From 6f83795e6ce46f5c5fda5896d71e695f27beacc4 Mon Sep 17 00:00:00 2001 From: Lorenzo Gaifas Date: Thu, 5 Oct 2023 02:10:40 +0200 Subject: [PATCH] ensure optics grup always exists --- src/cs2star/cs2star.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/cs2star/cs2star.py b/src/cs2star/cs2star.py index 5f12092..cd3cf3b 100755 --- a/src/cs2star/cs2star.py +++ b/src/cs2star/cs2star.py @@ -49,6 +49,7 @@ @click.option("--swapxy/--no-swapxy", default=True, help="swap x and y axes") @click.option("--inverty/--no-inverty", default=False, help="invert y axis") @click.option("--invertx/--no-invertx", default=False, help="invert x axis") +@click.version_option() def main( job_dir, dest_dir, @@ -235,6 +236,8 @@ def main( cleaning = progress.add_task("Cleaning up micrograph data...", total=3) # also, optics are changed to 1-based indexing by pyem in parse_cryosparc_2_cs so we match it # and we do it before the opticgroupname is generated from it + if "rlnOpticsGroup" not in df_mic.columns: + df_mic["rlnOpticsGroup"] = 0 df_mic["rlnOpticsGroup"] += 1 df_mic = pyem.star.check_defaults(df_mic, inplace=True) progress.update(cleaning, advance=1)