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rivetTDA / rivet

RIVET is a tool for Topological Data Analysis, in particular two-parameter persistent homology.
GNU General Public License v3.0
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Resizing Issue #49

Closed mlesnick closed 7 years ago

mlesnick commented 8 years ago

Originally reported by: M L (GitHub: mlesnick)

A few months ago, I shared some of Chris Baldassano's neuro data with Matthew, to ask him to do a 0-D persistence computation for me.

Now that I have my new Linux machine, I decided to try the 1-D version of this computation. It ran quickly (15x15 bins) but did not display properly. Matthew explained that this was because I didn't include labels in my input file. (The old format did not require labels, but we updated the input format in the last few months).

However, now I have fixed that issue with the input, and I am still getting roughly the same problem (now using 25x25 bins). See attached file and screenshot. Note that no upper bound for x coordinate is displayed. I would guess that this is related.

Screenshot from 2016-04-27 11-00-25.png

mlesnick commented 8 years ago

Original comment by Matthew Wright (GitHub: mlwright84):

The exception_test branch has been merged into master, so this issue is resolved.

mlesnick commented 8 years ago

Original comment by M L (GitHub: mlesnick):

At Matthew Points out, this is an artifact of a small error in the new exception handling code (negative numbers not handled properly), which has been fixed in the exception_test branch.

We can mark as resolve when that code is merged into the main branch,

mlesnick commented 8 years ago

Original comment by M L (GitHub: mlesnick):

When I saved the RIVET file and open in a text editor, I see there is only one x-grade: 0.
This presumably should make clear where the bug is.

mlesnick commented 8 years ago

Original comment by Matthew Wright (GitHub: mlwright84):

Hmmm. It's not immediately clear to me why this is happening. I will look into it!

mlesnick commented 8 years ago

Original comment by M L (GitHub: mlesnick):

I have reopened the issue and edited the description, as I see a similar bug even after fixing my input to include the label.

mlesnick commented 8 years ago

Original comment by M L (GitHub: mlesnick):

Not a

mlesnick commented 8 years ago

Original comment by M L (GitHub: mlesnick):

Interesting. I forgot about the change in input format. Thanks for explaining. Feel free to mark as ``resolved."

Perhaps we could require that the first character of a label is neither a digit, nor "-" nor ".", and exit otherwise?

A warning is also seems be a good alternative, though since RIVET is already verbose and sometimes moves very quickly, perhaps the warning could be missed. Anyway it's your call.

mlesnick commented 8 years ago

Original comment by Matthew Wright (GitHub: mlwright84):

Maybe RIVET should display a warning if it interprets a string of numbers as an axis label. What do you think?

mlesnick commented 8 years ago

Original comment by Matthew Wright (GitHub: mlwright84):

Thanks for pointing this out also. The improper labeling is occurring because the input file does not provide a label for the horizontal axis. RIVET is interpreting line 4 of the file as the axis label, but this line contains data. Adding a new line 4 with an axis label should fix this problem.

This issue showed up now because in January we changed the way that the axis label is specified. The current file format specification is available at http://rivet.online/wp/doc/input-data/ .