moved update_s_region_ out of jwst, altered step flow logic

jwst/assign_wcs/assign_wcs.py

@@ -1,7 +1,8 @@
 import logging
 import importlib
 from gwcs.wcs import WCS
-from .util import (update_s_region_spectral, update_s_region_imaging,
+from stcal.alignment.util import update_s_region_imaging
+from .util import (update_s_region_spectral,
                    update_s_region_nrs_ifu, update_s_region_mrs)
 from ..lib.exposure_types import IMAGING_TYPES, SPEC_TYPES, NRS_LAMP_MODE_SPEC_TYPES
 from ..lib.dispaxis import get_dispersion_direction

jwst/assign_wcs/util.py

@@ -17,6 +17,7 @@
 from gwcs.wcstools import grid_from_bounding_box
 from gwcs import utils as gwutils
 from stpipe.exceptions import StpipeExitException
+from stcal.alignment.util import update_s_region_keyword
 
 from stdatamodels.jwst.datamodels import WavelengthrangeModel
 from stdatamodels.jwst.transforms.models import GrismObject
@@ -789,32 +790,6 @@ def bounding_box_from_subarray(input_model):
     return bbox
 
 
-def update_s_region_imaging(model):
-    """
-    Update the ``S_REGION`` keyword using ``WCS.footprint``.
-    """
-
-    bbox = model.meta.wcs.bounding_box
-
-    if bbox is None:
-        bbox = wcs_bbox_from_shape(model.data.shape)
-        model.meta.wcs.bounding_box = bbox
-
-    # footprint is an array of shape (2, 4) as we
-    # are interested only in the footprint on the sky
-    footprint = model.meta.wcs.footprint(bbox, center=True, axis_type="spatial").T
-    # take only imaging footprint
-    footprint = footprint[:2, :]
-
-    # Make sure RA values are all positive
-    negative_ind = footprint[0] < 0
-    if negative_ind.any():
-        footprint[0][negative_ind] = 360 + footprint[0][negative_ind]
-
-    footprint = footprint.T
-    update_s_region_keyword(model, footprint)
-
-
 def compute_footprint_spectral(model):
     """
     Determine spatial footprint for spectral observations using the instrument model.
@@ -888,23 +863,6 @@ def update_s_region_nrs_slit(slit):
     slit.meta.wcsinfo.spectral_region = spectral_region
 
 
-def update_s_region_keyword(model, footprint):
-    """ Update the S_REGION keyword.
-    """
-    s_region = (
-        "POLYGON ICRS "
-        " {0:.9f} {1:.9f}"
-        " {2:.9f} {3:.9f}"
-        " {4:.9f} {5:.9f}"
-        " {6:.9f} {7:.9f}".format(*footprint.flatten()))
-    if "nan" in s_region:
-        # do not update s_region if there are NaNs.
-        log.info("There are NaNs in s_region, S_REGION not updated.")
-    else:
-        model.meta.wcsinfo.s_region = s_region
-        log.info("Update S_REGION to {}".format(model.meta.wcsinfo.s_region))
-
-
 def compute_footprint_nrs_ifu(dmodel, mod):
     """
     Determine NIRSPEC IFU footprint using the instrument model.

jwst/cube_build/cube_build_step.py

@@ -7,7 +7,7 @@
 from . import cube_build
 from . import ifu_cube
 from . import data_types
-from ..assign_wcs.util import update_s_region_keyword
+from stcal.alignment.util import update_s_region_keyword
 import time
 
 __all__ = ["CubeBuildStep"]

jwst/lib/set_telescope_pointing.py

@@ -72,11 +72,12 @@
 from scipy.interpolate import interp1d
 
 from stdatamodels.jwst import datamodels
+from stcal.alignment.util import update_s_region_keyword
 
 from .exposure_types import IMAGING_TYPES, FGS_GUIDE_EXP_TYPES
 from .set_velocity_aberration import compute_va_effects_vector
 from .siafdb import SIAF, SiafDb
-from ..assign_wcs.util import update_s_region_keyword, calc_rotation_matrix
+from ..assign_wcs.util import calc_rotation_matrix
 from ..assign_wcs.pointing import v23tosky
 from ..lib.engdb_tools import ENGDB_Service
 from ..lib.pipe_utils import is_tso

jwst/resample/resample_step.py

@@ -11,6 +11,7 @@
 from . import resample
 from ..stpipe import Step
 from ..assign_wcs import util
+from stcal.alignment.util import update_s_region_imaging
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -94,7 +95,7 @@ def process(self, input):
         for model in result:
             model.meta.cal_step.resample = 'COMPLETE'
             self.update_fits_wcs(model)
-            util.update_s_region_imaging(model)
+            update_s_region_imaging(model)
             model.meta.asn.pool_name = input_models.asn_pool_name
             model.meta.asn.table_name = input_models.asn_table_name
 

jwst/tweakreg/tests/test_multichip_jwst.py

@@ -14,6 +14,7 @@
 
 from tweakwcs.correctors import JWSTWCSCorrector
 from tweakwcs.imalign import align_wcs
+from tweakwcs import imalign
 
 from stdatamodels.jwst.datamodels import ImageModel
 
@@ -224,7 +225,7 @@ def test_multichip_jwst_alignment(monkeypatch):
     # 2. test_multichip_alignment_step() does not have access to 'fit_info'
     #    in the meta data and so test_multichip_jwst_alignment() can test
     #    the fit more extensively.
-    monkeypatch.setattr(tweakreg_step, 'align_wcs', _align_wcs)
+    monkeypatch.setattr(imalign, 'align_wcs', _align_wcs)
     monkeypatch.setattr(tweakreg_step, 'make_tweakreg_catalog', _make_tweakreg_catalog)
 
     w1 = _make_gwcs_wcs(os.path.join(data_path, 'wfc3_uvis1.hdr'))
@@ -294,7 +295,7 @@ def test_multichip_jwst_alignment(monkeypatch):
 
 
 def test_multichip_alignment_step(monkeypatch):
-    monkeypatch.setattr(tweakreg_step, 'align_wcs', _align_wcs)
+    monkeypatch.setattr(imalign, 'align_wcs', _align_wcs)
     monkeypatch.setattr(tweakreg_step, 'make_tweakreg_catalog', _make_tweakreg_catalog)
 
     # image 1
@@ -404,6 +405,8 @@ def test_multichip_alignment_step(monkeypatch):
     # step._is_wcs_correction_small = lambda x, y: True
 
     mr, m1, m2 = step.process(mc)
+    for im in [mr, m1, m2]:
+        assert im.meta.cal_step.tweakreg == 'COMPLETE'
 
     wc1 = m1.meta.wcs
     wc2 = m2.meta.wcs
@@ -422,7 +425,7 @@ def test_multichip_alignment_step(monkeypatch):
 
 
 def test_multichip_alignment_step_abs(monkeypatch):
-    monkeypatch.setattr(tweakreg_step, 'align_wcs', _align_wcs)
+    monkeypatch.setattr(imalign, 'align_wcs', _align_wcs)
     monkeypatch.setattr(tweakreg_step, 'make_tweakreg_catalog', _make_tweakreg_catalog)
 
     refcat_path = os.path.join(data_path, 'ref.ecsv')

jwst/tweakreg/tweakreg_step.py

@@ -249,10 +249,10 @@ def process(self, input):
 
         # wrapper to stcal tweakreg routines
         # step skip conditions should throw TweakregError from stcal
-        try:
+        if n_groups > 1:
+            try:
             # relative alignment of images to each other (if more than one group)
-            if n_groups > 1:
-                correctors, local_align_failed = \
+                correctors = \
                     twk.relative_align(correctors,
                                        enforce_user_order=self.enforce_user_order,
                                        expand_refcat=self.expand_refcat,
@@ -265,14 +265,19 @@ def process(self, input):
                                        separation=self.separation,
                                        tolerance=self.tolerance,
                                        xoffset=self.xoffset,
-                                       yoffset=self.yoffset,
-                                       align_to_abs_refcat=align_to_abs_refcat)
-            else:
+                                       yoffset=self.yoffset,)
+            except twk.TweakregError as e:
+                self.log.warning(str(e))
                 local_align_failed = True
+            else:
+                local_align_failed = False
+        else:
+            local_align_failed = True
 
-            # absolute alignment to the reference catalog
-            # can (and does) occur after alignment between groups
-            if align_to_abs_refcat:
+        # absolute alignment to the reference catalog
+        # can (and does) occur after alignment between groups
+        if align_to_abs_refcat:
+            try:
                 correctors = \
                     twk.absolute_align(correctors, self.abs_refcat, images[0],
                                        abs_minobj=self.abs_minobj,
@@ -285,20 +290,23 @@ def process(self, input):
                                        abs_tolerance=self.abs_tolerance,
                                        save_abs_catalog=self.save_abs_catalog,
                                        abs_catalog_output_dir=self.output_dir,
-                                       local_align_failed=local_align_failed,
                                             )
 
-            # one final pass through all the models to update them based
-            # on the results of this step
-            self._apply_tweakreg_solution(images, correctors,
-                                        align_to_abs_refcat=align_to_abs_refcat)
+            except twk.TweakregError as e:
+                self.log.warning(str(e))
+                for model in images:
+                    model.meta.cal_step.tweakreg = "SKIPPED"
+                return images 
 
-        except twk.TweakregError as e:
-            self.log.error(str(e))
+        if local_align_failed and not align_to_abs_refcat:    
             for model in images:
                 model.meta.cal_step.tweakreg = "SKIPPED"
             return images
 
+        # one final pass through all the models to update them based
+        # on the results of this step
+        self._apply_tweakreg_solution(images, correctors,
+                                    align_to_abs_refcat=align_to_abs_refcat)
         return images