GENDIS import problem

[mmar30]

Hi,

I have problems with importing modules from gendis, when I run this code I get the following error:

from gendis.genetic import GeneticExtractor
genetic_extractor = GeneticExtractor(population_size=50, iterations=25, verbose=False, 
                                     normed=False, add_noise_prob=0.3, add_shapelet_prob=0.3, 
                                     wait=10, plot='notebook', remove_shapelet_prob=0.3, 
                                     crossover_prob=0.66, n_jobs=4)

ERROR:

Traceback (most recent call last):
  File "/Users/maria/PycharmProjects/gendis_new/main.py", line 1, in <module>
    from gendis.genetic import GeneticExtractor
  File "/Users/maria/PycharmProjects/gendis_new/gendis/genetic.py", line 35, in <module>
    from gendis.pairwise_dist import _pdist
ImportError: No module named 'gendis.pairwise_dist'

Process finished with exit code 1

I’ve installed gendis sucessfully with Python 3.5. OS: Mojave 10.14.3

[GillesVandewiele]

Hello @mmar30

There indeed seems to be a problem with the latest release (I will try to fix this asap). Did you install in through pip or by cloning and running setup?

Another option would be to install a older (but slower) version of gendis:

`pip install gendis==1.0.91

[mmar30]

Thank you! I installed it by cloning and running setup. Now I've tried to run the script with gendis 1.0.91, but I still get the same error.

[GillesVandewiele]

Sorry, I made a typo there. It should have been pip install gendis==1.0.9

(and remove the GENDIS directory from your PycharmProject). It should be noted that this version will be 10x slower...

Another option would be to fix the imports in the genetic.py manually.

[mmar30]

Now it works with gendis 1.0.9. Thank you :)

[GillesVandewiele]

I think I made a fix for the import problems today, @mmar30 can you try to install pip install gendis==1.0.12 to see if it works? That version should be much faster since the bottleneck is written in Cython.

May I ask what you are using shapelets for by the way? And have you tried any other extraction techniques than GENDIS?

[mmar30]

This works too, thanks! I'm comparing different libraries for analysing gait patterns with shapelets.

[GillesVandewiele]

Cool! I would be very interested in that comparison ;) are there any preliminary results yet?

[mmar30]

Not yet, but I can tell you when I have some :)

[GillesVandewiele]

Would be greatly appreciated. Thanks!