plog.py -- now ignored data flagged as JUNK

'flagcloud' can flag data in a reduce file as junk; plog now ignores such data.
HiPERCAM · Mar 5, 2021 · c14cf4f · c14cf4f
1 parent ae0977e
commit c14cf4f
Showing 1 changed file with 13 additions and 10 deletions.
diff --git a/hipercam/scripts/plog.py b/hipercam/scripts/plog.py
@@ -71,9 +71,12 @@ def plog(args=None):
 
     .. Note::
 
-       Points with negative errors are ignored. Be careful with linked
-       apertures where all x, y, FWHM, beta automatically have negative errors
-       since they are not fitted.
+       Points marked bad, or flagged as having bad times or junk are
+       ignored. i.e.  bitmask = BAD_TIME | JUNK is passed to every
+       invocation of Tseries.mplot.  Be careful with linked apertures
+       where all x, y, FWHM, beta automatically have negative errors
+       since they are not fitted. See |flagcloud| for how to flag up
+       junk data.
 
     """
 
@@ -155,28 +158,28 @@ def plog(args=None):
         dat2 = hlog.tseries(ccd2, aper2, pname2)
         if scheme == "b":
             # plots both together
-            dat1.mplot(plt, "b", bitmask=hcam.BAD_TIME)
-            dat2.mplot(plt, "r", bitmask=hcam.BAD_TIME)
+            dat1.mplot(plt, "b", bitmask=hcam.BAD_TIME|hcam.JUNK)
+            dat2.mplot(plt, "r", bitmask=hcam.BAD_TIME|hcam.JUNK)
             xlabel = "Time [MJD]"
             ylabel = "{:s} & {:s}".format(lab1, lab2)
 
         elif scheme == "r":
             # ratio
             ratio = dat1 / dat2
-            ratio.mplot(plt, "b", bitmask=hcam.BAD_TIME)
+            ratio.mplot(plt, "b", bitmask=hcam.BAD_TIME|hcam.JUNK)
             xlabel = "Time [MJD]"
             ylabel = "{:s} / {:s}".format(lab1, lab2)
 
         elif scheme == "d":
             # difference
             diff = dat1 - dat2
-            diff.mplot(plt, "b", bitmask=hcam.BAD_TIME)
+            diff.mplot(plt, "b", bitmask=hcam.BAD_TIME|hcam.JUNK)
             xlabel = "Time [MJD]"
             ylabel = "{:s} - {:s}".format(lab1, lab2)
 
         elif scheme == "s":
-            mask1 = dat1.get_mask(bitmask=hcam.BAD_TIME, invert=True)
-            mask2 = dat1.get_mask(bitmask=hcam.BAD_TIME, invert=True)
+            mask1 = dat1.get_mask(bitmask=hcam.BAD_TIME|hcam.JUNK, invert=True)
+            mask2 = dat1.get_mask(bitmask=hcam.BAD_TIME|hcam.JUNK, invert=True)
             ok = ~mask1 & ~mask2
             plt.errorbar(
                 dat1.y[ok], dat2.y[ok], dat2.ye[ok], dat1.ye[ok], ".", capsize=0
@@ -186,7 +189,7 @@ def plog(args=None):
 
     else:
         # just one
-        dat1.mplot(plt, bitmask=hcam.BAD_TIME)
+        dat1.mplot(plt, bitmask=hcam.BAD_TIME|hcam.JUNK)
         xlabel = "Time [MJD]"
         ylabel = lab1