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fix(config): compute vit_normalization inline, not via ptychoml (client/replay envs lack it) #49

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Merged
Garrett Bischof (gwbischof) merged 1 commit into from
Jun 9, 2026
Merged

fix(config): compute vit_normalization inline, not via ptychoml (client/replay envs lack it) #49

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17 changes: 8 additions & 9 deletions scripts/config_from_tiled.py
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Original file line number Diff line number Diff line change
Expand Up @@ -565,21 +565,20 @@ def load_config_from_tiled(
slice=[slice(0, n_sample), slice(None), slice(None)]
)
import numpy as _np
from ptychoml import compute_intensity_normalization
# Max raw intensity with hot pixels excluded — the same constant
# hxn_to_vit writes per scan. compute_intensity_normalization
# raises ValueError when every sampled pixel exceeds the threshold.
try:
vit_normalization = compute_intensity_normalization(
_np.asarray(sample),
hot_pixel_count_threshold=HOT_PIXEL_THRESHOLD,
)
# hxn_to_vit writes per scan. Kept inline (not
# ptychoml.compute_intensity_normalization) because config_from_tiled
# runs in the client/replay pixi envs, which deliberately do NOT
# depend on ptychoml.
mask = sample <= HOT_PIXEL_THRESHOLD
if mask.any():
vit_normalization = float(_np.asarray(sample)[mask].max())
print(
f"[config_from_tiled] vit_normalization={vit_normalization:.1f} "
f"(max of {n_sample} frames, hot_pixel_threshold={HOT_PIXEL_THRESHOLD})",
file=sys.stderr,
)
except ValueError:
else:
print(
"WARNING: all sampled pixels exceed hot_pixel_threshold "
f"({HOT_PIXEL_THRESHOLD}); vit_normalization not set",
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