Minor CLI optimizations

phys2denoise/cli/run.py

@@ -90,7 +90,7 @@ def _get_parser():
         "--respiratory-pattern-variability",
         dest="metrics",
         action="append_const",
-        const=respiratory_pattern_variability,
+        const="respiratory_pattern_variability",
         help="Respiratory pattern variability. Requires the following "
         "input: window.",
         default=[],
@@ -100,7 +100,7 @@ def _get_parser():
         "--envelope",
         dest="metrics",
         action="append_const",
-        const=env,
+        const="env",
         help="Respiratory pattern variability calculated across a sliding "
         "window. Requires the following inputs: sample-rate, window and lags.",
         default=[],
@@ -416,6 +416,7 @@ def _get_parser():
     return parser
 
 
+@logger.catch()
 def main():
     """
     Main function to run the parser.
@@ -434,8 +435,7 @@ def main():
 
     logger.info(f"Running phys2denoise version: {__version__}")
 
-    LGR.debug(f"Arguments: {args}")
-    LGR.debug(f"Metrics to export: {args.metrics_to_export}")
+    LGR.debug(f"Arguments Provided: {args}")
 
     if args.metrics_to_export is None or args.metrics_to_export == "all":
         args.metrics_to_export = "all"
@@ -452,12 +452,13 @@ def main():
     args.slice_timings = (
         np.array(args.slice_timings) if args.slice_timings is not None else None
     )
+    args.lags = np.array(args.lags) if args.lags is not None else None
 
     metric_args = dict()
     for metric in args.metrics:
         metric_args[metric] = tasks.select_input_args(globals()[metric], vars(args))
 
-    logger.debug(f"Metric args: {metric_args}")
+    logger.debug(f"Metrics: {args.metrics}")
 
     wf = workflow.build(
         input_file=args.filename,

phys2denoise/metrics/chest_belt.py

@@ -1,6 +1,7 @@
 """Denoising metrics for chest belt recordings."""
 import numpy as np
 import pandas as pd
+from loguru import logger
 from physutils import io, physio
 from scipy.interpolate import interp1d
 from scipy.stats import zscore
@@ -229,6 +230,7 @@ def _respiratory_pattern_variability(data, window):
 
     # Convert window to Hertz
     window = int(window * data.fs)
+    logger.debug(f"Window size in samples: {window}")
 
     # Calculate RPV across a rolling window
 

phys2denoise/tasks.py

@@ -117,10 +117,17 @@ def export_metrics(
     if metrics == "all":
         LGR.info("Exporting all computed metrics")
         for metric in phys.computed_metrics.keys():
+            if metric == "respiratory_pattern_variability":
+                LGR.warning(
+                    f"respiratory_pattern_variability will not be exported, since it is a single value metric "
+                    f"and not a timeseries. RPV value is {phys.computed_metrics[metric].data}"
+                )
+                continue
             has_lags = (
                 True if "has_lags" in phys.computed_metrics[metric].args else False
             )
             prefix = outdir + f"/{metric}"
+            LGR.debug(f"Exporting {metric} to {prefix}")
             export_metric(
                 phys.computed_metrics[metric], phys.fs, tr, prefix, has_lags=has_lags
             )
@@ -131,10 +138,17 @@ def export_metrics(
             if metric not in phys.computed_metrics.keys():
                 LGR.warning(f"Metric {metric} not computed. Skipping")
                 continue
+            if metric == "respiratory_pattern_variability":
+                LGR.warning(
+                    f"respiratory_pattern_variability will not be exported, since it is a single value metric"
+                    f"and not a timeseries. RPV value is {phys.computed_metrics[metric]}"
+                )
+                continue
             has_lags = (
                 True if "has_lags" in phys.computed_metrics[metric].args else False
             )
             prefix = outdir + f"/{metric}"
+            LGR.debug(f"Exporting {metric} to {prefix}")
             export_metric(
                 phys.computed_metrics[metric],
                 phys.fs,