From edad2154809b8d43bd075f86fbb3ba8fdbc26a4f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Wed, 11 Jan 2023 16:21:21 +0000
Subject: [PATCH] change(aliby): rename Process._logger -> _log
---
src/agora/abc.py | 14 ++++++++------
src/aliby/pipeline.py | 8 ++++----
2 files changed, 12 insertions(+), 10 deletions(-)
diff --git a/src/agora/abc.py b/src/agora/abc.py
index 85bf4f3d..6c1fd343 100644
--- a/src/agora/abc.py
+++ b/src/agora/abc.py
@@ -200,6 +200,11 @@ class ProcessABC(ABC):
def run(self):
pass
+ def _log(self, message: str, level: str = "warn"):
+ # Log messages in the corresponding level
+ logger = logging.getLogger("aliby")
+ getattr(logger, level)(f"{self.__class__.__name__}: {message}")
+
def check_type_recursive(val1, val2):
same_types = True
@@ -230,10 +235,6 @@ class StepABC(ProcessABC):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
- @property
- def _logger(self):
- return logging.getLogger("aliby")
-
@abstractmethod
def _run_tp(self):
pass
@@ -245,8 +246,9 @@ class StepABC(ProcessABC):
if log:
t = perf_counter()
result = self._run_tp(tp, **kwargs)
- self._logger.debug(
- f"Timing:{self.__class__.__name__}:{perf_counter()-t}s"
+ self._log(
+ f"Timing:{self.__class__.__name__}:{perf_counter()-t}s",
+ "debug",
)
else:
result = self._run_tp(tp, **kwargs)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 1c6a03aa..dc1512c1 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -499,14 +499,14 @@ class Pipeline(ProcessABC):
frac_clogged_traps = self.check_earlystop(
filename, earlystop, steps["tiler"].tile_size
)
- logging.warn(
+ self._log(
f"{name}:Clogged_traps:{frac_clogged_traps}"
)
frac = np.round(frac_clogged_traps * 100)
pbar.set_postfix_str(f"{frac} Clogged")
else: # Stop if more than X% traps are clogged
- self._logger.warn(
+ self._log(
f"{name}:Analysis stopped early at time {i} with {frac_clogged_traps} clogged traps"
)
meta.add_fields({"end_status": "Clogged"})
@@ -521,7 +521,7 @@ class Pipeline(ProcessABC):
)
PostProcessor(filename, post_proc_params).run()
- self._logger.info("Analysis finished successfully.")
+ self._log("Analysis finished successfully.", "info")
return 1
except Exception as e: # bug during setup or runtime
@@ -678,7 +678,7 @@ class Pipeline(ProcessABC):
# If no previous segmentation and keep tiler
if filename.exists():
- self._logger.warn("IO: Result file exists.")
+ self._log("Result file exists.", "info")
if not ow["tiler"]:
steps["tiler"] = Tiler.from_hdf5(image, filename)
try:
--
GitLab