I have imported my fits table, hdul0, into python. I'm using astropy.table. I opened it with hdul0 = fits.open('filename').

hdul0data = Table(hdul0[1].data)

I have then made a scatter plot of two columns in the table, HDA and OII. I have made a cut-out region on the plot (a short vertical line and then an upwards sloping line from there), and I would like to select the points under that line, like slice them from the original fits table and move the slice into another fits table that I then save. This is what I have done, but it is not working.

x = hdul0data['HDA']
y = hdul0data['OII']
x1 = [2.5, 2.5] #the x values of the vertical line cut 
y1 = [0.0, 2.5] #the y values of the vertical line cut 
x2 = [2.5,16.0] #the x values of the sloping cut 
y2 = [2.5, 16.5] #the y values of the sloping cut  

slopy = np.interp(x, x2, y2)
myslice = np.where((x > 2.5) & (y < slopy))[0]

The error message I get is "RuntimeWarning: invalid value encountered in greater" (and the same for less).

Can anyone help? How do I slice my table and get the selected points into a new fits file? I think maybe part of the issue is that some of the data points in the HDA and OII columns are NaN, but I don't know how to get rid off it. I read I could use masked, but then I read it might not work with numpy.


Sample values of x and y:

x = [1.0, 6.2, 10.4, NaN, 2.8, NaN, 7.0] 
y = [10.3, NaN, 18.0, 22.9, 2.5, NaN, 31.8] 
  • $\begingroup$ I can't reproduce your error. Can you post some sample values of x and y? $\endgroup$
    – m13op22
    Commented Mar 21, 2019 at 14:34
  • $\begingroup$ @HS-nebula added sample values in the main post $\endgroup$
    – Joey
    Commented Mar 21, 2019 at 15:08
  • 1
    $\begingroup$ What version of Python are you using? $\endgroup$
    – m13op22
    Commented Mar 21, 2019 at 15:25
  • 2
    $\begingroup$ Are x and y actually Python lists or numpy.arrays? $\endgroup$
    – m13op22
    Commented Mar 21, 2019 at 15:59
  • $\begingroup$ I get a different error message TypeError: '>' not supported between instances of 'list' and 'float' $\endgroup$
    – usernumber
    Commented Feb 25, 2020 at 13:32


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