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updated dff generator to include more flexible arguments. Defaults re… #7

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updated dff generator to include more flexible arguments. Defaults re… #7

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9 changes: 6 additions & 3 deletions utils_video/generators.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import PIL.ImageFont
import PIL.Image
import PIL.ImageDraw
from scipy.ndimage.filters import gaussian_filter

from .utils import (
grid_size,
Expand All @@ -32,9 +33,9 @@
)


def dff(stack, size=None, font_size=16):
vmin = np.percentile(stack, 0.5)
vmax = np.percentile(stack, 99.5)
def dff(stack, size=None, font_size=16, pmin=0.5, pmax=99.5, vmin=None, vmax=None, blur=0):
vmin = np.percentile(stack, pmin) if vmin is None else vmin
vmax = np.percentile(stack, pmax)if vmax is None else vmax
norm = plt.Normalize(vmin, vmax)
cmap = plt.cm.jet

Expand All @@ -51,6 +52,8 @@ def dff(stack, size=None, font_size=16):

def frame_generator():
for frame in stack:
if blur:
frame = gaussian_filter(frame, (blur, blur))
frame = cmap(norm(frame))
frame = (frame * 255).astype(np.uint8)
frame = cv2.resize(frame, image_shape[::-1])
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