Integrate Loguru

peakdet/__init__.py

@@ -16,6 +16,8 @@
     "__version__",
 ]
 
+from loguru import logger
+
 from peakdet.analytics import HRV
 from peakdet.external import load_rtpeaks
 from peakdet.io import load_history, load_physio, save_history, save_physio
@@ -34,3 +36,5 @@
 
 __version__ = get_versions()["version"]
 del get_versions
+
+logger.disable("peakdet")

peakdet/cli/run.py

@@ -2,13 +2,16 @@
 import glob
 import os
 import sys
-import warnings
 
 import matplotlib
 
 matplotlib.use("WXAgg")
-from gooey import Gooey, GooeyParser
+import argparse
+import datetime
 
+from loguru import logger
+
+# from gooey import Gooey, GooeyParser
 import peakdet
 
 TARGET = "pythonw" if sys.platform == "darwin" else "python"
@@ -41,19 +44,11 @@
 }
 
 
-@Gooey(
-    program_name="Physio pipeline",
-    program_description="Physiological processing pipeline",
-    default_size=(800, 600),
-    target=TARGET,
-)
 def get_parser():
     """Parser for GUI and command-line arguments"""
-    parser = GooeyParser()
+    parser = argparse.ArgumentParser()
     parser.add_argument(
         "file_template",
-        metavar="Filename template",
-        widget="FileChooser",
         help="Select a representative file and replace all "
         'subject-specific information with a "?" symbol.'
         "\nFor example, subject_001_data.txt should "
@@ -67,28 +62,24 @@ def get_parser():
     )
     inp_group.add_argument(
         "--modality",
-        metavar="Modality",
         default="ECG",
         choices=list(MODALITIES.keys()),
         help="Modality of input data.",
     )
     inp_group.add_argument(
         "--fs",
-        metavar="Sampling rate",
         default=1000.0,
         type=float,
         help="Sampling rate of input data.",
     )
     inp_group.add_argument(
         "--source",
-        metavar="Source",
         default="rtpeaks",
         choices=list(LOADERS.keys()),
         help="Program used to collect the data.",
     )
     inp_group.add_argument(
         "--channel",
-        metavar="Channel",
         default=1,
         type=int,
         help="Which channel of data to read from data "
@@ -102,7 +93,6 @@ def get_parser():
     out_group.add_argument(
         "-o",
         "--output",
-        metavar="Filename",
         default="peakdet.csv",
         help="Output filename for generated measurements.",
     )
@@ -111,16 +101,13 @@ def get_parser():
         "--measurements",
         metavar="Measurements",
         nargs="+",
-        widget="Listbox",
         choices=list(ATTR_CONV.keys()),
         default=["Average NN intervals", "Standard deviation of NN intervals"],
-        help="Desired physiological measurements.\nChoose "
-        "multiple with shift+click or ctrl+click.",
+        help="Desired physiological measurements",
     )
     out_group.add_argument(
         "-s",
         "--savehistory",
-        metavar="Save history",
         action="store_true",
         help="Whether to save history of data processing " "for each file.",
     )
@@ -132,22 +119,45 @@ def get_parser():
     edit_group.add_argument(
         "-n",
         "--noedit",
-        metavar="Editing",
         action="store_true",
         help="Turn off interactive editing.",
     )
     edit_group.add_argument(
         "-t",
         "--thresh",
-        metavar="Threshold",
         default=0.2,
         type=float,
         help="Threshold for peak detection algorithm.",
     )
+    edit_group.add_argument(
+        "-debug",
+        "--debug",
+        dest="debug",
+        action="store_true",
+        help="Only print debugging info to log file. Default is False.",
+        default=False,
+    )
+    edit_group.add_argument(
+        "-quiet",
+        "--quiet",
+        dest="quiet",
+        action="store_true",
+        help="Only print warnings to log file. Default is False.",
+        default=False,
+    )
+    edit_group.add_argument(
+        "-verbose",
+        "--verbose",
+        dest="verbose",
+        action="store_true",
+        help="Print verbose error logs with diagnostics",
+        default=False,
+    )
 
     return parser
 
 
+@logger.catch
 def workflow(
     *,
     file_template,
@@ -159,7 +169,10 @@ def workflow(
     savehistory=True,
     noedit=False,
     thresh=0.2,
-    measurements=ATTR_CONV.keys()
+    measurements=ATTR_CONV.keys(),
+    verbose=False,
+    debug=False,
+    quiet=False,
 ):
     """
     Basic workflow for physiological data
@@ -190,17 +203,74 @@ def workflow(
     measurements : list, optional
         Which HRV-related measurements to save from data. See ``peakdet.HRV``
         for available measurements. Default: all available measurements.
+    verbose : bool, optional
+        Whether to include verbose logs when catching exceptions that include diagnostics
     """
+    outdir = os.path.dirname(output)
+    logger.info(f"Current path is {outdir}")
+
+    # Create logfile name
+    basename = "peakdet"
+    extension = "log"
+    isotime = datetime.datetime.now().strftime("%Y-%m-%dT%H%M%S")
+    logname = os.path.join(outdir, (basename + isotime + "." + extension))
+
+    logger.remove(0)
+    if quiet:
+        logger.add(
+            sys.stderr,
+            level="WARNING",
+            colorize=True,
+            backtrace=verbose,
+            diagnose=verbose,
+        )
+        logger.add(
+            logname,
+            level="WARNING",
+            colorize=False,
+            backtrace=verbose,
+            diagnose=verbose,
+        )
+    elif debug:
+        logger.add(
+            sys.stderr,
+            level="DEBUG",
+            colorize=True,
+            backtrace=verbose,
+            diagnose=verbose,
+        )
+        logger.add(
+            logname,
+            level="DEBUG",
+            colorize=False,
+            backtrace=verbose,
+            diagnose=verbose,
+        )
+    else:
+        logger.add(
+            sys.stderr,
+            level="INFO",
+            colorize=True,
+            backtrace=verbose,
+            diagnose=verbose,
+        )
+        logger.add(
+            logname,
+            level="INFO",
+            colorize=False,
+            backtrace=verbose,
+            diagnose=verbose,
+        )
 
     # output file
-    print("OUTPUT FILE:\t\t{}\n".format(output))
+    logger.info("OUTPUT FILE:\t\t{}".format(output))
     # grab files from file template
-    print("FILE TEMPLATE:\t{}\n".format(file_template))
+    logger.info("FILE TEMPLATE:\t{}".format(file_template))
     files = glob.glob(file_template, recursive=True)
 
     # convert measurements to peakdet.HRV attribute friendly names
     try:
-        print("REQUESTED MEASUREMENTS: {}\n".format(", ".join(measurements)))
+        logger.info("REQUESTED MEASUREMENTS: {}\n".format(", ".join(measurements)))
     except TypeError:
         raise TypeError(
             "It looks like you didn't select any of the options "
@@ -221,7 +291,7 @@ def workflow(
         # requested on command line, warn and use existing measurements so
         # as not to totally fork up existing file
         if eheader != head:
-            warnings.warn(
+            logger.warning(
                 "Desired output file already exists and requested "
                 "measurements do not match with measurements in "
                 "existing output file. Using the pre-existing "
@@ -238,7 +308,7 @@ def workflow(
         # iterate through all files and do peak detection with manual editing
         for fname in files:
             fname = os.path.relpath(fname)
-            print("Currently processing {}".format(fname))
+            logger.info("Currently processing {}".format(fname))
 
             # if we want to save history, this is the output name it would take
             outname = os.path.join(
@@ -281,6 +351,7 @@ def workflow(
 
 
 def main():
+    logger.enable("")
     opts = get_parser().parse_args()
     workflow(**vars(opts))
 

peakdet/editor.py

@@ -5,6 +5,7 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
+from loguru import logger
 from matplotlib.widgets import SpanSelector
 
 from peakdet import operations, utils
@@ -142,6 +143,7 @@ def on_edit(self, xmin, xmax, *, method):
 
         method accepts 'insert', 'reject', 'delete'
         """
+        logger.debug("Edited peaks with action: {}", method)
         if method not in ["insert", "reject", "delete"]:
             raise ValueError(f'Action "{method}" not supported.')
 
@@ -184,6 +186,7 @@ def undo(self):
 
         # pop off last edit and delete
         func, peaks = self.data._history.pop()
+        logger.debug(f"Undo previous action: {func}")
 
         if func == "reject_peaks":
             self.data._metadata["reject"] = np.setdiff1d(

peakdet/external.py

@@ -3,9 +3,8 @@
 Functions for interacting with physiological data acquired by external packages
 """
 
-import warnings
-
 import numpy as np
+from loguru import logger
 
 from peakdet import physio, utils
 
@@ -40,7 +39,7 @@ def load_rtpeaks(fname, channel, fs):
     """
 
     if fname.startswith("/"):
-        warnings.warn(
+        logger.warning(
             "Provided file seems to be an absolute path. In order "
             "to ensure full reproducibility it is recommended that "
             "a relative path is provided."

peakdet/io.py

@@ -5,9 +5,9 @@
 
 import json
 import os.path as op
-import warnings
 
 import numpy as np
+from loguru import logger
 
 from peakdet import physio, utils
 
@@ -61,18 +61,23 @@ def load_physio(data, *, fs=None, dtype=None, history=None, allow_pickle=False):
                 inp["history"] = list(map(tuple, inp["history"]))
         except (IOError, OSError, ValueError):
             inp = dict(data=np.loadtxt(data), history=[utils._get_call(exclude=[])])
+        logger.debug("Instantiating Physio object from a file")
         phys = physio.Physio(**inp)
     # if we got a numpy array, load that into a Physio object
     elif isinstance(data, np.ndarray):
+        logger.debug("Instantiating Physio object from numpy array")
         if history is None:
-            warnings.warn(
+            logger.warning(
                 "Loading data from a numpy array without providing a"
                 "history will render reproducibility functions "
                 "useless! Continuing anyways."
             )
         phys = physio.Physio(np.asarray(data, dtype=dtype), fs=fs, history=history)
     # create a new Physio object out of a provided Physio object
     elif isinstance(data, physio.Physio):
+        logger.debug(
+            "Instantiating a new Physio object from the provided Physio object"
+        )
         phys = utils.new_physio_like(data, data.data, fs=fs, dtype=dtype)
         phys._history += [utils._get_call()]
     else:
@@ -81,7 +86,7 @@ def load_physio(data, *, fs=None, dtype=None, history=None, allow_pickle=False):
     # reset sampling rate, as requested
     if fs is not None and fs != phys.fs:
         if not np.isnan(phys.fs):
-            warnings.warn(
+            logger.warning(
                 "Provided sampling rate does not match loaded rate. "
                 "Resetting loaded sampling rate {} to provided {}".format(phys.fs, fs)
             )
@@ -119,6 +124,7 @@ def save_physio(fname, data):
         np.savez_compressed(
             dest, data=data.data, fs=data.fs, history=hist, metadata=data._metadata
         )
+    logger.info(f"Saved {data} in {fname}")
 
     return fname
 
@@ -149,10 +155,11 @@ def load_history(file, verbose=False):
         history = json.load(src)
 
     # replay history from beginning and return resultant Physio object
+    logger.info(f"Replaying history from {file}")
     data = None
     for func, kwargs in history:
         if verbose:
-            print("Rerunning {}".format(func))
+            logger.info("Rerunning {}".format(func))
         # loading functions don't have `data` input because it should be the
         # first thing in `history` (when the data was originally loaded!).
         # for safety, check if `data` is None; someone could have potentially
@@ -203,13 +210,14 @@ def save_history(file, data):
 
     data = check_physio(data)
     if len(data.history) == 0:
-        warnings.warn(
+        logger.warning(
             "History of provided Physio object is empty. Saving "
             "anyway, but reloading this file will result in an "
             "error."
         )
     file += ".json" if not file.endswith(".json") else ""
     with open(file, "w") as dest:
         json.dump(data.history, dest, indent=4)
+    logger.info(f"Saved {data} history in {file}")
 
     return file