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Correct normalization #40

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Merged
jules-vanaret merged 3 commits into from
Jul 20, 2025
Merged

Correct normalization #40

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46e1e6e
pb saving channels separately on mac
aliceeeeeeeeee Feb 21, 2025
88ce0df
from Jules
aliceeeeeeeeee Jun 25, 2025
61959dd
Merge remote-tracking branch 'origin/main' into correct-normalization
jules-vanaret Jul 20, 2025
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8 changes: 8 additions & 0 deletions src/tapenade/preprocessing/_intensity_normalization.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,6 +142,14 @@ def _normalize_intensity(
array_norm[sl_norm]
) / np.nanmedian(array[sl])

if np.isnan(array_normalization_factor) or array_normalization_factor == 0 or np.isinf(array_normalization_factor):
print(
"Normalization factor is NaN or inf or zero. "
"Check whether the signals are not saturated by 0s."
)

array_normalization_factor = np.nanmean(array_norm[sl_norm]) / np.nanmean(array[sl])

array_norm = array_norm / array_normalization_factor

return array_norm
16 changes: 12 additions & 4 deletions src/tapenade/reconstruction/_reconstruct.py
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Expand Up @@ -148,14 +148,22 @@ def create_folders(
Path(folder_sample / "weights" / "before_trsf").mkdir(exist_ok=True)
Path(folder_sample / "weights" / "after_trsf").mkdir(exist_ok=True)

image_ref = io.imread(Path(folder_experiment) / f"{filename_ref}.tif")
image_float = io.imread(
# image_ref = io.imread(Path(folder_experiment) / f"{filename_ref}.tif")
# image_float = io.imread(
# Path(folder_experiment) / f"{filename_float}.tif"
# )
image_ref = tifffile.imread(Path(folder_experiment) / f"{filename_ref}.tif")
image_float = tifffile.imread(
Path(folder_experiment) / f"{filename_float}.tif"
)


if len(channels) > 1:
for ind_ch, ch in enumerate(channels):
imref = image_ref[:, :, :, ind_ch]
imfloat = image_float[:, :, :, ind_ch]
# imref = image_ref[:, :, :, ind_ch]
# imfloat = image_float[:, :, :, ind_ch]
imref=image_ref[:,ind_ch,:,:]
imfloat=image_float[:,ind_ch,:,:]
io.imsave(
Path(folder_sample) / "raw" / f"{filename_ref}_{ch}.tif",
imref, ##CAREFUL needs to be float32 or uint16 orint16 otherwise the blockmatching does not compute/save the result
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