[main] renaming main to convert, adding plot and timeline

oephys2nix/main.py

@@ -18,7 +18,7 @@ console = Console()
 
 
 @app.command()
-def main(
+def convert(
     data_path: Path = typer.Argument(
         ...,
         help="The source directory containing the Open Ephys data.",
@@ -92,32 +92,68 @@ def main(
         stim = StimulusToNix(open_ephys, str(relacs), str(nix_path))
         stim.create_repros_automatically()
         stim.print_table()
-        # stim.checks()
-
-        # if debug:
-        #     stim.plot_stimulus()
 
 
 @app.command()
 def timeline(
     data_path: Path = typer.Argument(
         ...,
-        help="The source directory containing the Open Ephys data.",
+        help="The source directory containing a dataset.",
         exists=True,
         file_okay=False,
         dir_okay=True,
         readable=True,
         resolve_path=True,
     ),
-):
+) -> None:
+    """Plot the timeline for a given dataset."""
+    dataset = list(Path(data_path).rglob("*.nix"))
+
+    if not dataset:
+        log.error("Did not find any dataset")
+        raise typer.Exit()
+    if len(dataset) > 1:
+        log.info(f"Found multiple datasets {len(dataset)} taking the first one")
+    dataset = rlx.Dataset(str(dataset[0]))
+    dataset.plot_timeline()
+    dataset.close()
+
+
+@app.command()
+def plot(
+    data_path: Path = typer.Argument(
+        ...,
+        help="The source directory containing the open-ephys and relacs data.",
+        exists=True,
+        file_okay=False,
+        dir_okay=True,
+        readable=True,
+        resolve_path=True,
+    ),
+) -> None:
+    """Plot the stimulus, TTL and the relacs stimulus.
+
+    You can run this if you converted already the nix-file.
+    """
     relacs_data_paths = list(Path(data_path).rglob("*relacs/*.nix"))
     if not relacs_data_paths:
         log.error("Did not find any relacs data")
         raise typer.Exit()
 
-    dataset = rlx.Dataset(str(relacs_data_paths[0]))
+    open_ephys_data_paths = list(Path(data_path).rglob("*open-ephys"))
-    dataset.plot_timeline()
+    if not open_ephys_data_paths:
-    dataset.close()
+        log.error("Did not find any open-ephys data")
+        raise typer.Exit()
+
+    nix_file_name = relacs_data_paths[0].parent.name.split("_")[0] + "-recording.nix"
+    nix_path = relacs_data_paths[0].parent.parent / nix_file_name
+    if not nix_path.is_file:
+        log.error("Did not find any converted nix file")
+        raise typer.Exit()
+
+    stim = StimulusToNix(open_ephys_data_paths[0], str(relacs_data_paths[0]), str(nix_path))
+    stim.plot_stimulus()
+    stim.close()
 
 
 if __name__ == "__main__":