Merge branch 'develop' into slitless_flats

doc/releases/1.16.1dev.rst

@@ -36,6 +36,20 @@ Instrument-specific Updates
 
 - Improved LRIS frame typing, including the typing of slitless flats and sky flats.
 - Improved HIRES frame typing and configuration setup.
+- Updated X-Shooter detector gain and read noise to come from header, and
+  updated plate scales to the most recent values from the manual.  Detailed
+  changes are:
+    - NIR arm:
+        - Platescale updated from 0.197 to 0.245 arcsec/pixel
+        - Dark current updated from 0. to 72. e-/pixel/hr
+        - Gain updated from 2.12 to 2.29 e-/DN
+    - VIS arm:
+        - Platescale updated from an order-dependent value, to being 0.154
+          arcsec/pixel for all orders
+    - UVB arm:
+        - Platescale updated from an order-dependent value, to being 0.164
+          arcsec/pixel for all orders
+
 
 Script Changes
 --------------
@@ -57,6 +71,8 @@ Script Changes
   function (before only optimal extraction was used).
 - Added ``pypeit_show_pixflat`` script to inspect the (slitless) pixel flat
   generated during the reduction and stored in ``data/pixelflats``.
+- Added ``pypeit_chk_flexure`` script to check both spatial and spectral flexure applied to
+  the reduced data.
 
 Datamodel Changes
 -----------------

pypeit/core/findobj_skymask.py

@@ -1278,6 +1278,7 @@ def ech_objfind(image, ivar, slitmask, slit_left, slit_righ, slit_spat_id, order
         det=det,
         inmask=inmask, 
         std_trace=std_trace,
+        ncoeff=ncoeff,
         specobj_dict=specobj_dict,
         snr_thresh=snr_thresh,
         show_peaks=show_peaks, 

pypeit/core/flexure.py

@@ -17,6 +17,7 @@
 from astropy import stats
 from astropy import units
 from astropy.io import ascii
+from astropy.table import Table
 import scipy.signal
 import scipy.optimize as opt
 from scipy import interpolate
@@ -36,7 +37,7 @@
 from pypeit.datamodel import DataContainer
 from pypeit.images.detector_container import DetectorContainer
 from pypeit.images.mosaic import Mosaic
-from pypeit import specobj, specobjs
+from pypeit import specobj, specobjs, spec2dobj
 from pypeit import wavemodel
 
 from IPython import embed
@@ -1394,6 +1395,80 @@ def sky_em_residuals(wave:np.ndarray, flux:np.ndarray,
     return dwave[m], diff[m], diff_err[m], los[m], los_err[m]
 
 
+def flexure_diagnostic(file, file_type='spec2d', flexure_type='spec', chk_version=False):
+    """
+    Print the spectral or spatial flexure of a spec2d or spec1d file
+    Args:
+        file (:obj:`str`, `Path`_):
+            Filename of the spec2d or spec1d file to check
+        file_type (:obj:`str`, optional):
+            Type of the file to check. Options are 'spec2d' or 'spec1d'. Default is 'spec2d'.
+        flexure_type (:obj:`str`, optional):
+            Type of flexure to check. Options are 'spec' or 'spat'. Default is 'spec'.
+        chk_version (:obj:`bool`, optional):
+            If True, raise an error if the datamodel version or type check failed.
+            If False, throw a warning only. Default is False.
+
+    Returns:
+        :obj:`astropy.table.Table` or :obj:`float`:
+        - If file_type is 'spec2d' and flexure_type is 'spec', return a table with the spectral flexure
+        - If file_type is 'spec2d' and flexure_type is 'spat', return the spatial flexure
+        - If file_type is 'spec1d', return a table with the spectral flexure
+
+    """
+
+    # value to return
+    return_flex = None
+
+    if file_type == 'spec2d':
+        # load the spec2d file
+        allspec2D = spec2dobj.AllSpec2DObj.from_fits(file, chk_version=chk_version)
+        # Loop on Detectors
+        for det in allspec2D.detectors:
+            print('')
+            print('=' * 50 + f'{det:^7}' + '=' * 51)
+            # get and print the spectral flexure
+            if flexure_type == 'spec':
+                spec_flex = allspec2D[det].sci_spec_flexure
+                spec_flex.rename_column('sci_spec_flexure', 'global_spec_shift')
+                if np.all(spec_flex['global_spec_shift'] != None):
+                    spec_flex['global_spec_shift'].format = '0.3f'
+                # print the table
+                spec_flex.pprint_all()
+                # return the table
+                return_flex = spec_flex
+            # get and print the spatial flexure
+            if flexure_type == 'spat':
+                spat_flex = allspec2D[det].sci_spat_flexure
+                # print the value
+                print(f'Spat shift: {spat_flex}')
+                # return the value
+                return_flex = spat_flex
+    elif file_type == 'spec1d':
+        # no spat flexure in spec1d file
+        if flexure_type == 'spat':
+            msgs.error("Spat flexure not available in the spec1d file, try with a spec2d file")
+        # load the spec1d file
+        sobjs = specobjs.SpecObjs.from_fitsfile(file, chk_version=chk_version)
+        spec_flex = Table()
+        spec_flex['NAME'] = sobjs.NAME
+        spec_flex['global_spec_shift'] = sobjs.FLEX_SHIFT_GLOBAL
+        if np.all(spec_flex['global_spec_shift'] != None):
+            spec_flex['global_spec_shift'].format = '0.3f'
+        spec_flex['local_spec_shift'] = sobjs.FLEX_SHIFT_LOCAL
+        if np.all(spec_flex['local_spec_shift'] != None):
+            spec_flex['local_spec_shift'].format = '0.3f'
+        spec_flex['total_spec_shift'] = sobjs.FLEX_SHIFT_TOTAL
+        if np.all(spec_flex['total_spec_shift'] != None):
+            spec_flex['total_spec_shift'].format = '0.3f'
+        # print the table
+        spec_flex.pprint_all()
+        # return the table
+        return_flex = spec_flex
+
+    return return_flex
+
+
 # TODO -- Consider separating the methods from the DataContainer as per calibrations
 class MultiSlitFlexure(DataContainer):
     """

pypeit/display/display.py

@@ -60,7 +60,7 @@ def connect_to_ginga(host='localhost', port=9000, raise_err=False, allow_new=Fal
             # was just instantiated for a maximum number of iterations.
             # If the connection is remains unsuccessful, an error is
             # thrown stating that the connection timed out.
-            maxiter = int(1e6)
+            maxiter = int(3e4)
             for i in range(maxiter):
                 try:
                     viewer = grc.RemoteClient(host, port)
@@ -72,8 +72,9 @@ def connect_to_ginga(host='localhost', port=9000, raise_err=False, allow_new=Fal
                     break
             if i == maxiter-1:
                 msgs.error('Timeout waiting for ginga to start.  If window does not appear, type '
-                           '`ginga --modules=RC,SlitWavelength` on the command line.  In either case, wait for '
-                           'the ginga viewer to open and try the pypeit command again.')
+                           '`ginga --modules=RC,SlitWavelength` on the command line.  In either '
+                           'case, wait for the ginga viewer to open and try the pypeit command '
+                           'again.')
             return viewer
 
         if raise_err:

pypeit/scripts/__init__.py

@@ -9,6 +9,7 @@
 from pypeit.scripts import chk_alignments
 from pypeit.scripts import chk_edges
 from pypeit.scripts import chk_flats
+from pypeit.scripts import chk_flexure
 from pypeit.scripts import chk_tilts
 from pypeit.scripts import chk_for_calibs
 from pypeit.scripts import chk_noise_1dspec

pypeit/scripts/chk_flexure.py

@@ -0,0 +1,63 @@
+"""
+This script displays the flexure (spatial or spectral) applied to the science data.
+
+.. include common links, assuming primary doc root is up one directory
+.. include:: ../include/links.rst
+"""
+
+from pypeit.scripts import scriptbase
+
+
+class ChkFlexure(scriptbase.ScriptBase):
+
+    @classmethod
+    def get_parser(cls, width=None):
+        parser = super().get_parser(description='Print QA on flexure to the screen',
+                                    width=width)
+
+        parser.add_argument('input_file', type=str, nargs='+', help='One or more PypeIt spec2d or spec1d file')
+        inp = parser.add_mutually_exclusive_group(required=True)
+        inp.add_argument('--spec', default=False, action='store_true', help='Check the spectral flexure')
+        inp.add_argument('--spat', default=False, action='store_true', help='Check the spatial flexure')
+        parser.add_argument('--try_old', default=False, action='store_true',
+                            help='Attempt to load old datamodel versions.  A crash may ensue..')
+        return parser
+
+    @staticmethod
+    def main(args):
+
+        from IPython import embed
+        from astropy.io import fits
+        from pypeit import msgs
+        from pypeit.core import flexure
+
+        chk_version = not args.try_old
+
+        # Loop over the input files
+        for in_file in args.input_file:
+
+            msgs.info(f'Checking fluxure for file: {in_file}')
+
+            # What kind of file are we??
+            hdul = fits.open(in_file)
+            head0 = hdul[0].header
+            file_type = None
+            if 'PYP_CLS' in head0.keys() and head0['PYP_CLS'].strip() == 'AllSpec2DObj':
+                file_type = 'spec2d'
+            elif 'DMODCLS' in head0.keys() and head0['DMODCLS'].strip() == 'SpecObjs':
+                file_type = 'spec1d'
+            else:
+                msgs.error("Bad file type input!")
+
+            # Check the flexure
+            flexure.flexure_diagnostic(in_file, file_type=file_type, flexure_type='spat' if args.spat else 'spec',
+                                       chk_version=chk_version)
+
+            #  space between files for clarity
+            print('')
+
+
+
+
+
+