JP-3355 added parameter to extract 1d to override srctype and use poi…

…nt source extraction (#7883)

CHANGES.rst

@@ -1,7 +1,12 @@
 1.12.1 (unreleased)
 ===================
 
-- 
+extract_1d
+----------
+
+- For MIRS MRS IFU data allow the user to set the src_type and allow 
+  the user to scale the extraction radius between 0.5 to 3.0 FWHM [#7883]
+
 
 1.12.0 (2023-09-18)
 ===================
@@ -112,6 +117,7 @@ extract_1d
 - Use ``source_{x/y}pos`` metadata to center extraction region for NIRSpec
   (non-IFU) data; use dithered pointing info for MIRI LRS fixed slit data. [#7796]
 
+
 extract_2d
 ----------
 

docs/jwst/extract_1d/arguments.rst

@@ -109,6 +109,19 @@ The ``extract_1d`` step has the following step-specific arguments.
   Switch to select whether or not to run 1d residual fringe correction on the
   extracted 1d spectrum (MIRI MRS only). Default is ``False``.
 
+``--ifu_set_srctype``
+  A string that can be used to override the extraction method for the source_type
+  given by the SRCTYPE keyword. The allowed values are POINT and EXTENDED. The SRCTYPE keyword is
+  not changed, instead the extraction method used is based on this parameter setting. This is
+  only allowed for MIRI MRS IFU data. 
+
+``--ifu_rscale``
+   A float designating the number of PSF FWHMs to use for the extraction radius. This
+   is a MIRI MRS only paramenter. Values accepted are between 0.5 to 3.0. The default extraction
+   size is set to 2 * FWHM. Values below 2 will result in a smaller
+   radius, a value of 2 results in no change to radius and a value above 2 results in a larger
+   extraction radius.  
+
 ``--soss_atoca``
   This is a NIRISS-SOSS algorithm-specific parameter; if True, use the ATOCA
   algorithm to treat order contamination. Default is ``True``.

jwst/extract_1d/extract.py

@@ -2547,6 +2547,8 @@ def run_extract1d(
         center_xy: Union[float, None],
         ifu_autocen: Union[bool, None],
         ifu_rfcorr: Union[bool, None],
+        ifu_set_srctype: str,
+        ifu_rscale: float,
         was_source_model: bool = False,
 ) -> DataModel:
     """Extract 1-D spectra.
@@ -2607,6 +2609,16 @@ def run_extract1d(
         Switch to select whether or not to apply a 1d residual fringe correction
         for MIRI MRS IFU spectra.  Default is False.
 
+    ifu_set_srctype : str
+        For MIRI MRS IFU data override srctype and set it to either POINT or EXTENDED.
+
+    ifu_rscale: float
+        For MRS IFU data a value for changing the extraction radius. The value provided is the number of PSF
+        FWHMs to use for the extraction radius. Values accepted are between 0.5 to 3.0. The
+        default extraction size is set to 2 * FWHM. Values below 2 will result in a smaller
+        radius, a value of 2 results in no change to the radius and a value above 2 results in a larger
+        extraction radius.
+
     was_source_model : bool
         True if and only if `input_model` is actually one SlitModel
         obtained by iterating over a SourceModelContainer.  The default
@@ -2655,6 +2667,8 @@ def run_extract1d(
         center_xy,
         ifu_autocen,
         ifu_rfcorr,
+        ifu_set_srctype,
+        ifu_rscale,
         was_source_model,
     )
 
@@ -2717,6 +2731,8 @@ def do_extract1d(
         center_xy: Union[int, None] = None,
         ifu_autocen: Union[bool, None] = None,
         ifu_rfcorr: Union[bool, None] = None,
+        ifu_set_srctype: str = None,
+        ifu_rscale: float = None,
         was_source_model: bool = False
 ) -> DataModel:
     """Extract 1-D spectra.
@@ -2787,6 +2803,16 @@ def do_extract1d(
         Switch to select whether or not to apply a 1d residual fringe correction
         for MIRI MRS IFU spectra.  Default is False.
 
+    ifu_set_srctype : str
+        For MIRI MRS IFU data override srctype and set it to either POINT or EXTENDED.
+
+    ifu_rscale: float
+        For MRS IFU data a value for changing the extraction radius. The value provided is the number of PSF
+        FWHMs to use for the extraction radius. Values accepted are between 0.5 to 3.0. The
+        default extraction size is set to 2 * FWHM. Values below 2 will result in a smaller
+        radius, a value of 2 results in no change to the radius and a value above 2 results in a larger
+        extraction radius.
+
     was_source_model : bool
         True if and only if `input_model` is actually one SlitModel
         obtained by iterating over a SourceModelContainer.  The default
@@ -2994,9 +3020,12 @@ def do_extract1d(
             if source_type is None:
                 source_type = "UNKNOWN"
 
+            if ifu_set_srctype is not None and input_model.meta.exposure.type == 'MIR_MRS':
+                source_type = ifu_set_srctype
+                log.info(f"Overriding source type and setting it to = {ifu_set_srctype}")
             output_model = ifu.ifu_extract1d(
                 input_model, extract_ref_dict, source_type, subtract_background,
-                bkg_sigma_clip, apcorr_ref_model, center_xy, ifu_autocen, ifu_rfcorr
+                bkg_sigma_clip, apcorr_ref_model, center_xy, ifu_autocen, ifu_rfcorr, ifu_rscale
             )
 
         else:

jwst/extract_1d/extract_1d_step.py

@@ -81,6 +81,16 @@ class Extract1dStep(Step):
         Switch to select whether or not to apply a 1d residual fringe correction
         for MIRI MRS IFU spectra.  Default is False.
 
+    ifu_set_srctype : str
+        For MIRI MRS IFU data override srctype and set it to either POINT or EXTENDED.
+
+    ifu_rscale : float
+        For MRS IFU data a value for changing the extraction radius. The value provided is
+        the number of PSF FWHMs to use for the extraction radius. Values accepted are between
+        0.5 to 3.0. The default extraction size is set to 2 * FWHM. Values below 2 will result
+        in a smaller radius, a value of 2 results in no change to the radius and a value above
+        2 results in a larger extraction radius.
+
     soss_atoca : bool, default=False
         Switch to toggle extraction of SOSS data with the ATOCA algorithm.
         WARNING: ATOCA results not fully validated, and require the photom step
@@ -149,6 +159,8 @@ class Extract1dStep(Step):
     apply_apcorr = boolean(default=True)  # apply aperture corrections?
     ifu_autocen = boolean(default=False) # Auto source centering for IFU point source data.
     ifu_rfcorr = boolean(default=False) # Apply 1d residual fringe correction
+    ifu_set_srctype = option("POINT", "EXTENDED", None, default=None) # user-supplied source type
+    ifu_rscale = float(default=None, min=0.5, max=3) # Radius in terms of PSF FWHM to scale extraction radii
     soss_atoca = boolean(default=True)  # use ATOCA algorithm
     soss_threshold = float(default=1e-2)  # TODO: threshold could be removed from inputs. Its use is too specific now.
     soss_n_os = integer(default=2)  # minimum oversampling factor of the underlying wavelength grid used when modeling trace.
@@ -217,6 +229,21 @@ def process(self, input):
             input_model.meta.cal_step.extract_1d = 'SKIPPED'
             return input_model
 
+        if self.ifu_rfcorr:
+            if input_model.meta.exposure.type != "MIR_MRS":
+                self.log.warning("The option to apply a residual refringe correction is"
+                                 f" not supported for {input_model.meta.exposure.type} data.")
+
+        if self.ifu_rscale is not None:
+            if input_model.meta.exposure.type != "MIR_MRS":
+                self.log.warning("The option to change the extraction radius is"
+                                 f" not supported for {input_model.meta.exposure.type} data.")
+
+        if self.ifu_set_srctype is not None:
+            if input_model.meta.exposure.type != "MIR_MRS":
+                self.log.warning("The option to change the source type is"
+                                 f" not supported for {input_model.meta.exposure.type} data.")
+
         # ______________________________________________________________________
         # Do the extraction for ModelContainer - this might only be WFSS data
         if isinstance(input_model, ModelContainer):
@@ -260,6 +287,8 @@ def process(self, input):
                         self.center_xy,
                         self.ifu_autocen,
                         self.ifu_rfcorr,
+                        self.ifu_set_srctype,
+                        self.ifu_rscale,
                         was_source_model=was_source_model
                     )
                     # Set the step flag to complete
@@ -296,6 +325,8 @@ def process(self, input):
                             self.center_xy,
                             self.ifu_autocen,
                             self.ifu_rfcorr,
+                            self.ifu_set_srctype,
+                            self.ifu_rscale,
                             was_source_model=was_source_model,
                         )
                         # Set the step flag to complete in each MultiSpecModel
@@ -335,6 +366,8 @@ def process(self, input):
                     self.center_xy,
                     self.ifu_autocen,
                     self.ifu_rfcorr,
+                    self.ifu_set_srctype,
+                    self.ifu_rscale,
                     was_source_model=was_source_model,
                 )
 
@@ -476,6 +509,8 @@ def process(self, input):
                     self.center_xy,
                     self.ifu_autocen,
                     self.ifu_rfcorr,
+                    self.ifu_set_srctype,
+                    self.ifu_rscale,
                     was_source_model=False,
                 )
 

jwst/extract_1d/ifu.py

@@ -37,7 +37,7 @@
 
 def ifu_extract1d(input_model, ref_dict, source_type, subtract_background,
                   bkg_sigma_clip, apcorr_ref_model=None, center_xy=None,
-                  ifu_autocen=False, ifu_rfcorr=False):
+                  ifu_autocen=False, ifu_rfcorr=False, ifu_rscale=None):
     """Extract a 1-D spectrum from an IFU cube.
 
     Parameters
@@ -77,6 +77,13 @@ def ifu_extract1d(input_model, ref_dict, source_type, subtract_background,
         Switch to select whether or not to apply a 1d residual fringe correction
         for MIRI MRS IFU spectra.  Default is False.
 
+    ifu_rscale: float
+        For MRS IFU data a value for changing the extraction radius. The value provided is the number of PSF
+        FWHMs to use for the extraction radius. Values accepted are between 0.5 to 3.0. The
+        default extraction size is set to 2 * FWHM. Values below 2 will resuls in a smaller
+        radius, a value of 2 results in no change to radius and a value above 2 results in a larger
+        extraction radius.
+
     Returns
     -------
     output_model : MultiSpecModel
@@ -108,14 +115,17 @@ def ifu_extract1d(input_model, ref_dict, source_type, subtract_background,
 
     extract_params = get_extract_parameters(ref_dict, bkg_sigma_clip, slitname)
 
-    # Add info about IFU auto-centroiding and residual fringe correction to extract_params for use later
+    # Add info about IFU auto-centroiding, residual fringe correction and extraction radius scale
+    # to extract_params for use later
     extract_params['ifu_autocen'] = ifu_autocen
     extract_params['ifu_rfcorr'] = ifu_rfcorr
+    extract_params['ifu_rscale'] = ifu_rscale
 
     # If the user supplied extraction center coords,
     # load them into extract_params for use later.
     extract_params['x_center'] = None
     extract_params['y_center'] = None
+
     if center_xy is not None:
         if len(center_xy) == 2:
             extract_params['x_center'] = float(center_xy[0])
@@ -515,6 +525,10 @@ def extract_ifu(input_model, source_type, extract_params):
         outer_bkg = extract_params['outer_bkg'].flatten()
         radius = extract_params['radius'].flatten()
 
+        if ((input_model.meta.instrument.name == 'MIRI') & (extract_params['ifu_rscale'] is not None)):
+            radius = radius * extract_params['ifu_rscale']/2.0
+            log.info("Scaling radius by factor =  %g", extract_params['ifu_rscale'] / 2.0)
+
         frad = interp1d(wave_extract, radius, bounds_error=False, fill_value="extrapolate")
         radius_match = frad(wavelength)
         # radius_match is in arc seconds - need to convert to pixels
@@ -741,14 +755,14 @@ def extract_ifu(input_model, source_type, extract_params):
         # Determine which MRS channel the spectrum is from
         thischannel = input_model.meta.instrument.channel
         # Valid single-channel values
-        validch=['1','2','3','4']
+        validch = ['1', '2', '3', '4']
         # Embed all calls to residual fringe code in a try/except loop as the default behavior
         # if problems are encountered should be to not apply this optional step
         try:
             # If a valid single channel, specify it in call to residual fringe code
             if (thischannel in validch):
                 temp_flux = rfutils.fit_residual_fringes_1d(temp_flux, wavelength, channel=thischannel,
-                                              dichroic_only=False, max_amp=None)
+                                                            dichroic_only=False, max_amp=None)
             # Otherwise leave channel blank
             else:
                 temp_flux = rfutils.fit_residual_fringes_1d(temp_flux, wavelength,