agiovann / calblitz Goto Github PK

Hi!

thanks to have created this very nice project. I am getting into it and would be much happy to contribute.
For now, I made some corrections in the README and try to make the test_software.py to work.
After minor adjustment, I end up with the script running well until the call of computeDFF.
Here a ZeroDivisionError since the downsampfact variable in computeDFF is set that way:

 downsampfact=int(secsWindow*1./self.fr);

which set to zero since self.fr~15

I tried to remove the integer cast but then other error appear...
What would be the proper way to repair this?

Cheers,
Guillaume

Upon import calblitz in python I always get the error 'segmentation fault (core dumped)' using Ubuntu 15.10. Anybody else run into this issue?

It seems to originate somewhere with numpy but I cannot for the life of me figure out what is wrong. Changing the version of numpy doesn't seem to change anything. When I run using GDB I get the following....

Program received signal SIGSEGV, Segmentation fault.
0x00007ffff1abae20 in PyArray_API ()
   from /home/francisco/anaconda2/lib/python2.7/site-packages/numpy/core/multiarray.so

Any ideas? Anybody successfully using CalBlitz with Ubuntu 15?

Just installed and tried running the test.

(calblitz) afonsob-lm1:CalBlitz afonsob$ python test_software.py
loading movie...
motion correcting...
/Users/afonsob/CalBlitz/calblitz/movies.py:194: UserWarning: Casting the array to float 32
warnings.warn('Casting the array to float 32')
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/Users/afonsob/CalBlitz/calblitz/movies.py:284: UserWarning: Casting the array to float 32
warnings.warn('Casting the array to float 32')
cubic interpolation
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Traceback (most recent call last):
File "test_software.py", line 38, in
m=m.crop(crop_top=max_h,crop_bottom=-min_h+1,crop_left=max_w,crop_right=-min_w,crop_begin=0,crop_end=0)
File "/Users/afonsob/CalBlitz/calblitz/movies.py", line 396, in crop
return self[crop_begin:t-crop_end,crop_top:h-crop_bottom,crop_left:w-crop_right]
TypeError: slice indices must be integers or None or have an index method

if tifffile.__version__ < '0.7.0':
    raise Exception('You need libtiff version >= 0.7.0, run pip install tifffile --upgrade')

This lexicographical comparison should be changed now that tiffile has hit version 0.10.0 -- maybe a package such as described at http://stackoverflow.com/questions/11887762/compare-version-strings ?