Merge branch 'trm-dev'

Bringing a bunch of recent changes into the master branch.

docs/change_log_0.22.0_1.0.0.rst

@@ -1,4 +1,4 @@
-.. changelog created on Wed 26 May 15:43:37 BST 2021
+.. changelog created on Wed  2 Jun 15:19:03 BST 2021
 
 .. include:: globals.rst
 

docs/makingmovies.rst

@@ -43,7 +43,9 @@ raw data, run0005.fits sat.
   trim = False
   ccd = 2
   bias = bias3x3_slow.hcm
+  dark = none
   flat = none
+  fmap = none
   defect = none
   log = run0005.log
   targ = 1
@@ -84,7 +86,9 @@ Once you have the stills, you still need to actually make the movie. I use the c
 which would find any files of the form 'run0005_0340.png' starting
 from 'run0005_0123.png'. 'ffmpeg' has a million-and-one options and
 there be ways to tweak it, but this does a reasonable job I find.
+You can loop the movie with something like:
 
+  ``ffmpeg -start_number 3 -i run0011_%04d.png -filter_complex loop=5:362 -c:v libx264 -pix_fmt yuv420p movie.mp4 -y``
 
-
+which would add 6 loops.
 

docs/reduction.rst

@@ -536,3 +536,35 @@ no one prescription that works for all cases. Faint targets normally require
 different settings from bright ones for the best results (e.g. smaller target
 aperture radii). Very faint target may benefit from optimal extraction, while
 brighter ones can look worse.
+
+Specific errors
+---------------
+
+I hope to list commonly encountered error traces here.
+
+Mis-matching calibration files
+..............................
+
+An error message such as this::
+
+  nrtplot ../run0012
+  first - first frame to plot [1]: \
+  1, utc= 2021-05-10 03:01:12.777 (ok), Traceback (most recent call last):
+    File "/home/phsaap/.local/bin/nrtplot", line 8, in <module>
+      sys.exit(nrtplot())
+    File "/home/phsaap/.local/lib/python3.9/site-packages/hipercam/scripts/nrtplot.py", line 836, in nrtplot
+      bias = bias.crop(mccd)
+    File "/home/phsaap/.local/lib/python3.9/site-packages/hipercam/ccd.py", line 795, in crop
+      tmccd[cnam] = self[cnam].crop(ccd)
+    File "/home/phsaap/.local/lib/python3.9/site-packages/hipercam/ccd.py", line 552, in crop
+      raise HipercamError(
+  hipercam.core.HipercamError: failed to find any enclosing window for window label = E1
+
+is a good sign that you have a problem with a mis-match between a
+calibration file and the data. In this case the bias frame selected
+was taken with 2x2 binning while the data were unbinned, and so it was
+impossible for it to recover. NB The code does attempt to go the other
+way, i.e.  to bin up 1x1 into 2x2 if need be, although this can only
+ever be approximate.  The other way for this message to occur is you
+try to use windowed calibration data which does not span the windows
+of the data.

hipercam/ccd.py

@@ -710,7 +710,9 @@ def read(cls, fname):
 
         """
         with fits.open(fname) as hdul:
-            return cls.rhdul(hdul)
+            mccd = cls.rhdul(hdul)
+        mccd.head['FILENAME'] = fname
+        return mccd
 
     @classmethod
     def rhdul(cls, hdul):

hipercam/cline.py

@@ -78,7 +78,6 @@
 
 # next two lines allow tab completion of file names
 import readline
-
 readline.parse_and_bind("tab: complete")
 
 from .core import HipercamError, HipercamWarning
@@ -764,8 +763,8 @@ def get_value(
         if multipleof != None and value % multipleof != 0:
             raise ClineError(str(value) + " is not a multiple of " + str(multipleof))
 
-        # update appropriate set of defaults. In the case of Fnames, strip the
-        # extension
+        # update appropriate set of defaults. In the case of Fnames,
+        # strip the extension
         if self._rpars[param]["g_or_l"] == Cline.GLOBAL:
             if isinstance(defval, Fname):
                 self._gpars[param] = defval.noext(value)
@@ -842,7 +841,8 @@ def __new__(cls, root, ext="", ftype=OLD, exist=True):
 
         """
 
-        if ftype != Fname.OLD and ftype != Fname.NEW and ftype != Fname.NOCLOBBER:
+        if ftype != Fname.OLD and ftype != Fname.NEW and \
+           ftype != Fname.NOCLOBBER:
             raise ClineError("ftype must be either OLD, NEW or NOCLOBBER")
 
         # store root with no extension
@@ -854,9 +854,9 @@ def __new__(cls, root, ext="", ftype=OLD, exist=True):
         return fname
 
     def __init__(self, root, ext="", ftype=OLD, exist=True):
-        """Initialiser. In the following text items in capitals such as 'OLD' are
-        static variables so that one should use hipercam.cline.Fname.OLD or
-        equivalent to refer to them.
+        """Initialiser. In the following text items in capitals such as 'OLD'
+        are static variables so that one should use
+        hipercam.cline.Fname.OLD or equivalent to refer to them.
 
         Arguments::
 
@@ -868,14 +868,14 @@ def __init__(self, root, ext="", ftype=OLD, exist=True):
              extension, e.g. '.dat'
 
           ftype : (int)
-             If exist=True and ftype=OLD, the file :must: exist. If exist=False, the file may or may
-             not exist already.
+             If exist=True and ftype=OLD, the file :must: exist. If
+             exist=False, the file may or may not exist already.
 
           exist : (bool)
              If True, the file must exist.
 
-        ext, ftype and exist are stored as identically-named attributes. 'root'
-        is stored as the base string.
+        ext, ftype and exist are stored as identically-named
+        attributes. 'root' is stored as the base string.
 
         """
 
@@ -884,16 +884,16 @@ def __init__(self, root, ext="", ftype=OLD, exist=True):
         self.exist = exist
 
     def __call__(self, fname):
-        """Given a potential file name, this first ensures that it has the correct
-        extension, and then tests for its existence if need be, depending upon
-        the values of `ftype` and `exist` defined at instantiation.
+        """Given a potential file name, this first ensures that it has the
+        correct extension, and then tests for its existence if need
+        be, depending upon the values of `ftype` and `exist` defined
+        at instantiation.
 
         Arguments::
 
-           fname : (string)
-
-              file name. The extension associated with the :class:`Fname` will
-              be added if necessary.
+           fname : str
+              file name. The extension associated with the
+              :class:`Fname` will be added if necessary.
 
         Returns the file name to use. Raises a ClineError exception if there
         are problems.
@@ -926,7 +926,6 @@ def __getnewargs__(self):
         """
         return (str(self), self.ext, self.ftype, self.exist)
 
-
 class ClineError(HipercamError):
     """For throwing exceptions from hipercam.cline"""
 

hipercam/core.py

@@ -54,7 +54,7 @@
 # Version of the reduce file in operation (used by 'reduce' and 'genred')
 # Format: YYYYMMDD(.#) where the optional .# part is an integer to allow for
 # multiple versions in a day, although that should be rare I hope.
-REDUCE_FILE_VERSION = "20210523"
+REDUCE_FILE_VERSION = "20210602"
 
 # Standard file extensions
 FIELD = ".fld"

hipercam/fringe.py

@@ -234,10 +234,13 @@ def scale(self, ccd, ccdref, nhalf, rmin=None, rmax=None, reset=False, verbose=F
                 ' '.join([f'{rat:.3f}' for rat in np.sort(ratios)])
             )
 
-        if rmin is not None:
+        if rmin is not None and rmax is not None:
+            ratios[(ratios < rmin) & (ratios > rmax)] = np.nan
+        elif rmin is not None:
             ratios[ratios < rmin] = np.nan
-        if rmax is not None:
+        elif rmax is not None:
             ratios[ratios > rmax] = np.nan
+
         return np.nanmedian(ratios)
 
 class MccdFringePair(Group):

hipercam/hcam.py

@@ -587,6 +587,12 @@ def __init__(self, fname, server=False, full=True):
             if "DEC" in hd:
                 self.thead["DEC"] = hd.get_full("DEC")
 
+            if "RADEG" in hd:
+                self.thead["RADEG"] = hd.get_full("RADEG")
+
+            if "DECDEG" in hd:
+                self.thead["DECDEG"] = hd.get_full("DECDEG")
+
             if "INSTRPA" in hd:
                 self.thead["INSTRPA"] = hd.get_full("INSTRPA")
 
@@ -596,6 +602,12 @@ def __init__(self, fname, server=False, full=True):
             if "ESO DET GPS" in hd:
                 self.thead["GPS"] = hd.get_full("ESO DET GPS")
 
+            if "INSTRUME" in hd:
+                self.thead["INSTRUME"] = hd.get_full("INSTRUME")
+
+            if "TELESCOP" in hd:
+                self.thead["TELESCOP"] = hd.get_full("TELESCOP")
+
             self.thead["XBIN"] = hd.get_full("ESO DET BINX1")
             self.thead["YBIN"] = hd.get_full("ESO DET BINY1")
             self.thead["SPEED"] = hd.get_full("ESO DET SPEED")
@@ -1067,7 +1079,7 @@ def __call__(self, nframe=None):
             # mode or intermediate junk frames in the case of NSKIP>0
             ch["DSTATUS"] = (
                 (self.nframe > self.ndwins) and (self.nframe % ch["NCYCLE"] == 0),
-                "Valid data (else junk frame)",
+                "Valid data or not",
             )
 
             # Get time at centre of exposure. Some care here to store a
@@ -1410,7 +1422,7 @@ def __call__(self, nframe=None):
 
         Arguments::
 
-           nframe : int | none
+           nframe : int | None
               frame number to get, starting at 1. 0 for the last (complete)
               frame. 'None' indicates that the next frame is wanted.
 
@@ -1460,30 +1472,31 @@ def __call__(self, nframe=None):
 
         # update the internal frame counter
         self.nframe += 1
+
+        # set the reset status to save effort if next time
+        # we simply want the next frame
         self.reset = False
 
         return tbytes
 
     def set(self, nframe=1):
         """Resets the position so that we are just about to read
         the timing data of nframe, but does not read them unlike
-        __call__
+        __call__. Set the internal "reset" flag if needed.
 
         Arguments::
 
-           nframe : int | none
+           nframe : int | None
               frame number to get, starting at 1. 0 for the last (complete)
-              frame. 'None' indicates that the next frame is wanted.
+              frame. 'None' indicates just read whatever is the next frame.
 
-        Returns:: the timing bytes of the frame
+        Returns:: the frame number of entry
         """
 
         old_frame = self.nframe
 
-        if nframe is None:
-            # just read whatever frame we are now on
-            self.reset = False
-        else:
+        if nframe is not None:
+
             if nframe == 0:
                 # go for the last one
                 nframe = self.ntotal()