def __exit__(self, except_type, except_value, except_trace):
if except_type is javabridge.JavaException:
raise NotSupportedError('File format is not supported.')
if except_value:
sys.stdout.write('The following error occurred:\n%s' %
str(except_value))
for tb in traceback.format_tb(except_trace):
sys.stdout.write(tb)
def create_run_batches(self, args):
'''Creates job descriptions for parallel computing.
Parameters
----------
args: tmlib.workflow.align.args.AlignBatchArguments
step-specific arguments
Returns
-------
generator
job descriptions
Raises
------
ValueError
when `args.ref_wavelength` does not exist across all cycles
'''
job_count = 0
with tm.utils.ExperimentSession(self.experiment_id) as session:
cycles = session.query(tm.Cycle).all()
if not (len(cycles) > 1):
raise NotSupportedError(
'Alignment requires more than one cycle.')
if args.ref_cycle >= len(cycles):
raise JobDescriptionError(
'Cycle index must not exceed total number of cycles.')
site_ids = session.query(tm.Site.id).\
order_by(tm.Site.id).\
all()
batches = self._create_batches(site_ids, args.batch_size)
for batch in batches:
job_count += 1
input_ids = {
'reference_file_ids': list(),
'target_file_ids': defaultdict(list)
}
for cycle in cycles:
n = session.query(tm.ChannelImageFile.id).\
join(tm.Cycle).\
join(tm.Channel).\
filter(tm.Cycle.id == cycle.id).\
filter(tm.Channel.wavelength == args.ref_wavelength).\
filter(~tm.Site.omitted).\
count()
if n == 0:
raise ValueError(
'No image files found for cycle %d and '
'wavelength "%s"' %
(cycle.id, args.ref_wavelength))
for s in batch:
files = session.query(tm.ChannelImageFile.id).\
join(tm.Site).\
join(tm.Cycle).\
join(tm.Channel).\
filter(tm.Site.id == s).\
filter(tm.Cycle.id == cycle.id).\
filter(tm.Channel.wavelength == args.ref_wavelength).\
filter(~tm.Site.omitted).\
all()
if not files:
# We don't raise an Execption here, because
# there may be situations were an aquisition
# failed at a given site in one cycle, but
# is present in the other cycles.
logger.warning('no files for site %d and cycle %d',
s, cycle.id)
continue
ids = [f.id for f in files]
if cycle.index == args.ref_cycle:
input_ids['reference_file_ids'].extend(ids)
input_ids['target_file_ids'][cycle.id].extend(ids)
yield {
'id': job_count,
'input_ids': input_ids,
'illumcorr': args.illumcorr,
'robust_align': args.robust_align,
'rescale_percentile': args.rescale_percentile
}