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Nan to zero frames #502

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Nan to zero frames #502

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3006a71
nan_to_num
tayllatheodoro Oct 27, 2025
9571216
Merge branch 'main' into nan_to_zero_frames
tayllatheodoro Oct 27, 2025
b0279de
using dask.array nan_to_num instead of np's
srivarra Oct 28, 2025
a1a1a07
removed commented line
srivarra Oct 28, 2025
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2 changes: 2 additions & 0 deletions waveorder/cli/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
from typing import Tuple

import click
import dask.array as da
import numpy as np
import torch
from iohub.ngff import Position, open_ome_zarr
Expand Down Expand Up @@ -128,6 +129,7 @@ def apply_inverse_to_zyx_and_save(
f"All values at t={t_idx} are zero or Nan, skipping reconstruction."
)
return
czyx_uint16_numpy = da.nan_to_num(czyx_uint16_numpy).compute()

# convert to np.int32 (torch doesn't accept np.uint16), then convert to tensor float32
czyx_data = torch.tensor(np.int32(czyx_uint16_numpy), dtype=torch.float32)
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