segmentation fault 11 when attempting to convert numpy ndarray to .avi video using PyAV module

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segmentation fault 11 when attempting to convert numpy ndarray to .avi video using PyAV module



I receive a Segmentation fault 11 error when trying to convert numpy arrays to a video file. I am using the PyAV module, whose documentation can be found at http://mikeboers.github.io/PyAV/



the line


frame = av.VideoFrame.from_ndarray(image)



converts the 512 x 512 numpy array successfully into the frame object defined in PyAV. It is the next line which causes the segmentation fault


for packet in stream.encode(frame):
container.mux(packet)



Would someone be able to direct me towards what might be causing the segmentation fault in this line? I have checked through the issues raised on the PyAV homepage, but I can't find anything which looks similar.



My Script to convert a numpy nd array into an avi video


import tifffile as tf
import sys
import av
from skimage.color import gray2rgb


sys.path.append('/Users/MarcusF/PyAV')?



#Here I import a ImageJ compatible hyper stack into a 1900 x 512 x 512 numpy array


with tf.TiffFile('/Users/MarcusF/Desktop/260522_CecB- PCPG vesicles- after
flushing_1_MMStack_Pos6.ome.tif') as tif:
images = tif.asarray()



#These images have binned pixels, i believe they are stored as uint16 type not uint8 i try to change this


images = images/np.max(images)
images = images *255
images = images.astype('uint8')



** At this point use of the av module starts **


fps = 30


container = av.open('/Users/MarcusF/Desktop/OLA2.avi','w')
stream = container.add_stream('mpeg4', rate=fps)
stream.width = images.shape[2]
stream.height = images.shape[1]
stream.pix_fmt = 'yuv420p'


for image in images:
frame = av.VideoFrame.from_ndarray(image)

for packet in stream.encode(frame):
container.mux(packet)



^^^^^^AT THIS POINT the kernel dies when running in Jupyter notebooks. I tried running in python from the mac terminal and python quits and i receive a notification of SEGMENTATION FAULT 11



remainder of script, error occurs before this runs I believe


for packet in stream.encode():
container.mux(packet)

#Close the file
container.close()









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