Fix logging message in NIRSpec assign_wcs

and turn all invalid interval warning into error

Capture log and emit different message
and catch RuntimeWarning

Author: pllim

jwst/assign_wcs/nirspec.py

@@ -5,9 +5,10 @@
 """
 
 import logging
-import numpy as np
 import copy
+import warnings
 
+import numpy as np
 from astropy.modeling import models
 from astropy.modeling.models import Mapping, Identity, Const1D, Scale, Tabular1D
 from astropy import units as u
@@ -2211,7 +2212,9 @@ def _get_y_range(open_slits):
             transform, wavelength_range, slit_ymin=slit_y_low, slit_ymax=slit_y_high
         )
 
-    slit_wcs.bounding_box = bb
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", category=RuntimeWarning, message="Invalid interval")
+        slit_wcs.bounding_box = bb
     return slit_wcs
 
 

jwst/msaflagopen/msaflag_open.py

@@ -1,16 +1,16 @@
 """Flag pixels affected by open MSA shutters in NIRSpec exposures."""
 
 import json
-import numpy as np
 import logging
+import warnings
 from pathlib import Path
 
+import numpy as np
 from gwcs.wcs import WCS
-
 from stdatamodels.jwst import datamodels
 from stdatamodels.jwst.transforms.models import Slit
 
-from ..assign_wcs.nirspec import slitlets_wcs, _nrs_wcs_set_input_lite, _get_transforms
+from jwst.assign_wcs.nirspec import slitlets_wcs, _nrs_wcs_set_input_lite, _get_transforms
 
 log = logging.getLogger(__name__)
 log.setLevel(logging.DEBUG)
@@ -43,9 +43,12 @@ def do_correction(input_model, shutter_refname, wcs_refnames):
     """
     # Create a list of failed open slitlets from the msaoper reference file
     failed_slitlets = create_slitlets(shutter_refname)
+    log.info("%d failed open shutters", len(failed_slitlets))
 
     # Flag the stuck open shutters
-    output_model = flag(input_model, failed_slitlets, wcs_refnames)
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", category=RuntimeWarning, message="Invalid interval")
+        output_model = flag(input_model, failed_slitlets, wcs_refnames)
     output_model.meta.cal_step.msa_flagging = "COMPLETE"
 
     return output_model

jwst/msaflagopen/msaflagopen_step.py

@@ -1,9 +1,12 @@
-from stdatamodels.jwst import datamodels
+import logging
 
+from stdatamodels.jwst import datamodels
 from stpipe.crds_client import reference_uri_to_cache_path
 
 from jwst.stpipe import Step
 from jwst.assign_wcs import AssignWcsStep
+from jwst.assign_wcs.nirspec import log as nirspec_log
+from jwst.lib.basic_utils import LoggingContext
 from jwst.msaflagopen import msaflag_open
 
 __all__ = ["MSAFlagOpenStep"]
@@ -50,7 +53,10 @@ def process(self, input_data):
             wcs_reffile_names = create_reference_filename_dictionary(input_model)
 
             # Do the DQ flagging
-            result = msaflag_open.do_correction(input_model, self.reference_name, wcs_reffile_names)
+            with LoggingContext(nirspec_log, level=logging.WARNING):
+                result = msaflag_open.do_correction(
+                    input_model, self.reference_name, wcs_reffile_names
+                )
 
             # set the step status to complete
             result.meta.cal_step.msa_flagging = "COMPLETE"

pyproject.toml

@@ -239,6 +239,7 @@ filterwarnings = [
     "error::ResourceWarning",
     "error::DeprecationWarning",
     "error::stdatamodels.exceptions.ValidationWarning",
+    "error:Invalid interval",
     "ignore:Models in math_functions:astropy.utils.exceptions.AstropyUserWarning",
 ]