def order(filename):
core_name = os.path.splitext(filename)[0]
vid_name = filename
data_name = core_name + '.hdf5'
out_name = core_name + '_check_order.png'
data = dataframes.DataStore(data_name)
crop = data.metadata['crop']
vid = video.ReadVideo(vid_name)
frame = 100
im = images.crop_img(vid.find_frame(frame), crop)
circles = data.df.loc[frame, ['x', 'y', 'r', 'order_r', 'order_i']]
circles['order_mag'] = np.abs(circles.order_r + 1j * circles.order_i)
circles = circles[['x', 'y', 'r', 'order_mag']].values
out = images.draw_circles(im, circles)
out = images.add_colorbar(out)
images.display(out)
images.save(out, out_name)
from Generic.video import ReadVideo
from Generic.images import display
if __name__ == '__main__':
readvid = ReadVideo()
for i in range(readvid.num_frames):
frame = readvid.read_next_frame()
display(frame)
"""
if preprocess:
grayscale_img = images.bgr_2_grayscale(img)
binary_img = adaptive_threshold(grayscale_img,
block_size=block_size,
constant=constant,
mode=mode)
# noise removal
kernel = np.ones((3, 3), np.uint8)
opening = cv2.morphologyEx(binary_img,
cv2.MORPH_OPEN,
kernel,
iterations=2)
# sure background area
sure_bg = cv2.dilate(opening, kernel, iterations=3)
else:
binary_img = img
dist_transform = cv2.distanceTransform(binary_img, cv2.DIST_L2, 5)
return dist_transform
if __name__ == '__main__':
from Generic import images
from Generic import video
read_vid = video.ReadVideo(
'/media/ppzmis/data/ActiveMatter/bacteria_plastic/bacteria.avi')
im = read_vid.read_next_frame()
images.display(im, title='a')
self._setup_process(width, height)
self.process.stdin.write(frame)
self.frame_no += 1
def _setup_process(self, width, height):
self.process = (ffmpeg.input(
'pipe:',
format='rawvideo',
pix_fmt='rgb24',
s='{}x{}'.format(width, height),
r=50).output(self.filename,
pix_fmt='yuv420p',
vcodec='libx264',
preset=self.preset,
video_bitrate=self.video_bitrate,
r=self.framerate).overwrite_output().run_async(
pipe_stdin=True, quiet=False))
def close(self):
self.process.stdin.close()
self.process.wait()
if __name__ == "__main__":
from Generic import images
input_video = '/media/ppzmis/data/ActiveMatter/bacteria_plastic/bacteria.mp4'
vid = ReadVideoFFMPEG(input_video)
for f in range(10):
frame = vid.read_frame()
images.display(frame)
from Generic import images
im = images.load("/media/data/Data/Logs/2020_1_15_15_29/0_mean.png", 0)
# %%
images.display(im)
# %%
# images.ThresholdGui(im)
# %%
threshold = images.threshold(im, 200)
images.display(threshold)
# %%
dilate = images.dilate(threshold, (5, 5))
# dilate = threshold
images.display(dilate)
# %%
opening = images.opening(dilate, (13, 13))
opening = images.opening(dilate, (21, 21))
images.display(opening)
# %%
center = images.center_of_mass(threshold)
im0 = images.draw_circle(im, center[0], center[1], 5)
im0 = images.draw_circle(im0,
im0.shape[1] // 2,
im0.shape[0] // 2,
5,
color=images.BLUE)