From 45b657765ca06ceea2ed586f7de157b6166316c4 Mon Sep 17 00:00:00 2001 From: Jonas Braun Date: Fri, 23 Apr 2021 13:04:25 +0200 Subject: [PATCH] updated dff generator to include more flexible arguments. Defaults remain the same. --- utils_video/generators.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/utils_video/generators.py b/utils_video/generators.py index 1ab1109..68803b1 100644 --- a/utils_video/generators.py +++ b/utils_video/generators.py @@ -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, @@ -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 @@ -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])