Re: Bottleneck distances


Dmitriy Morozov
 

Hi Adam,

Can you please report this issue on GitHub, so I don't lose track of it?

Thanks.
Dmitriy

On Thu, May 17, 2018 at 12:27 PM, Adam Spannaus <aspannau@...> wrote:
Dimitri,

Apologies for all the emails, but I found, what I believe to be an error in the R-implementation. It appears that when computing the wasserstein distance, the R version does not take the pth root of the value. I believe it computes the norm to the pth power.

Thanks again,
Adam

On May 17, 2018, at 2:19 PM, Adam Spannaus <aspannau@...> wrote:

Hi Dimitri,

Thanks for looking into it. If it helps, by looking at the distance between the same persistence diagram, even with a ‘inf’, gives the correct value of 0.

On another note, would you happen to know, of can point me in a direction, as to why the computation of Wasserstein distances with the same diagrams is different in the TDA R package as compared with your implementation?

Thanks for your assistance,
Adam

On May 15, 2018, at 7:42 PM, Dmitriy Morozov <dmitriy@...> wrote:

Never mind. I can reproduce the problem:

import dionysus as d
dgm1 = d.Diagram([(1,2), (3,4), (1., float('inf'))])
dgm2 = d.Diagram([(0,2), (3,5), (2., float('inf'))])
d.bottleneck_distance(dgm1,dgm2)

I'll look into it. Let me meanwhile point out that you can construct a diagram out of a list of tuples of point coordinates. So you could always generate a list of points in the diagram and then generate a new diagram, tweaking the points however you like. So that could be a temporary workaround.

BTW, TDA package in R uses Dionysus 1, so it has nothing in common with the code used in Dionysus 2.

On Tue, May 15, 2018 at 3:12 PM, Dmitriy Morozov <dmitriy@...> wrote:
Can you send an example code or diagram?

On Tue, May 15, 2018 at 7:34 AM,  <aspannau@...> wrote:
Hi Dimitri,

I am having an issue when computing the bottleneck distance between two diagrams. When both persistence diagrams have a point that has inf as its death time, the bottleneck distance seems to hang and not return a value. When computing these same values using the TDA package in R, I am able to compute these same distances, as it sets some finite number for the death at inf.  Also, since the death time is an attribute, I cannot change it in my code to be some large number.

Thanks for the assistance,
Adam











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