RuntimeError Using CNMF Module

[kevinpan0127]

I am running the CNMF module on motion corrected tiff image. I am getting a runtime error. Below is entire traceback, thank you very much!

C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint8 = np.dtype([("qint8", np.int8, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint8 = np.dtype([("quint8", np.uint8, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint16 = np.dtype([("qint16", np.int16, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint16 = np.dtype([("quint16", np.uint16, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint32 = np.dtype([("qint32", np.int32, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorflow\python\framework\dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. np_resource = np.dtype([("resource", np.ubyte, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint8 = np.dtype([("qint8", np.int8, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint8 = np.dtype([("quint8", np.uint8, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint16 = np.dtype([("qint16", np.int16, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint16 = np.dtype([("quint16", np.uint16, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint32 = np.dtype([("qint32", np.int32, 1)]) C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\tensorboard\compat\tensorflow_stub\dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. np_resource = np.dtype([("resource", np.ubyte, 1)]) Traceback (most recent call last): File "", line 1, in File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 105, in spawn_main exitcode = _main(fd) File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 114, in _main prepare(preparation_data) File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 225, in prepare _fixup_main_from_path(data['init_main_from_path']) File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 277, in _fixup_main_from_path run_name="__mp_main") File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\runpy.py", line 263, in run_path pkg_name=pkg_name, script_name=fname) File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\runpy.py", line 96, in _run_module_code mod_name, mod_spec, pkg_name, script_name) File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "c:\users\panyi\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\viewer\modules\batch_run_modules\CNMF.py", line 34, in from mesmerize.common.utils import HdfTools File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\init.py", line 1, in from .analysis import * File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\analysis\init.py", line 3, in from .math import cross_correlation, drfft_dtw, tvregdiff File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\site-packages\mesmerize\analysis\math\drfft_dtw.py", line 17, in raw_curve: np.ndarray = None, rf_curve: np.ndarray = None) -> list: File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\context.py", line 56, in Manager m.start() File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\managers.py", line 513, in start self._process.start() File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\process.py", line 105, in start self._popen = self._Popen(self) File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\context.py", line 322, in _Popen return Popen(process_obj) File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\popen_spawn_win32.py", line 33, in init__ prep_data = spawn.get_preparation_data(process_obj._name) File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 143, in get_preparation_data _check_not_importing_main() File "C:\Users\panyi\anaconda3\envs\mesmerize\lib\multiprocessing\spawn.py", line 136, in _check_not_importing_main is not going to be frozen to produce an executable.''') RuntimeError: An attempt has been made to start a new process before the current process has finished its bootstrapping phase.

    This probably means that you are not using fork to start your
    child processes and you have forgotten to use the proper idiom
    in the main module:

        if __name__ == '__main__':
            freeze_support()
            ...

    The "freeze_support()" line can be omitted if the program
    is not going to be frozen to produce an executable.

===== 2020.12.28 21:12:31 =====

[kushalkolar]

@kevinpan0127 Thanks for posting the issue, I'll try to fix this within a few days.

[kevinpan0127]

Hi @kushalkolar! I was wondering if there is any update on solving this issue? Thank you very much for your time!

[neurowookie]

Hi @kushalkolar , I'm having the same issue. Any luck in fixing it?

[kushalkolar]

@kevinpan0127 @neurowookie sorry for the delay, I didn't have access to a windows machine for testing. Fixed in master, will make a new release soon :)

[kushalkolar]

@kevinpan0127 @neurowookie now fixed in the v0.5.0 release.