def testListAggregatePullNoFRET():
pull_list = experiment.List(pulls).not_has('fret')
aggregated = datatypes.TrapData.aggregate(pull_list.get('trap'))
assert type(aggregated) == datatypes.TrapData
rows, cols = aggregated.shape
total_rows = sum(p.shape[0] for p in pull_list.get('trap'))
assert total_rows == rows
def test_collapse_two_exp_with_filename(self):
filename = 'test'
test_list = experiment.List(map(experiment.Pulling, self.to_collapse))
for p in test_list:
p.metadata['filename'] = filename
collapsed = test_list.collapse()
self.assertEqual(collapsed.filename, filename + '_collapsed')
def test_collapse_on_two_exp_with_trap_data(self):
test_list = experiment.List(map(experiment.Pulling, self.to_collapse))
collapsed = test_list.collapse()
print collapsed.trap
correct = datatypes.TrapData.aggregate(self.to_collapse)
print correct
self.assertItemsEqual(collapsed.trap.data.flat, correct.data.flat)
self.assertEqual(collapsed.filename, 'collapsed')
def testListCall():
pull_list = experiment.List(pulls)
def testFunc():
return True
for p in pull_list:
p.testFunc = testFunc
assert pull_list.call('testFunc') == [True] * len(pull_list)
def byMolecule(directory='./',
exp_type=experiment.Pulling,
fromMatch=('', ),
**metadata):
"""Return a generator (iterator) which yields experiment.List for all molecules in given directory."""
assert issubclass(exp_type, experiment.Base)
assert isinstance(fromMatch, (tuple, list))
assert isinstance(directory, str)
with ChangeDirectory(directory):
flist = filter(exp_type.filenameMatchesType,
experiment.filelist(*fromMatch))
filelist = groupby(flist, lambda f: fileIO.parseFilename(f)[:4])
for mol, group in filelist:
with ChangeDirectory(directory):
dirname = path.basename(directory)
date_ = dir_to_date(dirname)
metadata.setdefault('date', date_)
yield experiment.List(
map(lambda f: exp_type.fromFile(f, **metadata), group))
def testListGet():
pull_list = experiment.List(pulls)
info = pull_list.get('filename')
assert set(info) == set(LOADED_FILES)
def testListAggregatePull():
pull_list = experiment.List(pulls)
aggregated = datatypes.TrapData.aggregate(pull_list.get('trap'))
rows, cols = aggregated.shape
total_rows = sum(p.shape[0] for p in pull_list.get('trap'))
assert total_rows == rows
def testList():
pulls = [Mock(autospec=experiment.Pulling)] * 3
pull_list = experiment.List(pulls)
assert pull_list == pulls
def groupMolecules(exps):
group_iter = groupby(exps, lambda p: p.info[:4])
for info, group in group_iter:
yield experiment.List(group)