Skip to content

Added --no-summaries and --no-update options to run_remodel #655

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
VisLab merged 1 commit into from
Apr 25, 2023
Merged

Added --no-summaries and --no-update options to run_remodel #655

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
29 changes: 18 additions & 11 deletions hed/tools/remodeling/cli/run_remodel.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@


def get_parser():
""" Create a parser for the run_remodel command-line arguments.
""" Create a parser for the run_remodel command-line arguments.

Returns:
argparse.ArgumentParser: A parser for parsing the command line arguments.
Expand All @@ -35,10 +35,14 @@ def get_parser():
help="Name of the default backup for remodeling")
parser.add_argument("-nb", "--no-backup", action='store_true', dest="no_backup",
help="If present, the operations are run directly on the files with no backup.")
parser.add_argument("-ns", "--no-summaries", action='store_true', dest="no_summaries",
help="If present, the summaries are not saved, but rather discarded.")
parser.add_argument("-nu", "--no-update", action='store_true', dest="no_update",
help="If present, the files are not saved, but rather discarded.")
parser.add_argument("-r", "--hed-versions", dest="hed_versions", nargs="*", default=[],
help="Optional list of HED schema versions used for annotation, include prefixes.")
parser.add_argument("-s", "--save-formats", nargs="*", default=['.json', '.txt'], dest="save_formats",
help="Format for saving any summaries, if any. If empty, then no summaries are saved.")
help="Format for saving any summaries, if any. If no summaries are to be written, use the -ns option.")
parser.add_argument("-t", "--task-names", dest="task_names", nargs="*", default=[], help="The names of the task.")
parser.add_argument("-v", "--verbose", action='store_true',
help="If present, output informative messages as computation progresses.")
Expand All @@ -50,18 +54,18 @@ def get_parser():


def parse_arguments(arg_list=None):
""" Parse the command line arguments or arg_list if given.
""" Parse the command line arguments or arg_list if given.

Parameters:
arg_list (list): List of command line arguments as a list.

Returns:
Object: Argument object
List: A list of parsed operations (each operation is a dictionary).

Raises:
ValueError - If the operations were unable to be correctly parsed.

"""
parser = get_parser()
args = parser.parse_args(arg_list)
Expand All @@ -85,7 +89,7 @@ def parse_arguments(arg_list=None):

def run_bids_ops(dispatch, args):
""" Run the remodeler on a BIDS dataset.

Parameters:
dispatch (Dispatcher): Manages the execution of the operations.
args (Object): The command-line arguments as an object.
Expand All @@ -109,7 +113,8 @@ def run_bids_ops(dispatch, args):
if args.verbose:
print(f"Events {events_obj.file_path} sidecar {sidecar}")
df = dispatch.run_operations(events_obj.file_path, sidecar=sidecar, verbose=args.verbose)
df.to_csv(events_obj.file_path, sep='\t', index=False, header=True)
if not args.no_update:
df.to_csv(events_obj.file_path, sep='\t', index=False, header=True)


def run_direct_ops(dispatch, args):
Expand All @@ -133,7 +138,8 @@ def run_direct_ops(dispatch, args):
if args.task_names and not BackupManager.get_task(args.task_names, file_path):
continue
df = dispatch.run_operations(file_path, verbose=args.verbose, sidecar=sidecar)
df.to_csv(file_path, sep='\t', index=False, header=True)
if not args.no_update:
df.to_csv(file_path, sep='\t', index=False, header=True)


def main(arg_list=None):
Expand Down Expand Up @@ -169,7 +175,8 @@ def main(arg_list=None):
save_dir = None
if args.work_dir:
save_dir = os.path.realpath(os.path.join(args.work_dir, Dispatcher.REMODELING_SUMMARY_PATH))
dispatch.save_summaries(args.save_formats, individual_summaries=args.individual_summaries, summary_dir=save_dir)
if not args.no_summaries:
dispatch.save_summaries(args.save_formats, individual_summaries=args.individual_summaries, summary_dir=save_dir)


if __name__ == '__main__':
Expand Down