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Apply clipping to user initial model if not a cube #677

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Merged
stephen-riggs merged 1 commit into from
Oct 13, 2025
Merged

Apply clipping to user initial model if not a cube #677

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33 changes: 32 additions & 1 deletion src/murfey/server/feedback.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1151,6 +1151,34 @@ def _resize_intial_model(
executables: Dict[str, str],
env: Dict[str, str],
) -> None:
with mrcfile.open(input_path) as input_mrc:
input_size_x = input_mrc.nx
input_size_y = input_mrc.ny
input_size_z = input_mrc.nz
if executables.get("clip") and not input_size_x == input_size_y == input_size_z:
# If the initial model is not a cube, do some padding
clip_proc = subprocess.run(
[
f"{executables['clip']}",
"resize",
"-ox",
str(max(input_size_x, input_size_y, input_size_z)),
"-oy",
str(max(input_size_x, input_size_y, input_size_z)),
"-oz",
str(max(input_size_x, input_size_y, input_size_z)),
str(input_path),
str(input_path.with_suffix("_cube.mrc")),
],
capture_output=True,
text=True,
env=env,
)
input_path = input_path.with_suffix("_cube.mrc")
if clip_proc.returncode:
logger.error(
f"Clipping initial model {input_path} failed \n {clip_proc.stdout}"
)
if executables.get("relion_image_handler"):
comp_proc = subprocess.run(
[
Expand All @@ -1168,6 +1196,9 @@ def _resize_intial_model(
text=True,
env=env,
)
logger.info(
f"Initial model rescaling finished with code {comp_proc.returncode}"
)
with mrcfile.open(output_path) as rescaled_mrc:
rescaled_mrc.header.cella = (
downscaled_pixel_size,
Expand Down Expand Up @@ -1223,7 +1254,7 @@ def _register_3d_batch(message: dict, _db, demo: bool = False):
if not rescaled_initial_model_path.is_file():
_resize_intial_model(
*_downscaled_box_size(
message["particle_diameter"],
relion_options["particle_diameter"],
relion_options["angpix"],
),
provided_initial_model,
Expand Down