[BUG] Cell detection fails on Windows about cellfinder HOT 7 CLOSED

It would be good to see if someone else gets this error too.

from cellfinder.

Hi, I also have problems for the cell detection using Windows. The error message is:
` C:\Users\Asus>cellfinder -s C:\Users\Asus\Desktop\cellfinder_folder\signal -b C:\Users\Asus\Desktop\cellfinder_folder\anatomy -o C:\Users\Asus\Desktop\cellfinder_folder\result_cellfinder -x 1.625 -y 1.625 -z 4 --no-standard-space --soma-diameter 6 --ball-xy-size 4 --ball-z-size 4 --ball-overlap-fraction 0.4 --save-planes --no-classification
2020-04-27 12:49:13 PM - INFO - MainProcess fancylog.py:265 - Starting logging
2020-04-27 12:49:13 PM - INFO - MainProcess fancylog.py:267 - Multiprocessing-logging module found. Logging from all processes
2020-04-27 12:49:13 PM - INFO - MainProcess main.py:64 - Skipping registration
2020-04-27 12:49:13 PM - INFO - MainProcess main.py:110 - Detecting cell candidates
Processing planes: 0%| | 0/300 [00:00<?, ?it/s]Traceback (most recent call last):
File "C:\Users\Asus\Anaconda3\envs\cellfinderenv\Scripts\cellfinder-script.py", line 11, in
load_entry_point('cellfinder', 'console_scripts', 'cellfinder')()
File "c:\users\asus\cellfinder\cellfinder\main.py", line 91, in main
run_all(args, what_to_run)
File "c:\users\asus\cellfinder\cellfinder\main.py", line 112, in run_all
detect.main(args)
File "c:\users\asus\cellfinder\cellfinder\detect\detect.py", line 114, in main
bf_process.start() # needs to be started before the loop
File "C:\Users\Asus\Anaconda3\envs\cellfinderenv\lib\multiprocessing\process.py", line 112, in start
self._popen = self._Popen(self)
File "C:\Users\Asus\Anaconda3\envs\cellfinderenv\lib\multiprocessing\context.py", line 223, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "C:\Users\Asus\Anaconda3\envs\cellfinderenv\lib\multiprocessing\context.py", line 322, in _Popen
return Popen(process_obj)
File "C:\Users\Asus\Anaconda3\envs\cellfinderenv\lib\multiprocessing\popen_spawn_win32.py", line 89, in init
reduction.dump(process_obj, to_child)
File "C:\Users\Asus\Anaconda3\envs\cellfinderenv\lib\multiprocessing\reduction.py", line 60, in dump
ForkingPickler(file, protocol).dump(obj)
File "stringsource", line 2, in View.MemoryView._memoryviewslice.reduce_cython
TypeError: no default reduce due to non-trivial cinit
Processing planes: 0%| | 0/300 [00:00<?, ?it/s]

(cellfinderenv) C:\Users\Asus>Traceback (most recent call last):
File "", line 1, in
File "C:\Users\Asus\Anaconda3\envs\cellfinderenv\lib\multiprocessing\spawn.py", line 105, in spawn_main
exitcode = _main(fd)
File "C:\Users\Asus\Anaconda3\envs\cellfinderenv\lib\multiprocessing\spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
EOFError: Ran out of input`

from cellfinder.

Issue seems to be that the cython classes need to be pickled for multiprocessing, and the automatic method isn't working on Windows. Looks like it might need custom __reduce__ methods

from cellfinder.

Yes, I came to the same conclusion. Issue seems to be solved if you create the 3 cython classes inside the process method of Mp3DFilter. I know is not an elegant solution and I just worked around the problem, but it works.

from cellfinder.

Would you mind submitting a PR?

from cellfinder.

sure!

from cellfinder.

Release candidate out : pip install cellfinder==0.3.12rc0

from cellfinder.