Merge pull request #1884 from pypeit/msc_ar_slits

Fixes problem with definition of image locations in mosaics

doc/api/pypeit.scripts.run_to_calibstep.rst

@@ -0,0 +1,8 @@
+pypeit.scripts.run\_to\_calibstep module
+========================================
+
+.. automodule:: pypeit.scripts.run_to_calibstep
+   :members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:

doc/help/pypeit_run_to_calibstep.rst

@@ -0,0 +1,36 @@
+.. code-block:: console
+
+    $ pypeit_run_to_calibstep -h
+    usage: pypeit_run_to_calibstep [-h] [--science_frame SCIENCE_FRAME]
+                                   [--calib_group CALIB_GROUP] [--det DET]
+                                   [-v VERBOSITY] [-r REDUX_PATH] [-s]
+                                   pypeit_file step
+    
+    Run PypeIt to a single calibration step for an input frame
+    
+    positional arguments:
+      pypeit_file           PypeIt reduction file (must have .pypeit extension)
+      step                  Calibration step to perform. Valid steps are: align,
+                            arc, bias, bpm, dark, flats, scattlight, slits, tiltimg,
+                            tilts, wv_calib
+    
+    options:
+      -h, --help            show this help message and exit
+      --science_frame SCIENCE_FRAME
+                            Raw science frame to reduce as listed in your PypeIt
+                            file, e.g. b28.fits.gz. Either this or the calib_group
+                            must be provided
+      --calib_group CALIB_GROUP
+                            Calibration group ID to reduce. Either this or the frame
+                            must be provided
+      --det DET             Detector to reduce
+      -v VERBOSITY, --verbosity VERBOSITY
+                            Verbosity level between 0 [none] and 2 [all]
+      -r REDUX_PATH, --redux_path REDUX_PATH
+                            Path to directory for the reduction. Only advised for
+                            testing
+      -s, --show            Show reduction steps via plots (which will block further
+                            execution until clicked on) and outputs to ginga.
+                            Requires remote control ginga session via "ginga
+                            --modules=RC,SlitWavelength &"
+    

doc/help/run_pypeit.rst

@@ -4,7 +4,7 @@
     usage: run_pypeit [-h] [-v VERBOSITY] [-r REDUX_PATH] [-m] [-s] [-o] [-c]
                       pypeit_file
     
-    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.17.1.dev2+g6e8b74d14[0m
+    ##  [1;37;42mPypeIt : The Python Spectroscopic Data Reduction Pipeline v1.17.2.dev152+gd5ab50fca[0m
     ##  
     ##  Available spectrographs include:
     ##   aat_uhrf, bok_bc, gemini_flamingos1, gemini_flamingos2,

doc/releases/1.17.2dev.rst

@@ -60,6 +60,8 @@ Bug Fixes
   the spectrum is extracted even when `pixelflat_model` does not exist.
 - The variance cube previously had a cubic term, and this has been changed
   to a quadratic term. This has been cross-checked with simple subpixel calculations.
+- Fixes bug associated with trying to remove or add slits for reductions that
+  mosaic multiple detectors.
 - Fix Setup GUI sizing issues on MacOS.
 - Fixed a bug with ``pypeit_identify`` when the number of echelle orders has
   more than two digits.

pypeit/core/parse.py

@@ -335,3 +335,134 @@ def str2list(inp, length=None):
             indices += [int(grp)]
     return np.unique(indices).tolist()
 
+
+def parse_image_location(inp, spec):
+    """
+    Parse a colon-separated string with a detector/mosaic identifier and a
+    series of floats.
+    
+    This function should be used to parse a *single* image location.  Multiple
+    image locations are generally separated by semi-colons; the ``inp`` string
+    provided *must not* contain semi-colons.
+
+    This is primarily used for two purposes: setting locations in a
+    PypeIt-reduced image (e.g., adding or removing slits) or to define a manual
+    extraction aperture (see :ref:`manual`).
+
+    Parameters
+    ----------
+    inp : :obj:`str`
+        Colon-separated string with a detector identifier and 2 to 3 numbers.
+        **Must not contain semi-colons.**
+    spec : :class:`~pypeit.spectrographs.spectrograph.Spectrograph`
+        Spectrograph class used to interpret the detector/mosaic identifier.
+
+    Returns
+    -------
+    :obj:`tuple`
+        Flag that detector integer as negative, the detector identifier returned
+        as a string (e.g., DET01, MSC01), and the set of floats.
+
+    Raises
+    ------
+    PypeItError
+        Raised if the ``inp`` string contains a semi-colon, if a mosaic is
+        identified that is not valid for the provided spectrograph, or if there
+        is an issue constructing the detector/mosaic identifier.
+
+    Examples
+    --------
+    Setup, where ``keck_nires`` is just used as an example of a single detector
+    spectrograph.
+
+        >>> from pypeit.spectrographs.util import load_spectrograph
+        >>> from pypeit.core import parse
+        >>> spec = load_spectrograph('keck_nires')
+
+    The detector can be negative:
+
+        >>> parse.parse_image_location('-1:34.5:400.1:4', spec)
+        (True, 'DET01', 34.5, 400.1, 4.0)
+
+    or positive:
+
+        >>> parse.parse_image_location('1:34.5:400.1:4', spec)
+        (False, 'DET01', 34.5, 400.1, 4.0)
+
+    This will fail because ``(1,2,3)`` is not an allowed mosaic for ``keck_nires``.
+
+        >>> try:
+        ...     parse.parse_image_location('(1,2,3):34.5:400.1:4', spec)
+        ... except:
+        ...     print('failed')
+        [ERROR]   :: (1, 2, 3) is not a valid mosaic for keck_nires.
+        failed
+
+    Now for a mosaic:
+    
+        >>> spec = load_spectrograph('gemini_gmos_south_ham')
+        >>> parse.parse_image_location('(1,2,3):34.5:400.1:4', spec)
+        (False, 'MSC01', 34.5, 400.1, 4.0)
+        >>> parse.parse_image_location('(-1,-2,-3):34.5:400.1:4', spec)
+        (True, 'MSC01', 34.5, 400.1, 4.0)
+        >>> parse.parse_image_location('2:34.5:400.1', spec)
+        (False, 'DET02', 34.5, 400.1)
+    
+    """
+    if ';' in inp:
+        msgs.error(f'Image location string provided ({inp}) includes a semi-colon!')
+    # Split the components of the string
+    _inp = inp.split(':')
+
+    # Get the detector integer(s); det will be a list of a single number (no
+    # mosaic) or >= 2 numbers (mosaic)
+    det = tuple(int(d) for d in _inp[0].strip('()').split(','))
+
+    # check if the detector integers are negative
+    neg = np.all([d < 0 for d in det])
+    if neg:
+        det = tuple(-d for d in det)
+
+    if len(det) > 1 and det not in spec.allowed_mosaics:
+        msgs.error(f'{det} is not a valid mosaic for {spec.name}.')
+    elif len(det) > 1 and det in spec.allowed_mosaics:
+        # we use detname, which is a string (e.g., 'DET01', 'MSC01')
+        detname = spec.get_det_name(det)
+    elif len(det) == 1:
+        detname = spec.get_det_name(det[0])
+    else:
+        msgs.error(f'Unable to parse detector identifier in: {inp}')
+
+    return (neg, detname) + tuple(float(p) for p in _inp[1:])
+
+
+def fix_config_par_image_location(par):
+    """
+    Fix mosaic image locations as parsed by `configobj`_.
+
+    When, e.g., defining a slit to remove, the user sets:
+
+    .. code-block:: ini
+
+        rm_slits = (1,2,3):1500:331; (1,2,3):1500:635
+
+    The `configobj`_ parser turns this into ``['(1', '2', '3):1500:331; (1',
+    '2', '3):1500:635']``.  This function converts this back to the expected
+    format: ``['(1,2,3):1500:331', '(1,2,3):1500:635']``.
+
+    Parameters
+    ----------
+    par : :obj:`str`, :obj:`list`
+        List of strings parsed by `configobj`_.
+
+    Returns
+    -------
+    :obj:`list`
+        The corrected image-location definitions.
+    """
+    # Ensure list type; avoid running ','.join(par) on a string!
+    _par = [par] if isinstance(par, str) else par
+    # Simply join all the entries with a comma (removed by the configobj parser)
+    # and instead split at the semi-colon and remove leading/trailing whitespace:
+    return list(map(str.strip, (','.join(_par)).split(';')))
+

pypeit/core/trace.py

@@ -24,7 +24,9 @@
 from pypeit import msgs
 from pypeit import utils
 from pypeit import sampling
-from pypeit.core import moment, pydl, arc
+from pypeit.core import arc
+from pypeit.core import moment
+from pypeit.core import pydl
 
 # TODO: Some of these functions could probably just live in pypeit.edges