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Initial model resizing fixes #709

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Merged
stephen-riggs merged 2 commits into from
Dec 8, 2025
Merged

Initial model resizing fixes #709

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c0b7b6f
Initial model size should be read from header
stephen-riggs Dec 8, 2025
e299993
Adjusted box size calculation for initial model
stephen-riggs Dec 8, 2025
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16 changes: 9 additions & 7 deletions src/murfey/server/feedback.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1115,12 +1115,12 @@ def _find_initial_model(visit: str, machine_config: MachineConfig) -> Path | Non


def _downscaled_box_size(
particle_diameter: int, pixel_size: float
particle_diameter_ang: float, pixel_size: float
) -> Tuple[int, float]:
particle_diameter = particle_diameter_ang / pixel_size
box_size = int(math.ceil(1.2 * particle_diameter))
box_size = box_size + box_size % 2
for small_box_pix in (
48,
64,
96,
128,
Expand All @@ -1145,9 +1145,9 @@ def _downscaled_box_size(
# Don't go larger than the original box
if small_box_pix > box_size:
return box_size, pixel_size
# If Nyquist freq. is better than 8.5 A, use this downscaled box, else step size
# If Nyquist freq. is better than 7.5 A, use this downscaled box, else step size
small_box_angpix = pixel_size * box_size / small_box_pix
if small_box_angpix < 4.25:
if small_box_angpix < 3.75:
return small_box_pix, small_box_angpix
raise ValueError(f"Box size is too large: {box_size}")

Expand All @@ -1161,9 +1161,9 @@ def _resize_intial_model(
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
input_size_x = input_mrc.header.nx
input_size_y = input_mrc.header.ny
input_size_z = input_mrc.header.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(
Expand Down Expand Up @@ -1198,6 +1198,8 @@ def _resize_intial_model(
str(downscaled_box_size),
"--rescale_angpix",
str(downscaled_pixel_size),
"--force_header_angpix",
str(downscaled_pixel_size),
"--o",
str(output_path),
],
Expand Down
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