Merge branch 'main' of https://whale.am28.uni-tuebingen.de/git/awendt/oephys2nix

oephys2nix/logging.py

@@ -5,14 +5,28 @@ from rich.logging import RichHandler
 DEFAULT_LOG_LEVEL = "DEBUG"
 
 
-def setup_logging(logger: logging.Logger, level=DEFAULT_LOG_LEVEL):
+def setup_logging(logger: logging.Logger, verbosity: int):
+    level = logging.WARNING  # Default level
+
+    if verbosity == 0:
+        level = logging.ERROR
+    elif verbosity == 1:
+        level = logging.INFO
+    elif verbosity >= 2:
+        level = logging.DEBUG
+        print("Debugging enabled.")
+    else:
+        print("Invalid verbosity level. Defaulting to WARNING.")
+
     if logger.hasHandlers():
         logger.handlers.clear()
-    stream_handler = RichHandler(rich_tracebacks=True, show_path=False)
+    stream_handler = RichHandler(rich_tracebacks=True, show_path=level == logging.DEBUG)
     stream_handler.setLevel(level)
     fmt_shell = "%(filename)s:%(lineno)d - %(message)s"
     shell_formatter = logging.Formatter(fmt_shell)
     stream_handler.setFormatter(shell_formatter)
     logger.addHandler(stream_handler)
     logger.setLevel(level)
+    logger.propagate = False
+    # logging.basicConfig(level=level, handlers=[stream_handler], force=True)
     logging.getLogger(__name__).info(f"Logging configured with level {level}.")

oephys2nix/main.py

@@ -1,5 +1,6 @@
 import logging
 from pathlib import Path
+from typing import Annotated
 
 import nixio
 import typer
@@ -12,7 +13,6 @@ from oephys2nix.tonix import RawToNix
 
 app = typer.Typer()
 log = logging.getLogger(__name__)
-setup_logging(log, level="DEBUG")
 console = Console()
 
 
@@ -30,8 +30,11 @@ def main(
     no_ttl: bool = typer.Option(False, help="For recordings that did not have a ttl pulse"),
     overwrite: bool = typer.Option(default=True, help="Overwrites nix file"),
     debug: bool = typer.Option(default=True, help="Shows more information and plots the results"),
+    verbose: Annotated[int, typer.Option("--verbose", "-v", count=True)] = 0,
 ) -> None:
     """Combines open ephys data with relacs data from data_path to a new nix file."""
+
+    setup_logging(logging.getLogger("oephys2nix"), verbosity=verbose)
     log.info(f"Selected data_path is {data_path}")
     open_ephys_data_paths = list(Path(data_path).rglob("*open-ephys"))
     relacs_data_paths = list(Path(data_path).rglob("*relacs/*.nix"))
@@ -88,10 +91,10 @@ def main(
         stim = StimulusToNix(open_ephys, str(relacs), str(nix_path))
         stim.create_repros_automatically()
         stim.print_table()
-        stim.checks()
+        # stim.checks()
 
-        if debug:
-            stim.plot_stimulus()
+        # if debug:
+        #     stim.plot_stimulus()
 
 
 if __name__ == "__main__":

oephys2nix/stimulus_recreation.py

@@ -15,11 +15,9 @@ from rich.table import Table
 from rlxnix.plugins.efish.utils import extract_am
 from scipy import signal
 
-from oephys2nix.logging import setup_logging
 from oephys2nix.metadata import create_dict_from_section, create_metadata_from_dict
 
 log = logging.getLogger(__name__)
-setup_logging(log, level="DEBUG")
 console = Console()
 
 
@@ -452,8 +450,6 @@ class StimulusToNix:
         for repro_r, repro_n in zip(self.dataset.repro_runs(), nix_data_set.repro_runs()):
             if repro_n.name.split("_")[0] not in important_repros:
                 continue
-            embed()
-            exit()
 
             if "FileStimulus" in repro_n.name:
                 repro_n.stimulus_folder = "/home/alexander/stimuli/whitenoise/"

oephys2nix/tonix.py

@@ -11,7 +11,6 @@ from oephys2nix.logging import setup_logging
 from oephys2nix.metadata import create_dict_from_section, create_metadata_from_dict
 
 log = logging.getLogger(__name__)
-setup_logging(log, level="DEBUG")
 
 
 class RawToNix: