def tst_dump_empty_sweep(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.model.crystal import crystal_model
from uuid import uuid4
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 3))))
imageset.set_beam(Beam((1, 0, 0)))
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 3), (0.0, 1.0)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=1)
experiments = ExperimentListFactory.from_imageset_and_crystal(
imageset, crystal)
dump = ExperimentListDumper(experiments)
filename = 'temp%s.json' % uuid4().hex
dump.as_json(filename)
experiments2 = ExperimentListFactory.from_json_file(filename,
check_format=False)
self.check(experiments, experiments2)
print 'OK'
class TestImageSweep(object):
def __init__(self):
pass
def get_file_list(self):
import libtbx.load_env
import os
from dxtbx.imageset import SweepFileList
try:
dials_regression = libtbx.env.dist_path('dials_regression')
except KeyError, e:
print 'FAIL: dials_regression not configured'
return
path = os.path.join(dials_regression, 'centroid_test_data')
# Non-sequential Filenames and image indices
template = os.path.join(path, 'centroid_%04d.cbf')
array_range = (0, 9)
filenames = SweepFileList(template, array_range)
return filenames
def tst_from_datablock(self):
from dxtbx.imageset import ImageSweep, NullReader, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
from dxtbx.datablock import DataBlockFactory
from dxtbx.model.crystal import crystal_model
imageset = ImageSweep(NullReader(SweepFileList("filename%01d.cbf", (0, 2))))
imageset.set_beam(Beam())
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1, 2), (0, 1)))
crystal = crystal_model((1, 0, 0), (0, 1, 0), (0, 0, 1), space_group_symbol=0)
datablock = DataBlockFactory.from_imageset(imageset)
experiments = ExperimentListFactory.from_datablock_and_crystal(
datablock, crystal)
assert(len(experiments) == 1)
assert(experiments[0].imageset is not None)
assert(experiments[0].beam is not None)
assert(experiments[0].detector is not None)
assert(experiments[0].goniometer is not None)
assert(experiments[0].scan is not None)
assert(experiments[0].crystal is not None)
print 'OK'
def tst_from_null_sweep(self):
from dxtbx.datablock import DataBlockFactory
from dxtbx.imageset import NullReader, ImageSweep, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
sweep = ImageSweep(
NullReader(SweepFileList("template_%2d.cbf", (0, 10))))
sweep.set_beam(Beam((0, 0, 1)))
sweep.set_detector(Detector())
sweep.set_goniometer(Goniometer((1, 0, 0)))
sweep.set_scan(Scan((1, 10), (0, 0.1)))
# Create the datablock
datablock = DataBlockFactory.from_imageset(sweep)
assert (len(datablock) == 1)
datablock = datablock[0]
sweeps = datablock.extract_sweeps()
assert (len(sweeps) == 1)
assert (sweeps[0].get_beam() == sweep.get_beam())
assert (sweeps[0].get_detector() == sweep.get_detector())
assert (sweeps[0].get_goniometer() == sweep.get_goniometer())
assert (sweeps[0].get_scan() == sweep.get_scan())
print 'OK'
class TestMultiFileReader(object):
def normal_file_list(self):
dials_regression = libtbx.env.dist_path('dials_regression')
path = os.path.join(dials_regression, 'centroid_test_data')
# Non-sequential Filenames and image indices
filenames = []
image_indices = range(1, 10)
for i in image_indices:
filenames.append(
os.path.join(path, 'centroid_000{0}.cbf'.format(i)))
return filenames
def sweep_file_list(self):
from dxtbx.imageset import SweepFileList
try:
dials_regression = libtbx.env.dist_path('dials_regression')
except KeyError, e:
print 'FAIL: dials_regression not configured'
return
path = os.path.join(dials_regression, 'centroid_test_data')
# Non-sequential Filenames and image indices
template = os.path.join(path, 'centroid_%04d.cbf')
array_range = (0, 9)
filenames = SweepFileList(template, array_range)
return filenames
def tst_cmp(self, filelist):
from dxtbx.imageset import SweepFileList
assert(filelist == filelist)
template = template = '%s%%0%dd%s' % ('filename', 5, '.cbf')
array_range = (0, 10)
filelist2 = SweepFileList(template, array_range)
assert(filelist != filelist2)
template = template = '%s%%0%dd%s' % ('filename2', 5, '.cbf')
array_range = (20, 50)
filelist3 = SweepFileList(template, array_range)
assert(filelist != filelist3)
template = template = '%s%%0%dd%s' % ('filename', 5, '.cbf')
array_range = (20, 50)
filelist4 = SweepFileList(template, array_range)
assert(filelist == filelist4)
print 'OK'
def get_file_list(self):
from dxtbx.imageset import SweepFileList
dials_regression = libtbx.env.dist_path('dials_regression')
path = os.path.join(dials_regression, 'centroid_test_data')
# Non-sequential Filenames and image indices
template = os.path.join(path, 'centroid_%04d.cbf')
array_range = (0, 9)
filenames = SweepFileList(template, array_range)
return filenames
def tst_null_reader_sweep(self):
from dxtbx.imageset import NullReader, ImageSweep, SweepFileList
from dxtbx.model import Beam, Detector, Goniometer, Scan
template = 'hello_world_%d.cbf'
paths = [template % 1]
# Create the null reader
reader = NullReader(SweepFileList(template, (0, 1)))
# Create the imageset
imageset = ImageSweep(reader)
# Try to get an item
try:
imageset[0]
assert(False)
except Exception:
print 'OK'
# Try to slice the imageset
imageset2 = imageset[0:1]
print 'OK'
# Try some functions which should work
assert(len(imageset) == 1)
assert(imageset == imageset)
assert(imageset.indices() == [0])
assert(imageset.is_valid())
assert(imageset.get_template() == template)
print 'OK'
# Get the image paths
assert(imageset.paths() == paths)
assert(imageset.get_path(0) == paths[0])
print 'OK'
imageset.set_beam(Beam())
imageset.set_detector(Detector())
imageset.set_goniometer(Goniometer())
imageset.set_scan(Scan((1,1), (0, 1)))
assert(isinstance(imageset.get_beam(), Beam))
assert(isinstance(imageset.get_detector(), Detector))
assert(isinstance(imageset.get_goniometer(), Goniometer))
assert(isinstance(imageset.get_scan(), Scan))
print 'OK'
def run(self):
from dxtbx.imageset import SweepFileList
# Create the template and array range
template = template = '%s%%0%dd%s' % ('filename', 5, '.cbf')
array_range = (20, 50)
# Create the sweep file list class
filelist = SweepFileList(template, array_range)
# Call a load of tests
self.tst_len(filelist, 30)
self.tst_template(filelist, template)
self.tst_array_range(filelist, array_range)
self.tst_indices(filelist, range(*array_range))
self.tst_is_index_in_range(filelist)
self.tst_get_filename(filelist)
self.tst_get_item(filelist)
self.tst_iter(filelist)
self.tst_cmp(filelist)
import os
from dxtbx.imageset import SweepFileList
try:
dials_regression = libtbx.env.dist_path('dials_regression')
except KeyError, e:
print 'FAIL: dials_regression not configured'
return
path = os.path.join(dials_regression, 'centroid_test_data')
# Non-sequential Filenames and image indices
template = os.path.join(path, 'centroid_%04d.cbf')
array_range = (0, 9)
filenames = SweepFileList(template, array_range)
return filenames
def run(self):
self.run_tests(self.normal_file_list())
self.run_tests(self.sweep_file_list())
def run_tests(self, filenames):
from dxtbx.imageset import MultiFileReader
from dxtbx.format.Registry import Registry
# Get the parameters we need
format_class = Registry.find(filenames[0])