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[main] adding convertion scripts

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This commit is contained in:
wendtalexander 2025-10-07 16:06:58 +02:00
parent f34cbc6cd2
commit 1af6fa4f7b
1 changed files with 36 additions and 21 deletions
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57
oephys2nix/main.py
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@ -7,6 +7,8 @@ from IPython import embed
from rich.console import Console from rich.console import Console
from oephys2nix.logging import setup_logging from oephys2nix.logging import setup_logging
from oephys2nix.stimulus_recreation import StimulusToNix
from oephys2nix.tonix import RawToNix
app = typer.Typer() app = typer.Typer()
log = logging.getLogger(__name__) log = logging.getLogger(__name__)
@ -25,30 +27,25 @@ def main(
readable=True, readable=True,
resolve_path=True, resolve_path=True,
), ),
ttl: bool = typer.Option( ttl: bool = typer.Option(default=True, help="For recordings that did not have a ttl pulse"),
default=True, help="For recordings that did not have a ttl pulse"
),
overwrite: bool = typer.Option(default=True, help="Overwrites nix file"), overwrite: bool = typer.Option(default=True, help="Overwrites 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 """Combines open ephys data with relacs data from data_path to a new nix file."""
"""
log.info(f"Selected data_path is {data_path}") log.info(f"Selected data_path is {data_path}")
open_ephys_data_paths = list(Path(data_path).rglob("*open-ephys")) 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( 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") log.error("Please check if both are present")
raise typer.Exit() raise typer.Exit()
for open_ephys, relacs in zip( for open_ephys, relacs in zip(open_ephys_data_paths, relacs_data_paths, strict=True):
open_ephys_data_paths, relacs_data_paths, strict=True nix_file_name = relacs.parent.name.split("_")[0] + "-recording.nix"
):
nix_file_name = relacs.name.split("_")[0] + "-recording.nix"
console.print( console.print(
f"Converting [bold cyan]{open_ephys.name}[/bold cyan] and " f"Converting [bold cyan]{open_ephys.name}[/bold cyan] and "
@ -56,20 +53,38 @@ def main(
f"[green]{nix_file_name}[/green]" 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 nix_path.exists and nix_path.is_file():
if overwrite: if overwrite:
log.warning("Overwriting nix file") 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: else:
log.error( log.error("Converted nix file already exits, and Overwrite is not enabled")
"Converted nix file already exits, and Overwrite is not enabled"
)
raise typer.Exit() raise typer.Exit()
else: else:
log.debug("Creating nix file") 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__": if __name__ == "__main__":