User Defined Cover

[leesteinberg]

Hi there

I can see that there is a TODO to implement a cover defining API. I was wondering what is the best way of creating a user-defined cover at the moment (if it is possible at all). From what I can tell, we are currently restricted to a (n_bins, overlap_perc) method. Is it possible to define a cover explicity (for one or more dimensions in the lens), using cutoff values or similar (like, setting the maximum and minimum values of the covering space in each dimension)? I ask because in its current implementation I think the [non-]presence of an outlier can skew the covering space quite drastically

Let me know what my options are for the covering space. I would also be interested to know the status of the above TODO. More information as to how the cover class currently works might also be useful if I was going to write my own.

Thanks!

Edit: I've modified the code such that you can pass kmapper.map a CoverBounds variable.
if CoverBounds == None: Normal behavior
However, CoverBounds can also be a (ndim_lens, 2) array, with min, max for every dimension of your lens. If the default behavior is fine for a particular dimension, pass it np.float('inf'), np.float('inf').

For example, if I have a lens in R2 and want to set the maximum and minimum of the second dimension to be 0 and 1, I can pass:
mapper.map(CoverBounds = np.array([[np.float('inf'), np.float('inf')],[0,1]])) and that should have the desired behavior.

Edit 2: Might change it so rather than inf detection, works off None detection in the CoverBounds array.

I think a system designed like this should produce exactly the same cover, independent of input data limits.

Devs - let me hear your thoughts on this - I can clean up and submit a pull request.

[sauln]

hi @leesteinberg. This sounds like a great new feature to add to the library.

Have you seen the cover class implementation? /kepler-mapper/cover.py?

To define your own cover, you could inherit from Cover and change the define_bins method:

class CoverBounds(Cover):
    def __init__(self, bounds):
          self.bounds = bounds

    def find_bins(self, data):
           # return a set of cover elements according to the new bins.

I would be happy to incorporate a pull request for this!

[leesteinberg]

Submitted pull request #98 implementing CoverBounds class as discussed.

Edit: @sauln I'll think about how to write a test later today...
Edit 2: Test written + added to pull request (it is a slow day at work...) CoverBounds class required slight modification for python 3.4 compatibility, but works now

[sauln]

Thanks for working on this @leesteinberg!