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Use contrast enhancement to improve registration #23

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Use contrast enhancement to improve registration #23

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95e7a8d
Add functions for contrast enhancement
lauraporta Jul 26, 2024
f34e6ee
Rename folder
lauraporta Jul 26, 2024
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35 changes: 35 additions & 0 deletions derotation/postprocessing/contrast_enhancement.py
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Original file line number Diff line number Diff line change
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from pathlib import Path

import numpy as np
import tifffile as tf
from skimage.exposure import rescale_intensity


def whole_video_contrast_enhancment(
tiff_path: Path, saturated_percentage: float
):
tiff = tf.imread(tiff_path)
v_min, v_max = np.percentile(
tiff, (saturated_percentage, 100 - saturated_percentage)
)

CE_tiff_path = np.zeros_like(tiff)
for i, frame in enumerate(tiff):
CE_tiff_path[i] = rescale_intensity(frame, in_range=(v_min, v_max))

return CE_tiff_path


def frame_by_frame_contrast_enhancement(
tiff_path: Path, saturated_percentage: float
):
tiff = tf.imread(tiff_path)

CE_tiff_path = np.zeros_like(tiff)
for i, frame in enumerate(tiff):
v_min, v_max = np.percentile(
frame, (saturated_percentage, 100 - saturated_percentage)
)
CE_tiff_path[i] = rescale_intensity(frame, in_range=(v_min, v_max))

return CE_tiff_path
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