Re: cellprofiler

[Mathieu Malaterre <mathieu.malaterre@gmail.com>]

On Mon, Dec 12, 2011 at 11:35 AM, Thouis Jones <thouis.jones@curie.fr> wrote:
> On Mon, Dec 12, 2011 at 11:20, Mathieu Malaterre
> <mathieu.malaterre@gmail.com> wrote:
>> I must be missing something, but it looks like CellProfiler.py is
>> still loading numpy directly from the main script:
>>
>> https://github.com/thouis/CellProfiler/blob/wrap-cppy-in-main/CellProfiler.py
>>
>> Am I looking at the right file ?
>
> You're looking at the right file, I just missed that change.  I just
> pushed a new version with the import moved into main().  Is that
> sufficient to fix the bug?

Nope...

WARNING:root:Distributed support disabled: please install nuageux
Traceback (most recent call last):
  File "/usr/share/pyshared/CellProfiler.py", line 495, in <module>
    main()
  File "/usr/share/pyshared/CellProfiler.py", line 169, in main
    import numpy as np
...


$ cat CellProfiler.py:
...
def main():
    options, args = parser.parse_args()

    import numpy as np
    #
    # CellProfiler expects NaN as a result during calculation
    #
    np.seterr(all='ignore')

Thanks,
-- 
Mathieu