Star should warn if input periodogram is not flattened or update docs.

[alexlyttle]

Context

When I tried passing the following periodogram to the star class,

pg = lc.to_periodogram(normalization='psd')

I got this output from star.run_asy_peakbag():

For comparison, when I passed the following periodogram, (flatten() is Lightkurves method to remove noise and smooth the periodogram)

pg = lc.to_periodogram(normalization='psd').flatten()

I get this:

Issue

PBjam docs suggests a periodogram with power in any units may be passed, but not that it needs to be flattened. Clearly the periodogram needs to be flattened for this to work, as that would explain the dodgy units in the plot.

Suggestion

1. (easy) Update the docs to specify the input periodogram must be flattened.
2. (additional) PBjam raises an error or warning if it detects that the input periodogram is not flattened.
3. (alternative) star flattens the periodogram if it is not already

[nielsenmb]

I think we should definitely recommend in the docs that the LC be flattened first. If I recall correctly the periodogram is flattened in session when reading in from text file, but may not be when providing a pg object. I don't recall putting any flattening in star. It could be a good idea to do so. Although we should check what the effect of flattening multiple times. Not sure how easy it would be to put in a flatten_detector. While you can easily compute mean/std of the psd, making it robust might be tough.

…

On Thu, 21 Nov 2019, 15:20 Alex Lyttle, ***@***.***> wrote: Context When I tried passing the following periodogram to the star class, pg = lc.to_periodogram(normalization='psd') I got this output from star.run_asy_peakbag(): [image: image] <https://user-images.githubusercontent.com/43786145/69348676-75c4f780-0c6e-11ea-830f-46967d6d4275.png> For comparison, when I passed the following periodogram, (flatten() is Lightkurves method to remove noise and smooth the periodogram) pg = lc.to_periodogram(normalization='psd').flatten() I get this: [image: image] <https://user-images.githubusercontent.com/43786145/69349790-4d3dfd00-0c70-11ea-9558-30256b369a5e.png> Issue PBjam docs suggests a periodogram with power in any units may be passed, but not that it needs to be flattened. Clearly the periodogram needs to be flattened for this to work, as that would explain the dodgy units in the plot. Suggestion 1. (easy) Update the docs to specify the input periodogram must be flattened. 2. (additional) PBjam raises an error or warning if it detects that the input periodogram is not flattened. 3. (alternative) star flattens the periodogram if it is not already — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#197?email_source=notifications&email_token=AEJWO33XGDVT6VI3PPDC3LTQU2RKDA5CNFSM4JQD4ZUKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H3EG4ZQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEJWO32TSPU5ZZQGELZ4QNDQU2RKDANCNFSM4JQD4ZUA> .

[nielsenmb]

I've put in a flatten method call in the init of star. Not the best procedure I guess, but it does the trick.

I tested flattening on the same spectrum 10x and it made no measureable difference after the first flattening (does this make sense?). It was a high SNR target, don't know if low SNR targets behave the same.

Tested on 4448777 and it works, feel free to close issue.