191 q6 channel based flagging

[mpound]

No description provided.

[astrofle]

Flags are subject to Exception: You can only have one channel selection rule. Remove the old rule before creating a new one.. Which limits how flags can be used. Can we remove this for flags?

[mpound]

yeah, that should be removed.

[mpound]

also note read/write of flags is not yet implemented

[mpound]

Somehow my description of this PR was never saved. It contains
Flag object, use of Flag object in GBTFITSLoad, applying flags to create data mask (saved in underlying SDF objects), passing of flags to calibration routines, creation of masks in output spectra, one proof of concept test.

[mpound]

I'm going to see if there is an easy patch for SpecPlot, but that should not hold up the review. Thanks.

[mpound]

Specplot should now not plot masked values.

from dysh.spectra.spectrum import Spectrum
f = Spectrum.fake_spectrum()
f.plot()
f.mask[1:100] = True
f.plot()

[mpound]

Updates to Spectrum.smooth and spectra.core.smooth to deal with masked data correctly.

[mpound]

had to undo changes to smooth because it breaks getps with smoothref.

[mpound]

See #415 for discussion of smoothing with masks

[astrofle]

astropy log messages are showing up now. Not sure why this is happening, since I did not set up a logger at all.

from pathlib import Path
from dysh.util.download import from_url
from dysh.fits.gbtfitsload import GBTFITSLoad
url = "http://www.gb.nrao.edu/dysh/example_data/mixed-fs-ps/data/TGBT24B_613_04.raw.vegas.trim.fits"
savepath = Path.cwd() / "data"
filename = from_url(url, savepath)
sdf = GBTFITSLoad(filename)
sdf.flags.clear()
sdf.flag(channel=[[100,10000]])
ps_sb = sdf.getps(scan=35, sig="T", apply_flags=True)#.timeaverage()
ps_sig = ps_sb.timeaverage()
    INFO: overwriting Masked Quantity's current mask with specified mask. [astropy.nddata.nddata]
    INFO: overwriting Masked Quantity's current mask with specified mask. [astropy.nddata.nddata]

[mpound]

Those are coming from the used of Masked. I haven't yet looked into turning them off, kind of annoying.