
result = procrunner.run_process([
'dials.export',
'format=json',
os.path.join(dials_regression, "centroid_test_data", "datablock.json"),
os.path.join(dials_regression, "centroid_test_data", "strong.pickle"),
])
assert result['exitcode'] == 0
assert result['stderr'] == ''
assert os.path.exists('rlp.json')
from dxtbx.datablock import DataBlockFactory
with open('rlp.json', 'rb') as f:
d = json.load(f)
assert d.keys() == ['imageset_id', 'datablocks', 'rlp',
'experiment_id'], d.keys()
assert d['rlp'][:3] == [0.123454, 0.57687, 0.186465], d['rlp'][:3]
assert d['imageset_id'][0] == 0
assert d['experiment_id'][0] == 0
assert len(d['datablocks']) == 1
db = DataBlockFactory.from_dict(d['datablocks'])
imgset = db[0].extract_imagesets()
assert len(imgset) == 1
def to_datablocks(self):
''' Return the experiment list as a datablock list.
This assumes that the experiment contains 1 datablock.'''
from dxtbx.datablock import DataBlockFactory
# Convert the experiment list to dict
obj = self.to_dict()
# Convert the dictionary to a datablock dictionary
obj['__id__'] = 'DataBlock'
for e in obj['experiment']:
iid = e['imageset']
imageset = obj['imageset'][iid]
if 'beam' in e:
imageset['beam'] = e['beam']
if 'detector' in e:
imageset['detector'] = e['detector']
if 'goniometer' in e:
imageset['goniometer'] = e['goniometer']
if 'scan' in e:
imageset['scan'] = e['scan']
# Remove the experiments
del obj['experiment']
# Create the datablock
return DataBlockFactory.from_dict([obj])
def test_json(self):
import json
from libtbx import easy_run
from os.path import exists
from libtbx.test_utils import approx_equal
from dxtbx.datablock import DataBlockFactory
# Call dials.export
easy_run.fully_buffered([
'dials.export',
'format=json',
self.datablock,
self.strong
]).raise_if_errors()
assert exists('rlp.json')
with open('rlp.json', 'rb') as f:
d = json.load(f)
assert d.keys() == ['imageset_id', 'datablocks', 'rlp', 'experiment_id'], d.keys()
assert d['rlp'][:3] == [0.123454, 0.57687, 0.186465], d['rlp'][:3]
assert d['imageset_id'][0] == 0
assert d['experiment_id'][0] == 0
assert len(d['datablocks']) == 1
db = DataBlockFactory.from_dict(d['datablocks'])
imgset = db[0].extract_imagesets()
assert len(imgset) == 1
# Call dials.export
easy_run.fully_buffered([
'dials.export',
'format=json',
self.experiments,
self.reflections,
'json.filename=integrated.json',
'n_digits=4',
'compact=False',
]).raise_if_errors()
assert exists('integrated.json')
with open('integrated.json', 'rb') as f:
d = json.load(f)
assert d.keys() == ['imageset_id', 'rlp', 'experiment_id'], d.keys()
assert d['rlp'][:3] == [-0.5975, -0.6141, 0.4702], d['rlp'][:3]
assert d['imageset_id'][0] == 0
assert d['experiment_id'][0] == 0
print 'OK'
def from_dict(obj, check_format=True, directory=None):
"""
Load an experiment list from a dictionary.
Args:
obj (dict):
Dictionary containing either ExperimentList or DataBlock
structure.
check_format (bool):
If True, the file will be read to verify metadata.
directory (str):
Returns:
ExperimentList: The dictionary converted
"""
try:
experiments = ExperimentList()
for db in DataBlockFactory.from_dict(
obj, check_format=check_format, directory=directory
):
experiments.extend(
ExperimentListFactory.from_datablock_and_crystal(db, None)
)
except Exception:
experiments = None
# Decode the experiments from the dictionary
if experiments is None:
experiments = ExperimentListDict(
obj, check_format=check_format, directory=directory
).decode()
# Check the list is consistent
assert experiments.is_consistent()
return experiments
def to_datablocks(self):
"""Return the experiment list as a datablock list.
This assumes that the experiment contains 1 datablock."""
# Datablock depends on model/__init__
from dxtbx.datablock import DataBlockFactory
# Convert the experiment list to dict
obj = self.to_dict()
# Convert the dictionary to a datablock dictionary
obj["__id__"] = "DataBlock"
for e in obj["experiment"]:
iid = e["imageset"]
imageset = obj["imageset"][iid]
if "beam" in e:
imageset["beam"] = e["beam"]
if "detector" in e:
imageset["detector"] = e["detector"]
if "goniometer" in e:
imageset["goniometer"] = e["goniometer"]
if "scan" in e:
imageset["scan"] = e["scan"]
if imageset["__id__"] in ("ImageSet", "ImageGrid"):
image_list = []
for file_index, filename in enumerate(imageset["images"]):
image_dict = collections.OrderedDict()
image_dict["filename"] = filename
image_dict["image"] = file_index
image_list.append(image_dict)
imageset["images"] = image_list
# Remove the experiments
del obj["experiment"]
# Create the datablock
return DataBlockFactory.from_dict([obj])
from __future__ import absolute_import, division, print_function
from dxtbx.datablock import DataBlockFactory, DataBlockDumper
import sys
from six.moves import range
fin = sys.argv[1]
px_size = 0.05 # in mm
dpx = [0, 0, 1, 1, 0, 1, 1, 0] # in px
dpy = [0, 0, 1, 1, 0, 1, 1, 0] # in px
db = DataBlockFactory.from_json_file(fin)
db0 = db[0]
dd = db0.to_dict()
for i in range(8):
x = dd['detector'][0]['panels'][i]['origin'][0] + dpx[i] * px_size
y = dd['detector'][0]['panels'][i]['origin'][1] + dpy[i] * px_size
dd['detector'][0]['panels'][i]['origin'] = (x, y, 0)
xx = DataBlockFactory.from_dict(dd)
yy = DataBlockDumper(xx)
yy.as_file('new_detector_geom.json')
