JP-3649 Fix cube build error when called from mrs_imatch and add depr…

…ecated warning for mrs_imatch (#8728)

CHANGES.rst

@@ -28,6 +28,8 @@ cube_build
 
 - Removed direct setting of the ``self.skip`` attribute from within the step
   itself. [#8600]
+
+- Fixed a bug when ``cube_build`` was called from the ``mrs_imatch`` step. [#8728]
 
 documentation
 -------------
@@ -55,6 +57,11 @@ master_background
 - Either of ``"background"`` or ``"bkg"`` in slit name now defines the slit
   as a background slit, instead of ``"bkg"`` only. [#8600]
 
+mrs_imatch
+----------
+
+- Added a deprecation warning and set the default to skip=True for the step. [#8728] 
+
 outlier_detection
 -----------------
 

docs/jwst/mrs_imatch/description.rst

@@ -8,6 +8,10 @@ Description
 
 Overview
 --------
+
+This step has been deprecated  and will be
+skipped by default in the calwebb_spec3 pipeline.
+
 The ``mrs_imatch`` step "matches" image intensities of several input
 2D MIRI MRS images by fitting polynomials to cube intensities (cubes built
 from the input 2D images), in such a way as to minimize - in the least squares

jwst/cube_build/ifu_cube.py

@@ -826,7 +826,7 @@ def build_ifucube_single(self):
 
                 coord1, coord2, corner_coord, wave, dwave, flux, err, slice_no, \
                     rois_pixel, roiw_pixel, weight_pixel, \
-                    softrad_pixel, scalerad_pixel = pixelresult
+                    softrad_pixel, scalerad_pixel, _, _ = pixelresult
 
                 build_cube = True
                 if wave is None:  # there is no valid data on the detector. Pixels are flagged as DO_NOT_USE.
@@ -870,6 +870,9 @@ def build_ifucube_single(self):
                     linear = 0
                     if self.linear_wavelength:
                         linear = 1
+                        x_det = None
+                        y_det = None
+                        debug_cube = -1
                     result = cube_wrapper_driz(instrument, flag_dq_plane,
                                                start_region, end_region,
                                                self.overlap_partial, self.overlap_full,
@@ -878,7 +881,8 @@ def build_ifucube_single(self):
                                                xi1, eta1, xi2, eta2, xi3, eta3, xi4, eta4,
                                                dwave,
                                                self.cdelt3_normal,
-                                               self.cdelt1, self.cdelt2, cdelt3_mean, linear)
+                                               self.cdelt1, self.cdelt2, cdelt3_mean, linear,
+                                               x_det, y_det, debug_cube)
 
                     spaxel_flux, spaxel_weight, spaxel_var, spaxel_iflux, _ = result
                     self.spaxel_flux = self.spaxel_flux + np.asarray(spaxel_flux, np.float64)

jwst/mrs_imatch/mrs_imatch_step.py

@@ -9,7 +9,6 @@
 import numpy as np
 
 from jwst.datamodels import ModelContainer
-
 from .. stpipe import Step
 from wiimatch.match import match_lsq
 from astropy.stats import sigma_clipped_stats as sigclip
@@ -29,16 +28,18 @@ class MRSIMatchStep(Step):
         # General sky matching parameters:
         bkg_degree = integer(min=0, default=1) # Degree of the polynomial for background fitting
         subtract = boolean(default=False) # subtract computed sky from 'images' cube data?
-
+        skip = boolean(default=True) # Step must be turned on by parameter reference or user
     """
 
     reference_file_types = []
 
     def process(self, images):
-        all_models2d = ModelContainer(images)
 
-        chm = {}
+        # Provide warning to user this code is deprecated
+        self.log.warning('mrs_imatch is deprecated')
 
+        chm = {}
+        all_models2d = ModelContainer(images)
         for m in all_models2d:
             ch = m.meta.instrument.channel
             if ch not in chm:

jwst/mrs_imatch/tests/test_configuration.py

@@ -70,9 +70,22 @@ def test_imatch_background_subtracted(tmp_cwd, miri_dither_ch12):
     # test if background subtracted - raise error
     with pytest.raises(ValueError):
         step = MRSIMatchStep()
-        step.run(new_container)
+        step.call(new_container, skip=False)
 
 
+def test_imatch_default_run(tmp_cwd, miri_dither_ch12):
+    """ Test mrs_imatch test is skipped by default """
+
+    all_models = ModelContainer(miri_dither_ch12)
+
+    # test if default running results in skipping step
+    step = MRSIMatchStep()
+    results = step.call(all_models)
+    n = len(all_models)
+    for i  in range(n):
+        assert results[i].meta.cal_step.mrs_imatch =='SKIPPED'
+
+
 def test_imatch_background_reset(tmp_cwd, miri_dither_ch12):
     """ Test if background polynomial is already determined - reset it"""