JP-3695: Clean up unnecessary copies (#8676)

Co-authored-by: Tyler Pauly <[email protected]>

CHANGES.rst

@@ -63,6 +63,11 @@ calwebb_detector1
 - Added the optional ``clean_flicker_noise`` step between ``jump`` and
   ``ramp_fit``. [#8669]
 
+change_migration
+----------------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 clean_flicker_noise
 -------------------
 
@@ -91,6 +96,11 @@ datamodels
 - Added `ModelLibrary` class to allow passing on-disk models between steps in the
   image3 pipeline. [#8683]
 
+dark_current
+------------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 documentation
 -------------
 
@@ -99,12 +109,24 @@ documentation
 - Updated description of association keyword `expname`: including path information
   in addition to the filename is discouraged, but allowed. [#8789]
 
+dq_init
+--------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 emicorr
 -------
 
 - Fixed a bug where MIRI EMI correction step would return NaNs when it was unable
   to compute a correction. [#8675]
 
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+first_frame
+-----------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 flat_field
 ----------
 
@@ -113,6 +135,11 @@ flat_field
 
 - Replaced deep copies of NIRSpec WCS objects within most loops [#8793]
 
+gain_scale
+----------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 general
 -------
 
@@ -126,12 +153,37 @@ general
 
 - bump dependency to use ``stcal 1.9.0`` [#8808]
 
+group_scale
+-----------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+ipc
+---
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+jump
+----
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 klip
 ----
 
 - Allowed klip to ingest a single shifted 3-D PSF model instead of a 4-D structure
   containing one shifted PSF per science integration. [#8747]
 
+lastframe
+---------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+linearity
+---------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 master_background
 -----------------
 
@@ -196,6 +248,11 @@ pathloss
 
 - Replaced deep copies of NIRSpec WCS objects within most loops [#8793]
 
+persistence
+-----------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 photom
 ------
 
@@ -232,6 +289,18 @@ ramp_fitting
 - Updated the flow of the detector 1 pipeline when selecting the ``LIKELY`` algorithm
   for ramp fitting.  The ramps must contain a minimum number of groups (4).[#8631]
 
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+refpix
+------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
+regtest
+-------
+
+- Added memory usage test for Detector1 pipeline. [#8676]
+
 resample
 --------
 
@@ -245,6 +314,11 @@ resample
 - Ensure that NaNs and DO_NOT_USE flags match up in all input data before
   resampling. [#8557]
 
+reset
+-----
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 resample_spec
 -------------
 
@@ -269,12 +343,19 @@ resample_spec
 - Ensure that NaNs and DO_NOT_USE flags match up in all input data before
   resampling. [#8557]
 
+rscd
+----
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 saturation
 ----------
 
 - Add option for using the readout pattern information to improve saturation flagging
   in grouped data. [#8731]
-
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 scripts
 -------
 
@@ -301,6 +382,11 @@ stpipe
 
 - Log jwst version at end of `Step.run`. [#8769]
 
+superbias
+---------
+
+- Removed unnecessary copies, and created a single copy at step.py level. [#8676]
+
 tso_photometry
 --------------
 

docs/jwst/emicorr/arguments.rst

@@ -12,9 +12,6 @@ The ``emicorr`` step has the following step-specific arguments.
     If True, the reference wavelength will be scaled to the
     data's phase amplitude.
 
-``--user_supplied_reffile`` (boolean, default=None)
-    This is to specify an ASDF-format user-created reference file.
-
 ``--save_intermediate_results``  (string, default=False)
     This is a boolean flag to specify whether to write a step output
     file with the EMI correction, and a reference file with all the

jwst/charge_migration/charge_migration.py

@@ -16,13 +16,13 @@
 CHLO_DNU = CHLO + DNU
 
 
-def charge_migration(input_model, signal_threshold):
+def charge_migration(output_model, signal_threshold):
     """
     Correct for chargemigration
 
     Parameters
     ----------
-    input_model : `~jwst.datamodels.RampModel`
+    output_model : `~jwst.datamodels.RampModel`
         The input science data to be corrected
 
     signal_threshold : float
@@ -35,11 +35,8 @@ def charge_migration(input_model, signal_threshold):
 
         DO_NOT_USE flags to groups exceeding signal_threshold
     """
-    data = input_model.data
-    gdq = input_model.groupdq
-
-    # Create the output model as a copy of the input
-    output_model = input_model.copy()
+    data = output_model.data
+    gdq = output_model.groupdq
 
     log.info('Using signal_threshold: %.2f', signal_threshold)
 

jwst/charge_migration/charge_migration_step.py

@@ -1,9 +1,8 @@
 #! /usr/bin/env python
 import logging
 
-from ..stpipe import Step
-
 from stdatamodels.jwst import datamodels
+from ..stpipe import Step
 
 from . import charge_migration
 
@@ -25,22 +24,24 @@ class ChargeMigrationStep(Step):
         skip = boolean(default=True)
     """
 
-    def process(self, input):
+    def process(self, step_input):
 
         # Open the input data model
-        with datamodels.RampModel(input) as input_model:
+        with datamodels.RampModel(step_input) as input_model:
+
             if (input_model.data.shape[1] < 3):  # skip step if only 1 or 2 groups/integration
                 log.info('Too few groups per integration; skipping charge_migration')
-
-                result = input_model
-                result.meta.cal_step.charge_migration = 'SKIPPED'
 
-                return result
+                input_model.meta.cal_step.charge_migration = 'SKIPPED'
+                return input_model
+
+            # Work on a copy
+            result = input_model.copy()
 
             # Retrieve the parameter value(s)
             signal_threshold = self.signal_threshold
 
-            result = charge_migration.charge_migration(input_model, signal_threshold)
+            result = charge_migration.charge_migration(result, signal_threshold)
             result.meta.cal_step.charge_migration = 'COMPLETE'
 
         return result

jwst/dark_current/dark_current_step.py

@@ -23,10 +23,10 @@ class DarkCurrentStep(Step):
 
     reference_file_types = ['dark']
 
-    def process(self, input):
+    def process(self, step_input):
 
         # Open the input data model
-        with datamodels.RampModel(input) as input_model:
+        with datamodels.RampModel(step_input) as input_model:
 
             # Get the name of the dark reference file to use
             self.dark_name = self.get_reference_file(input_model, 'dark')
@@ -36,9 +36,11 @@ def process(self, input):
             if self.dark_name == 'N/A':
                 self.log.warning('No DARK reference file found')
                 self.log.warning('Dark current step will be skipped')
-                result = input_model.copy()
-                result.meta.cal_step.dark = 'SKIPPED'
-                return result
+                input_model.meta.cal_step.dark = 'SKIPPED'
+                return input_model
+
+            # Work on a copy
+            result = input_model.copy()
 
             # Create name for the intermediate dark, if desired.
             dark_output = self.dark_output
@@ -49,7 +51,7 @@ def process(self, input):
                 )
 
             # Open the dark ref file data model - based on Instrument
-            instrument = input_model.meta.instrument.name
+            instrument = result.meta.instrument.name
             if instrument == 'MIRI':
                 dark_model = datamodels.DarkMIRIModel(self.dark_name)
             else:
@@ -58,20 +60,23 @@ def process(self, input):
             # Store user-defined average_dark_current in model, if provided
             # A user-defined value will take precedence over any value present
             # in dark reference file
-            self.set_average_dark_current(input_model, dark_model)
+            self.set_average_dark_current(result, dark_model)
 
             # Do the dark correction
-            result = dark_sub.do_correction(
-                input_model, dark_model, dark_output
+            correction = dark_sub.do_correction(
+                result, dark_model, dark_output
             )
 
-            out_data, dark_data = result
+            out_data, dark_data = correction
 
             if dark_data is not None and dark_data.save:
                 save_dark_data_as_dark_model(dark_data, dark_model, instrument)
-            dark_model.close()
 
-            out_ramp = dark_output_data_2_ramp_model(out_data, input_model)
+            out_ramp = dark_output_data_2_ramp_model(out_data, result)
+
+            # Cleanup
+            del dark_model
+            del result
 
         return out_ramp
 
@@ -140,7 +145,7 @@ def save_dark_data_as_dark_model(dark_data, dark_model, instrument):
     out_dark_model.close()
 
 
-def dark_output_data_2_ramp_model(out_data, input_model):
+def dark_output_data_2_ramp_model(out_data, out_model):
     """
     Convert computed output data from the dark step to a RampModel.
 
@@ -149,7 +154,7 @@ def dark_output_data_2_ramp_model(out_data, input_model):
     out_data: ScienceData
         Computed science data from the dark current step.
 
-    input_model: RampModel
+    out_model: RampModel
         The input ramp model from which to subtract the dark current.
 
     Return
@@ -161,10 +166,9 @@ def dark_output_data_2_ramp_model(out_data, input_model):
     if out_data.cal_step == "SKIPPED":
         # If processing was skipped in the lower-level routines,
         # just return the unmodified input model
-        input_model.meta.cal_step.dark_sub = "SKIPPED"
-        return input_model
+        out_model.meta.cal_step.dark_sub = "SKIPPED"
+        return out_model
     else:
-        out_model = input_model.copy()
         out_model.meta.cal_step.dark_sub = out_data.cal_step
         out_model.data = out_data.data
         out_model.groupdq = out_data.groupdq