JP-3858-superbias

.pre-commit-config.yaml

@@ -65,7 +65,6 @@ repos:
             jwst/spectral_leak/.* |
             jwst/srctype/.* |
             jwst/straylight/.* |
-            jwst/superbias/.* |
             jwst/tests/.* |
             jwst/tso_photometry/.* |
             jwst/wfs_combine/.* |

.ruff.toml

@@ -47,7 +47,6 @@ exclude = [
     "jwst/spectral_leak/**.py",
     "jwst/srctype/**.py",
     "jwst/straylight/**.py",
-    "jwst/superbias/**.py",
     "jwst/tso_photometry/**.py",
     "jwst/wfs_combine/**.py",
     "jwst/white_light/**.py",
@@ -147,7 +146,6 @@ ignore-fully-untyped = true  # Turn off annotation checking for fully untyped co
 "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/wfs_combine/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]
 "jwst/white_light/**.py" = ["D", "N", "A", "ARG", "B", "C4", "ICN", "INP", "ISC", "LOG", "NPY", "PGH", "PTH", "S", "SLF", "SLOT", "T20", "TRY", "UP", "YTT", "E501"]

jwst/superbias/__init__.py

@@ -1,3 +1,5 @@
+"""Subtract super-bias reference data from the input science data model."""
+
 from .superbias_step import SuperBiasStep
 
-__all__ = ['SuperBiasStep']
+__all__ = ["SuperBiasStep"]

jwst/superbias/bias_sub.py

@@ -1,6 +1,4 @@
-#
-#  Module for subtracting a super-bias image from science data sets
-#
+"""Module for subtracting a super-bias image from science data sets."""
 
 import numpy as np
 import logging
@@ -12,25 +10,20 @@
 
 def do_correction(input_model, bias_model):
     """
-    Short Summary
-    -------------
-    Execute all tasks for Super-Bias Subtraction
+    Execute all tasks for Super-Bias Subtraction.
 
     Parameters
     ----------
-    input_model: data model object
-        science data to be corrected
-
-    bias_model: super-bias model object
-        bias data
+    input_model : RampModel
+        Science data to be corrected
+    bias_model : SuperBiasModel
+        Bias data
 
     Returns
     -------
-    output_model: data model object
-        bias-subtracted science data
-
+    output_model : stdatamodels.jwst.datamodels.ramp.RampModel
+        Bias-subtracted science data
     """
-
     # Check for subarray mode and extract subarray from the
     # bias reference data if necessary
     if not reffile_utils.ref_matches_sci(input_model, bias_model):
@@ -42,33 +35,30 @@ def do_correction(input_model, bias_model):
     # Subtract the bias ref image from the science data
     output_model = subtract_bias(input_model, bias_model)
 
-    output_model.meta.cal_step.superbias = 'COMPLETE'
+    output_model.meta.cal_step.superbias = "COMPLETE"
 
     return output_model
 
 
 def subtract_bias(output, bias):
     """
-    Subtracts a superbias image from a science data set, subtracting the
-    superbias from each group of each integration in the science data.
+    Subtract the superbias image from each group of each integration in the science data.
+
     The DQ flags in the bias reference image are propagated into the science
-    data pixeldq array. The error array is unchanged.
+    data pixel DQ array. The error array is unchanged.
 
     Parameters
     ----------
-    output: data model object
-        the input science data
-
-    bias: superbias model object
-        the superbias image data
+    output : stdatamodels.jwst.datamodels.ramp.RampModel
+        Input science data
+    bias : stdatamodels.jwst.datamodels.superbias.SuperBiasModel
+        Superbias image data
 
     Returns
     -------
-    output: data model object
-        bias-subtracted science data
-
+    output : stdatamodels.jwst.datamodels.ramp.RampModel
+        Bias-subtracted science data
     """
-
     # combine the science and superbias DQ arrays
     output.pixeldq = np.bitwise_or(output.pixeldq, bias.dq)
 
@@ -81,8 +71,8 @@ def subtract_bias(output, bias):
     # If ZEROFRAME is present, subtract the super bias.  Zero values
     # indicate bad data, so should be kept zero.
     if output.meta.exposure.zero_frame:
-        wh_zero = np.where(output.zeroframe == 0.)
+        wh_zero = np.where(output.zeroframe == 0.0)
         output.zeroframe -= bias.data
-        output.zeroframe[wh_zero] = 0.  # Zero values indicate unusable data
+        output.zeroframe[wh_zero] = 0.0  # Zero values indicate unusable data
 
     return output

jwst/superbias/superbias_step.py

@@ -7,32 +7,40 @@
 
 
 class SuperBiasStep(Step):
-    """
-    SuperBiasStep: Performs super-bias subtraction by subtracting
-    super-bias reference data from the input science data model.
-    """
+    """Subtract super-bias reference data from the input science data model."""
 
     class_alias = "superbias"
 
     spec = """
-    """ # noqa: E501
+    """  # noqa: E501
 
-    reference_file_types = ['superbias']
+    reference_file_types = ["superbias"]
 
     def process(self, step_input):
-
+        """
+        Apply the superbias correction.
+
+        Parameters
+        ----------
+        step_input : str or stdatamodels.jwst.datamodels.ramp.RampModel
+            Either the path to the file or the science data model to be corrected.
+
+        Returns
+        -------
+        stdatamodels.jwst.datamodels.ramp.RampModel
+            Superbias-corrected science data model.
+        """
         # Open the input data model
         with datamodels.open(step_input) as input_model:
-
             # Get the name of the superbias reference file to use
-            self.bias_name = self.get_reference_file(input_model, 'superbias')
-            self.log.info('Using SUPERBIAS reference file %s', self.bias_name)
+            self.bias_name = self.get_reference_file(input_model, "superbias")
+            self.log.info("Using SUPERBIAS reference file %s", self.bias_name)
 
             # Check for a valid reference file
-            if self.bias_name == 'N/A':
-                self.log.warning('No SUPERBIAS reference file found')
-                self.log.warning('Superbias step will be skipped')
-                input_model.meta.cal_step.superbias = 'SKIPPED'
+            if self.bias_name == "N/A":
+                self.log.warning("No SUPERBIAS reference file found")
+                self.log.warning("Superbias step will be skipped")
+                input_model.meta.cal_step.superbias = "SKIPPED"
                 return input_model
 
             # Open the superbias ref file data model
@@ -43,7 +51,7 @@ def process(self, step_input):
 
             # Do the bias subtraction
             result = bias_sub.do_correction(result, bias_model)
-            result.meta.cal_step.superbias = 'COMPLETE'
+            result.meta.cal_step.superbias = "COMPLETE"
 
             # Cleanup
             del bias_model