Merge branch 'master' into speedupemicorr

CHANGES.rst

@@ -82,6 +82,9 @@ cube_build
 
 - Replaced deep copies of NIRSpec WCS objects within most loops. [#8793]
 
+- Allow the user to provide ra and dec shifts to apply for each file to fine
+  tune the WCS. [#8720]
+
 datamodels
 ----------
 

docs/jwst/cube_build/arguments.rst

@@ -91,6 +91,12 @@ The following arguments control the size and sampling characteristics of the out
 ``nspax_y``
   The odd integer number of spaxels to use in the y dimension of the tangent plane.
 
+``offset_file [string]``
+  The string contains the name of the file holding RA and Dec offsets to apply to each input file. This file
+  must be an asdf file with a specific format. For details on how to construct the offset file see
+  :ref:`offsets`. 
+
+
 ``coord_system [string]``
   The default IFU cubes are built on the ra-dec coordinate system (``coord_system=skyalign``). In these cubes north is up 
   and east is left. There are two other coordinate systems an IFU cube can be built on:
@@ -122,3 +128,42 @@ A parameter only used for investigating which detector pixels contributed to a c
 
   The string is the x,y,z value of the cube spaxel that is being investigated. The  numbering starts counting at 0.
   To print information to the screeen about the x = 10, y = 20, z = 35 spaxel the parameter string value is '10 20 35'.
+
+.. _offsets:
+
+Creating an offset file
+-----------------------
+
+The offset file is an ASDF formatted file :`<https://asdf-standard.readthedocs.io/>`_ stands for "Advanced Scientific Data.
+For each input file in the spec3 association used to build the IFU cubes, the offset file needs to have a
+corresponding right ascension and declination offset given in arc seconds.
+
+Below is an example of how to make an ASDF offset file. It is assumed the user has determined the
+offsets to apply to the data in each file. The offsets information is stored in three lists:
+`filename`, `raoffset` and `decoffset`.  The units of the Ra and Dec offsets 
+are required to be in the offset file and only the unit, `arcsec`, is allowed. The file names should
+not contain the directory path. The offset file can have any name, but it must have the `asdf` extension.
+
+An example of making an offset file for an association containing three files is:
+
+.. code-block:: python
+		
+   import asdf
+   import astropy.units as u
+   
+   filename = ['file1.fits', 'file2.fits', 'file3.fits']
+   raoffset = [0.0, -1.0, 1.0]
+   decoffset = [0.0, 1.0, -1.0]
+
+   tree = {
+    "units": str(u.arcsec),
+    "filename": filename,
+    "raoffset": raoffset,
+    "decoffset": decoffset
+    }
+    af = asdf.AsdfFile(tree)
+    af.write_to('offsets.asdf')
+    af.close()
+    
+
+

jwst/cube_build/cube_build_step.py

@@ -2,16 +2,16 @@
 """
 
 import time
-
 from jwst.datamodels import ModelContainer
 from jwst.lib.pipe_utils import match_nans_and_flags
-
 from . import cube_build
 from . import ifu_cube
 from . import data_types
+import asdf
 from ..assign_wcs.util import update_s_region_keyword
 from ..stpipe import Step, record_step_status
-
+from pathlib import Path
+from astropy import units 
 __all__ = ["CubeBuildStep"]
 
 
@@ -64,6 +64,7 @@ class CubeBuildStep (Step):
          search_output_file = boolean(default=false)
          output_use_model = boolean(default=true) # Use filenames in the output models
          suffix = string(default='s3d')
+         offset_file = string(default=None) # Filename containing a list of Ra and Dec offsets to apply to files. 
          debug_spaxel = string(default='-1 -1 -1') # Default not used
        """
 
@@ -235,7 +236,18 @@ def process(self, input):
                 self.output_type = 'channel'
         self.pars_input['output_type'] = self.output_type
         self.log.info(f'Setting output type to: {self.output_type}')
-
+# ________________________________________________________________________________
+# If an offset file is provided do some basic checks on the file and its contents.
+# The offset list contains a matching list to the files in the association
+# used in calspec3 (for offline cube building).
+# The offset list is an asdf file.
+        self.offsets = None
+
+        if self.offset_file is not None:
+            offsets = self.check_offset_file()
+            if offsets is not None:
+                self.offsets = offsets
+# ________________________________________________________________________________
 # Read in Cube Parameter Reference file
 # identify what reference file has been associated with these input
 
@@ -276,6 +288,7 @@ def process(self, input):
             'roiw': self.roiw,
             'wavemin': self.wavemin,
             'wavemax': self.wavemax,
+            'offsets': self.offsets,
             'skip_dqflagging': self.skip_dqflagging,
             'suffix': self.suffix,
             'debug_spaxel': self.debug_spaxel}
@@ -530,3 +543,64 @@ def read_user_input(self):
 # remove duplicates if needed
             self.pars_input['grating'] = list(set(self.pars_input['grating']))
 # ________________________________________________________________________________
+
+    def check_offset_file(self):
+        """Read in an optional ra and dec offset for each file.
+
+        Summary
+        ----------
+        Check that is file is asdf file.
+        Check the file has the correct format using an local schema file.
+        The schema file, ifuoffset.schema.yaml, is located in the jwst/cube_build directory.
+        For each file in the input  assocation check that there is a corresponding
+        file in the offset file.
+
+       """
+
+        # validate the offset file using the schema file
+        DATA_PATH = Path(__file__).parent
+
+        try:
+            af = asdf.open(self.offset_file, custom_schema=DATA_PATH/'ifuoffset.schema.yaml')
+        except:
+            schema_message = ('Validation Error for offset file. Fix the offset file. \n' + \
+                              'The offset file needs to have the same number of elements ' + \
+                              'in the three lists: filename, raoffset and decoffset.\n' +\
+                              'The units need to provided and only arcsec is allowed.')
+
+            raise Exception(schema_message)
+
+        offset_filename = af['filename']
+        offset_ra = af['raoffset']
+        offset_dec = af['decoffset']
+        # Note:
+        # af['units'] is checked by the schema validation. It must be arcsec or a validation error occurs.
+
+        # check that all the file names in input_model are in the offset filename
+        for model in self.input_models:
+            file_check = model.meta.filename
+            if file_check in offset_filename:
+                continue
+            else:
+                af.close()
+                raise ValueError('Error in offset file. A file in the assocation is not found in offset list %s', file_check)
+
+        # check that all the lists have the same length
+        len_file  = len(offset_filename)
+        len_ra = len(offset_ra)
+        len_dec = len(offset_dec)
+        if (len_file != len_ra or len_ra != len_dec or len_file != len_dec):
+            af.close()
+            raise ValueError('The offset file does not have the same number of values for filename, raoffset, decoffset')
+
+        offset_ra =   offset_ra* units.arcsec
+        offset_dec =   offset_dec* units.arcsec
+
+        # The offset file has passed tests so set the offset dictionary
+        offsets = {}
+        offsets['filename'] = offset_filename
+        offsets['raoffset'] = offset_ra
+        offsets['decoffset'] = offset_dec
+
+        af.close()
+        return offsets