From 1af6fa4f7bd59812d6ac5bf440a26e9b92e54764 Mon Sep 17 00:00:00 2001
From: wendtalexander <wendtalexander@protonmail.com>
Date: Tue, 7 Oct 2025 16:06:58 +0200
Subject: [PATCH] [main] adding convertion scripts

---
 oephys2nix/main.py | 57 +++++++++++++++++++++++++++++-----------------
 1 file changed, 36 insertions(+), 21 deletions(-)

diff --git a/oephys2nix/main.py b/oephys2nix/main.py
index 59d93a6..1b6d48e 100644
--- a/oephys2nix/main.py
+++ b/oephys2nix/main.py
@@ -7,6 +7,8 @@ from IPython import embed
 from rich.console import Console
 
 from oephys2nix.logging import setup_logging
+from oephys2nix.stimulus_recreation import StimulusToNix
+from oephys2nix.tonix import RawToNix
 
 app = typer.Typer()
 log = logging.getLogger(__name__)
@@ -25,30 +27,25 @@ def main(
         readable=True,
         resolve_path=True,
     ),
-    ttl: bool = typer.Option(
-        default=True, help="For recordings that did not have a ttl pulse"
-    ),
+    ttl: bool = typer.Option(default=True, help="For recordings that did not have a ttl pulse"),
     overwrite: bool = typer.Option(default=True, help="Overwrites nix file"),
-):
-    """
-    Combines open ephys data with relacs data from data_path to a new nix file
-    """
-
+    debug: bool = typer.Option(default=True, help="Shows more information and plots the results"),
+) -> None:
+    """Combines open ephys data with relacs data from data_path to a new nix file."""
     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"))
+    relacs_data_paths = list(Path(data_path).rglob("*relacs/*.nix"))
 
-    if not len(open_ephys_data_paths) == len(relacs_data_paths):
+    if len(open_ephys_data_paths) != len(relacs_data_paths):
         log.error(
-            f"Missmatch in data directory found open-ephys data {len(open_ephys_data_paths)} and relacs data {len(relacs_data_paths)}"
+            f"Missmatch in data directory found open-ephys data {len(open_ephys_data_paths)} "
+            f"and relacs data {len(relacs_data_paths)}"
         )
         log.error("Please check if both are present")
         raise typer.Exit()
 
-    for open_ephys, relacs in zip(
-        open_ephys_data_paths, relacs_data_paths, strict=True
-    ):
-        nix_file_name = relacs.name.split("_")[0] + "-recording.nix"
+    for open_ephys, relacs in zip(open_ephys_data_paths, relacs_data_paths, strict=True):
+        nix_file_name = relacs.parent.name.split("_")[0] + "-recording.nix"
 
         console.print(
             f"Converting [bold cyan]{open_ephys.name}[/bold cyan] and "
@@ -56,20 +53,38 @@ def main(
             f"[green]{nix_file_name}[/green]"
         )
 
-        nix_path = relacs.parent / nix_file_name
+        nix_path = relacs.parent.parent / nix_file_name
 
         if nix_path.exists and nix_path.is_file():
             if overwrite:
                 log.warning("Overwriting nix file")
-                nix_files = nixio.File(str(nix_file_name), nixio.FileMode.Overwrite)
+                nix_file = nixio.File(str(nix_path), nixio.FileMode.Overwrite)
             else:
-                log.error(
-                    "Converted nix file already exits, and Overwrite is not enabled"
-                )
+                log.error("Converted nix file already exits, and Overwrite is not enabled")
                 raise typer.Exit()
         else:
             log.debug("Creating nix file")
-            nix_files = nixio.File(str(nix_file_name), nixio.FileMode.Overwrite)
+            nix_file = nixio.File(str(nix_path), nixio.FileMode.Overwrite)
+
+        nix_file.close()
+
+        log.info("Appending raw data from relacs and open-ephys to new nix-file")
+        to_nix = RawToNix(open_ephys, str(relacs), str(nix_path))
+        to_nix.append_section()
+        to_nix.append_fish_lines()
+        to_nix.append_relacs_lines()
+        to_nix.append_raw_data()
+        to_nix.close()
+        log.info("Finished!")
+
+        log.info("Starting with stimulus recreation")
+        stim = StimulusToNix(open_ephys, str(relacs), str(nix_path))
+        stim.create_repros_automatically()
+        stim.print_table()
+        stim.checks()
+
+        if debug:
+            stim.plot_stimulus()
 
 
 if __name__ == "__main__":