diff --git a/phys2denoise/metrics/cardiac.py b/phys2denoise/metrics/cardiac.py index 40ebc47..0c102ec 100644 --- a/phys2denoise/metrics/cardiac.py +++ b/phys2denoise/metrics/cardiac.py @@ -1,5 +1,6 @@ """Denoising metrics for cardio recordings.""" import numpy as np +from loguru import logger from .. import references from ..due import due @@ -8,6 +9,7 @@ from .utils import convolve_and_rescale +@logger.catch def _cardiac_metrics(card, peaks, samplerate, metric, window=6, central_measure="mean"): """ Compute cardiac metrics. diff --git a/phys2denoise/metrics/utils.py b/phys2denoise/metrics/utils.py index 34fb21b..6005347 100644 --- a/phys2denoise/metrics/utils.py +++ b/phys2denoise/metrics/utils.py @@ -2,13 +2,11 @@ import logging import numpy as np +from loguru import logger from numpy.lib.stride_tricks import sliding_window_view as swv from scipy.interpolate import interp1d from scipy.stats import zscore -LGR = logging.getLogger(__name__) -LGR.setLevel(logging.INFO) - def print_metric_call(metric, args): """ @@ -33,7 +31,7 @@ def print_metric_call(metric, args): msg = f"{msg}\n" - LGR.info(msg) + logger.info(msg) def mirrorpad_1d(arr, buffer=250): @@ -58,7 +56,7 @@ def mirrorpad_1d(arr, buffer=250): post_mirror = np.take(mirror, idx, axis=0) except IndexError: len(arr) - LGR.warning( + logger.warning( f"Requested buffer size ({buffer}) is longer than input array length " f"({len(arr)}). Fixing buffer size to array length." ) diff --git a/phys2denoise/workflow.py b/phys2denoise/workflow.py index 170abeb..222c601 100644 --- a/phys2denoise/workflow.py +++ b/phys2denoise/workflow.py @@ -18,6 +18,7 @@ import numpy as np import pandas as pd +from loguru import logger from phys2denoise.cli.run import _get_parser from phys2denoise.metrics.cardiac import crf @@ -32,8 +33,8 @@ from . import __version__ from .due import Doi, due -LGR = logging.getLogger(__name__) -LGR.setLevel(logging.INFO) +# LGR = logging.getLogger(__name__) +# LGR.setLevel(logging.INFO) def save_bash_call(outdir): @@ -59,6 +60,7 @@ def save_bash_call(outdir): f.close() +@logger.catch def select_input_args(metric, metric_args): """ Retrieve required args for metric from a dictionary of possible arguments. @@ -112,6 +114,7 @@ def select_input_args(metric, metric_args): version=__version__, cite_module=True, ) +@logger.catch def phys2denoise( filename, outdir=".", @@ -182,8 +185,10 @@ def phys2denoise( ) version_number = __version__ - LGR.info(f"Currently running phys2denoise version {version_number}") - LGR.info(f"Input file is {filename}") + # LGR.info(f"Currently running phys2denoise version {version_number}") + # LGR.info(f"Input file is {filename}") + logger.info(f"Currently running phys2denoise version {version_number}") + logger.info(f"Input file is {filename}") # Check options to make them internally coherent pt. II # #!# This can probably be done while parsing? diff --git a/setup.cfg b/setup.cfg index 8b89352..8a0ce00 100644 --- a/setup.cfg +++ b/setup.cfg @@ -53,10 +53,13 @@ test = coverage devtools = pre-commit +logger = + loguru dev = %(devtools)s %(doc)s %(test)s + %(logger)s [options.entry_points] console_scripts =