Negative values for births and deaths

[scikit-tda]

Negative values for births and deaths

[sauln]

oh very weird. Thanks for bringing this up.

Does your distance matrix have negative values?

[christian-oreilly]

Right... I was using a correlation matrix, so you are totally right... with both positives and negative values. My bad. If it is expecting a distance metric it is not surprising that it would give weird results. Maybe I could suggest testing for positivity and throwing a warning if the input matrix has negative values... for dumb-proofing the function call and helping spotting eventual issues :) Thanks for the fast feedback and for your time.

[sauln]

Phew! I'm glad that was the problem.

The test and warning is a great idea and would probably save others in the future. If you'd like to submit a pull request with that implementation, I would readily review and merge!

[ctralie]

Note that our lower star image filtration often applies to negative scalar images, so that would trip the warning erroneously every time. It could be messy to deal with that

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On Sat, Nov 16, 2019, 1:24 AM Nathaniel Saul ***@***.***> wrote: Phew! I'm glad that was the problem. The test and warning is a great idea and would probably save others in the future. If you'd like to submit a pull request with that implementation, I would readily review and merge! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#88?email_source=notifications&email_token=AAJWDZVCXJBWRAVRCUWOUOTQT6GX7A5CNFSM4JN24V52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEHKWTQ#issuecomment-554609486>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJWDZVY7L3PWJFYE3HUSFLQT6GX7ANCNFSM4JN24V5Q> .

[christian-oreilly]

@sauln I can have a look at it.

@ctralie Could you provide an example of a function call that relates to that? Not knowing that much about ripser, it could take me some time to figure out what objects/functions/methods are related to your "lower start image filtration".

[ctralie]

We have two notebooks showing this use case https://github.com/scikit-tda/ripser.py/blob/master/docs/notebooks/Lower%20Star%20Image%20Filtrations.ipynb https://github.com/scikit-tda/ripser.py/blob/master/docs/notebooks/Lower%20Star%20Time%20Series.ipynb Because of this, I would vote against putting a warning for negative values, but thank you for offering!

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On Sat, Nov 16, 2019 at 8:53 AM christian-oreilly ***@***.***> wrote: @sauln <https://github.com/sauln> I can have a look at it. @ctralie <https://github.com/ctralie> Could you provide an example of a function call that relates to that? Not knowing that much about ripser, it could take me some time to figure out what objects/functions/methods are related to your "lower start image filtration". — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#88?email_source=notifications&email_token=AAJWDZQJGH7PTHMVXAMCRA3QT73OXA5CNFSM4JN24V52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEHSA2I#issuecomment-554639465>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJWDZS6KK4W7TOLU7DSQ7LQT73OXANCNFSM4JN24V5Q> .

[christian-oreilly]

Alright. Nice notebook @ctralie

So, no change for the moment. At least this ticket provides a minimum of documentation on the existence of negative birth and death time.