merylldindin/tdatoolbox

Topological Data Analysis toolkit, with examples

tdatoolbox's Issues

estimate_clusters function has an issue with persistence diagram

Persistence diagram does not appear from estimate_clusters function

Missing imports

Hi, thanks a lot for the code! I tried running ToMaTo.ipynb, but it failed because of a few missing imports. To get it to work, I modified the following:
clustering/clusters.py as follows:

def generate(self):
        from sklearn.datasets import make_blobs, make_circles, make_moons

def estimate_density(self, nbins=100, graph=False):
        from scipy.stats import gaussian_kde
        x,y = self.x.T
        den = gaussian_kde(self.x.T)

It works just fine with the above changes. Without the above changes, I got errors like the one below:

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-5-0dd55453a1ad> in <module>
      1 gen = ClusterGenerator(structure='anisotropy', randomize=45)
----> 2 clf = ToMaTo(*gen.generate())
      3 _ = clf.estimate_clusters(graph=True)

/usr/local/share/notebooks/TDAtest/TdaToolbox-master/clustering/clusters.py in generate(self)
     24         if self.structure == 'anisotropy':
     25 
---> 26             x,y = make_blobs(n_samples=self.n_samples, random_state=self.randomize)
     27             vec = [[0.60834549, -0.63667341], [-0.40887718, 0.85253229]]
     28             return np.dot(x, vec), y

NameError: name 'make_blobs' is not defined

clusting：Multidimensional data

The examples are all 2-dimensional data. Can you handle high-dimensional data?

functions missing in 3Dshape tutorial

Hi there, thank you for the nice toolbox. I was trying to run the 3D shape. However, there are some missing functions, e.g, functionize, build_landscapes. Could you please fix it? Thank you!

Clustering - Thoughts on a predict method?

Instead of fit_predict, any thoughts on creating a predict method?
Could be interesting for new (test) data..