diff --git a/pyproject.toml b/pyproject.toml index 928bb083408fbf24b26961bd1bff5bb7bc35f681..69c7a1058f2978c986ad1869391539847dd79ef9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "aliby" -version = "0.1.54" +version = "0.1.55" description = "Process and analyse live-cell imaging data" authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"] packages = [ diff --git a/src/agora/io/signal.py b/src/agora/io/signal.py index c0c3e840f171d8c092ffec03ee4efb0d841f5a92..4ea45539c8a5905e366604ce2c643271ffa00b22 100644 --- a/src/agora/io/signal.py +++ b/src/agora/io/signal.py @@ -1,3 +1,4 @@ +import logging import typing as t from copy import copy from functools import cached_property, lru_cache @@ -85,10 +86,10 @@ class Signal(BridgeH5): """Find the interval between time points (minutes).""" tinterval_location = "time_settings/timeinterval" with h5py.File(self.filename, "r") as f: - if tinterval_location in f: + if tinterval_location in f.attrs: return f.attrs[tinterval_location][0] else: - print( + logging.getlogger("aliby").warn( f"{str(self.filename).split('/')[-1]}: using default time interval of 5 minutes" ) return 5 diff --git a/src/postprocessor/chainer.py b/src/postprocessor/chainer.py index 831d5471b558cd574410d1b0d538de98838e7403..21693811c4d57dd38c7f5a11c2c0708f66ce423a 100644 --- a/src/postprocessor/chainer.py +++ b/src/postprocessor/chainer.py @@ -62,7 +62,7 @@ class Chainer(Signal): data = self.common_chains[dataset](**kwargs) else: # use Signal's get_raw - data = self.get_raw(dataset, in_minutes=in_minutes) + data = self.get_raw(dataset, in_minutes=in_minutes, lineage=True) if chain: data = self.apply_chain(data, chain, **kwargs) if retain: diff --git a/src/postprocessor/grouper.py b/src/postprocessor/grouper.py index 09bff52e5c22b54f5b6346a17a3d7e1a6cafc0af..6b9fa9ee56a1d77fa24ff3b29299ca352db34466 100644 --- a/src/postprocessor/grouper.py +++ b/src/postprocessor/grouper.py @@ -165,8 +165,6 @@ class Grouper(ABC): ): """Enable different threads for independent chains, particularly useful when aggregating multiple elements.""" if pool is None: - # Alan: why is None changed to 8 - # pool = 8 pass chainers = chainers or self.chainers if pool: