As I cannot (and need not) run a whole brain on my current machine I wanted to try those parts I need and where I expect your code to be faster than the one I previously used. I could confirm this for the skeletonization which works really well. But I am stuck with the segmentation/ binarization. This is my code using your function:
Traceback (most recent call last):
File "/home/saskra/anaconda3/envs/ClearMap_II/lib/python3.6/multiprocessing/queues.py", line 240, in _feed
send_bytes(obj)
File "/home/saskra/anaconda3/envs/ClearMap_II/lib/python3.6/multiprocessing/connection.py", line 200, in send_bytes
self._send_bytes(m[offset:offset + size])
File "/home/saskra/anaconda3/envs/ClearMap_II/lib/python3.6/multiprocessing/connection.py", line 393, in _send_bytes
header = struct.pack("!i", n)
struct.error: 'i' format requires -2147483648 <= number <= 2147483647
Any idea how to fix that, some parameter settings maybe?
OK, there seems to be an easy solution: Do not read the file in advance, just enter the path in the function call. And you have to convert Tif to Npy if your file is bigger than ~4GB.
As I cannot (and need not) run a whole brain on my current machine I wanted to try those parts I need and where I expect your code to be faster than the one I previously used. I could confirm this for the skeletonization which works really well. But I am stuck with the segmentation/ binarization. This is my code using your function:
And this is the error message:
Any idea how to fix that, some parameter settings maybe?