JP-3858-srctype

.pre-commit-config.yaml

@@ -63,7 +63,6 @@ repos:
             jwst/saturation/.* |
             jwst/scripts/.* |
             jwst/spectral_leak/.* |
-            jwst/srctype/.* |
             jwst/straylight/.* |
             jwst/superbias/.* |
             jwst/tests/.* |

.ruff.toml

@@ -45,7 +45,6 @@ exclude = [
     "jwst/saturation/**.py",
     "jwst/scripts/**.py",
     "jwst/spectral_leak/**.py",
-    "jwst/srctype/**.py",
     "jwst/straylight/**.py",
     "jwst/superbias/**.py",
     "jwst/tso_photometry/**.py",
@@ -145,7 +144,6 @@ ignore-fully-untyped = true  # Turn off annotation checking for fully untyped co
 "jwst/saturation/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/scripts/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/spectral_leak/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
-"jwst/srctype/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/straylight/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/superbias/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/tso_photometry/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]

jwst/srctype/__init__.py

@@ -1,3 +1,5 @@
+"""Determine if a spectroscopic source should be considered to be a point or extended object."""
+
 from .srctype_step import SourceTypeStep
 
-__all__ = ['SourceTypeStep']
+__all__ = ["SourceTypeStep"]

jwst/srctype/srctype.py

@@ -9,8 +9,7 @@
 
 def set_source_type(input_model, source_type=None):
     """
-    Set source_type based on APT input, user specification, exposure type,
-    or default values.
+    Set source_type based on APT input, user specification, exposure type, or default values.
 
     Parameters
     ----------
@@ -29,24 +28,29 @@
                   or `~jwst.datamodels.SlitModel`
         The updated model.
     """
-
     # Get the exposure type of the input model
     exptype = input_model.meta.exposure.type
     if exptype is None:
-        log.error('EXP_TYPE value not found in input')
-        raise RuntimeError('Step cannot be executed without an EXP_TYPE value')
+        log.error("EXP_TYPE value not found in input")
+        raise RuntimeError("Step cannot be executed without an EXP_TYPE value")
     else:
-        log.info(f'Input EXP_TYPE is {exptype}')
+        log.info(f"Input EXP_TYPE is {exptype}")
     # For exposure types that have a single source specification, get the
     # user-supplied source type from the selection they provided in the APT
-    if exptype in ['MIR_LRS-FIXEDSLIT', 'MIR_LRS-SLITLESS', 'MIR_MRS',
-                   'NRC_TSGRISM', 'NIS_SOSS', 'NRS_FIXEDSLIT',
-                   'NRS_BRIGHTOBJ', 'NRS_IFU']:
-
+    if exptype in [
+        "MIR_LRS-FIXEDSLIT",
+        "MIR_LRS-SLITLESS",
+        "MIR_MRS",
+        "NRC_TSGRISM",
+        "NIS_SOSS",
+        "NRS_FIXEDSLIT",
+        "NRS_BRIGHTOBJ",
+        "NRS_IFU",
+    ]:
         # Get info about the exposure, including whether it's a background
         # target and the dither pattern type
         bkg_target = input_model.meta.observation.bkgdtarg
-        if exptype == 'MIR_MRS':
+        if exptype == "MIR_MRS":
             patttype = input_model.meta.dither.optimized_for
         else:
             patttype = input_model.meta.dither.primary_type
@@ -59,13 +63,13 @@
         # SRCTYPE as both input and output (as before).
         try:
             user_type = input_model.meta.target.source_type_apt
-            log.info(f'Input SRCTYAPT = {user_type}')
+            log.info(f"Input SRCTYAPT = {user_type}")
             if user_type is None:
-                log.warning('SRCTYAPT keyword not found in input; using SRCTYPE instead')
+                log.warning("SRCTYAPT keyword not found in input; using SRCTYPE instead")
                 user_type = input_model.meta.target.source_type
                 input_model.meta.target.source_type_apt = user_type
         except AttributeError:
-            log.warning('SRCTYAPT keyword not found in input; using SRCTYPE instead')
+            log.warning("SRCTYAPT keyword not found in input; using SRCTYPE instead")
             user_type = input_model.meta.target.source_type
             input_model.meta.target.source_type_apt = user_type
 
@@ -74,49 +78,49 @@
             source_type = str(source_type).upper()
 
             # Check if the exposure type is a mode that allows setting
-            if exptype in ['MIR_LRS-FIXEDSLIT', 'MIR_LRS-SLITLESS',
-                           'MIR_MRS', 'NRC_TSGRISM', 'NRS_FIXEDSLIT',
-                           'NRS_BRIGHTOBJ', 'NRS_IFU']:
-
+            if exptype in [
+                "MIR_LRS-FIXEDSLIT",
+                "MIR_LRS-SLITLESS",
+                "MIR_MRS",
+                "NRC_TSGRISM",
+                "NRS_FIXEDSLIT",
+                "NRS_BRIGHTOBJ",
+                "NRS_IFU",
+            ]:
                 src_type = source_type
 
-            log.warning(f'Based on user-input, setting SRCTYPE = {src_type}')
+            log.warning(f"Based on user-input, setting SRCTYPE = {src_type}")
             input_model.meta.target.source_type = src_type
 
         elif bkg_target:
-
             # If this image is flagged as a BACKGROUND target, set the
             # source type to EXTENDED regardless of any other settings
-            src_type = 'EXTENDED'
-            log.info(f'Exposure is a background target; setting SRCTYPE = {src_type}')
+            src_type = "EXTENDED"
+            log.info(f"Exposure is a background target; setting SRCTYPE = {src_type}")
 
         elif pipe_utils.is_tso(input_model):
-
             # Treat all TSO exposures as a point source
-            src_type = 'POINT'
-            log.info(f'Input is a TSO exposure; setting SRCTYPE = {src_type}')
-
-        elif user_type in ['POINT', 'EXTENDED']:
+            src_type = "POINT"
+            log.info(f"Input is a TSO exposure; setting SRCTYPE = {src_type}")
 
+        elif user_type in ["POINT", "EXTENDED"]:
             # Use the value supplied by the user
             src_type = user_type
-            log.info(f'Using input source type = {src_type}')
-
-        elif (patttype is not None) and (('NOD' in patttype) or ('POINT-SOURCE' in patttype)):
+            log.info(f"Using input source type = {src_type}")
 
+        elif (patttype is not None) and (("NOD" in patttype) or ("POINT-SOURCE" in patttype)):
             # Set all nodded exposures to POINT source type
-            src_type = 'POINT'
-            log.info(f'Exposure is nodded; setting SRCTYPE = {src_type}')
+            src_type = "POINT"
+            log.info(f"Exposure is nodded; setting SRCTYPE = {src_type}")
 
         else:
-
             # Set a default value based on the exposure type
-            if exptype in ['MIR_MRS', 'NRS_IFU']:
-                src_type = 'EXTENDED'
+            if exptype in ["MIR_MRS", "NRS_IFU"]:
+                src_type = "EXTENDED"
             else:
-                src_type = 'POINT'
+                src_type = "POINT"
 
-            log.info(f'Input source type is unknown; setting default SRCTYPE = {src_type}')
+            log.info(f"Input source type is unknown; setting default SRCTYPE = {src_type}")
 
         # Set the source type in the global meta attribute
         input_model.meta.target.source_type = src_type
@@ -126,31 +130,29 @@
         if isinstance(input_model, datamodels.SlitModel):
             input_model.source_type = src_type
 
-        elif input_model.meta.exposure.type == 'NRS_FIXEDSLIT':
-
+        elif input_model.meta.exposure.type == "NRS_FIXEDSLIT":
             # NIRSpec fixed-slit is a special case: Apply the source type
             # determined above to only the primary slit (the one in which
             # the target is located). Set all other slits to the default
             # value, which for NRS_FIXEDSLIT is 'EXTENDED'.
-            default_type = 'EXTENDED'
+            default_type = "EXTENDED"
             primary_slit = input_model.meta.instrument.fixed_slit
-            log.debug(f' primary_slit = {primary_slit}')
+            log.debug(f" primary_slit = {primary_slit}")
             for slit in input_model.slits:
                 if slit.name == primary_slit:
                     slit.source_type = src_type
                     # Ensure x,y position reset to zero if source type is EXTENDED
-                    if src_type == 'EXTENDED':
+                    if src_type == "EXTENDED":
                         slit.source_xpos = 0.0
                         slit.source_ypos = 0.0
                 else:
                     slit.source_type = default_type
-                log.debug(f' slit {slit.name} = {slit.source_type}')
+                log.debug(f" slit {slit.name} = {slit.source_type}")
 
     # For NIRSpec MSA exposures, read the stellarity value for the
     # source in each extracted slit and set the point/extended value
     # based on the stellarity.
-    elif exptype == 'NRS_MSASPEC':
-
+    elif exptype == "NRS_MSASPEC":
         # Loop over the input slits
         for slit in input_model.slits:
             stellarity = slit.stellarity
@@ -159,38 +161,40 @@
             # a threshold value from a reference file. For now, the
             # threshold is hardwired.
             if stellarity < 0.0:
-                slit.source_type = 'POINT'
+                slit.source_type = "POINT"
             elif stellarity > 0.75:
-                slit.source_type = 'POINT'
+                slit.source_type = "POINT"
             else:
-                slit.source_type = 'EXTENDED'
+                slit.source_type = "EXTENDED"
 
-            log.info(f'source_id={slit.source_id}, stellarity={stellarity:.4f}, type={slit.source_type}')
+            log.info(
+                f"source_id={slit.source_id}, stellarity={stellarity:.4f}, type={slit.source_type}"
+            )
 
         # Remove the global target source type, so that it never mistakenly
         # gets used for MOS data, which should always use slit-specific values
         input_model.meta.target.source_type = None
 
     # Set all TSO exposures to POINT
     elif pipe_utils.is_tso(input_model):
-        src_type = 'POINT'
-        log.info(f'Input is a TSO exposure; setting default SRCTYPE = {src_type}')
+        src_type = "POINT"
+        log.info(f"Input is a TSO exposure; setting default SRCTYPE = {src_type}")
         input_model.meta.target.source_type = src_type
 
     # For WFSS modes check slit values of is_extended to set SRCTYPE
-    elif exptype in ['NIS_WFSS', 'NRC_WFSS']:
+    elif exptype in ["NIS_WFSS", "NRC_WFSS"]:
         for slit in input_model.slits:
             if slit.is_extended:
-                slit.source_type = 'EXTENDED'
+                slit.source_type = "EXTENDED"
             else:
-                slit.source_type = 'POINT'
-            log.info(f'source_id={slit.source_id}, type={slit.source_type}')
+                slit.source_type = "POINT"
+            log.info(f"source_id={slit.source_id}, type={slit.source_type}")
 
     # Unrecognized exposure type; set to UNKNOWN as default
     else:
-        log.warning(f'EXP_TYPE {exptype} not applicable to this operation')
-        src_type = 'UNKNOWN'
-        log.warning(f'Setting SRCTYPE = {src_type}')
+        log.warning(f"EXP_TYPE {exptype} not applicable to this operation")
+        src_type = "UNKNOWN"
+        log.warning(f"Setting SRCTYPE = {src_type}")
         input_model.meta.target.source_type = src_type
 
     # We're done

jwst/srctype/srctype_step.py

@@ -9,7 +9,8 @@
 
 class SourceTypeStep(Step):
     """
-    SourceTypeStep: Selects and sets a source type based on various inputs.
+    Select and sets a source type based on various inputs.
+
     The source type is used in later calibrations to determine the appropriate
     methods to use. Input comes from either the SRCTYAPT keyword value, which
     is populated from user info in the APT, or the NIRSpec MSA planning tool.
@@ -21,25 +22,37 @@
 
     spec = """
         source_type = option('POINT','EXTENDED', default=None)  # user-supplied source type
-    """ # noqa: E501
+    """
+
+    def process(self, step_input):
+        """
+        Determine the source type.
 
-    def process(self, input):
+        Parameters
+        ----------
+        step_input : str, IFUImageModel, MultiSlitModel, or SlitModel
+            Either the path to the file or the science data model to be corrected.
 
+        Returns
+        -------
+        datamodel : IFUImageModel, MultiSlitModel, or SlitModel
+            Data model with keyword “SRCTYPE” populated with either “POINT” or “EXTENDED”.
+        """
         if self.source_type is not None:
             self.source_type = self.source_type.upper()
 
         source_type = self.source_type  # retrieve command line override
 
-        input_model = datamodels.open(input)
+        input_model = datamodels.open(step_input)
 
         # Call the source selection routine
         result = set_source_type(input_model, source_type)
 
         # Set the step status in the output model
         if result is None:
             result = input_model
-            result.meta.cal_step.srctype = 'SKIPPED'
+            result.meta.cal_step.srctype = "SKIPPED"
         else:
-            result.meta.cal_step.srctype = 'COMPLETE'
+            result.meta.cal_step.srctype = "COMPLETE"
 
         return result