From ac7f44a872ff1c54ba5e0ae9dc36ad65623ef1ba Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Tue, 7 Mar 2023 20:01:39 +0000
Subject: [PATCH] change(tiler): print -> log
---
src/aliby/tile/tiler.py | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
index ea057235..43f4b397 100644
--- a/src/aliby/tile/tiler.py
+++ b/src/aliby/tile/tiler.py
@@ -13,6 +13,7 @@ A peak-identifying algorithm recovers the x and y-axis location of traps in the
The experiment is stored as an array with a standard indexing order of (Time, Channels, Z-stack, X, Y).
"""
+import logging
import re
import typing as t
import warnings
@@ -26,7 +27,7 @@ from skimage.registration import phase_cross_correlation
from agora.abc import ParametersABC, StepABC
from agora.io.writer import BridgeH5
-from aliby.io.image import ImageLocalOME, ImageDir, ImageDummy
+from aliby.io.image import ImageDummy
from aliby.tile.traps import segment_traps
@@ -578,7 +579,7 @@ class Tiler(StepABC):
"""Return index of reference channel."""
return self.get_channel_index(self.parameters.ref_channel)
- def get_channel_index(self, channel: str or int):
+ def get_channel_index(self, channel: str or int) -> int:
"""
Find index for channel using regex.
@@ -640,7 +641,7 @@ class Tiler(StepABC):
# Alan: do we need these as well as get_channel_index and get_channel_name?
-# self._log below is not defined
+# TODO homogenise these into a pair of functions
def find_channel_index(image_channels: t.List[str], channel: str):
"""
Access
@@ -649,7 +650,10 @@ def find_channel_index(image_channels: t.List[str], channel: str):
found = re.match(channel, ch, re.IGNORECASE)
if found:
if len(found.string) - (found.endpos - found.start()):
- self._log(f"Channel {channel} matched {ch} using regex")
+ logging.getLogger("aliby").log(
+ logging.WARNING,
+ f"Channel {channel} matched {ch} using regex",
+ )
return i
--
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