JP-2013 NIRSpec leakcal and nodded exposures

CHANGES.rst

@@ -6,6 +6,17 @@ documentation
 
 - Remove references to pub server [#7421]
 
+calwebb_spec2
+-------------
+
+- Subtract leakcal image from science and backgrounds and then background subtract [#7426]
+
+imprint
+-------
+
+- Add matching leakcal image and science/background image by using dither.position_number [#7426]
+
+
 1.9.1 (2023-01-03)
 ==================
 

docs/jwst/imprint/description.rst

@@ -9,8 +9,8 @@ MOS and IFU exposures by the MSA structure. This is accomplished by
 subtracting a dedicated exposure taken with all MSA shutters closed and the
 IFU entrance aperture blocked.
 
-The step has two input parameters: the target exposure and the imprint
-exposure. These arguments can be provided as either a file name
+The step has two input parameters: the target exposure and a list of imprint
+exposures.  These arguments can be provided as either a file name
 or a JWST data model.
 
 The SCI data array of the imprint exposure is subtracted from the SCI array

docs/jwst/pipeline/calwebb_spec2.rst

@@ -47,10 +47,10 @@ TSO exposures. The instrument mode abbreviations used in the table are as follow
 +==========================================================+=====+=====+=====+=====+=====+=====+======+======+========+=====+
 | :ref:`assign_wcs <assign_wcs_step>`                      | |c| | |c| | |c| | |c| | |c| | |c| |  |c| | |c|  |  |c|   | |c| |
 +----------------------------------------------------------+-----+-----+-----+-----+-----+-----+------+------+--------+-----+
-| :ref:`background <background_step>`                      | |c| | |c| | |c| | |c| |     | |c| |  |c| | |c|  |  |c|   |     |
-+----------------------------------------------------------+-----+-----+-----+-----+-----+-----+------+------+--------+-----+
 | :ref:`imprint <imprint_step>`                            |     | |c| | |c| |     |     |     |      |      |        |     |
 +----------------------------------------------------------+-----+-----+-----+-----+-----+-----+------+------+--------+-----+
+| :ref:`background <background_step>`                      | |c| | |c| | |c| | |c| |     | |c| |  |c| | |c|  |  |c|   |     |
++----------------------------------------------------------+-----+-----+-----+-----+-----+-----+------+------+--------+-----+
 | :ref:`msaflagopen <msaflagopen_step>`                    |     | |c| | |c| |     |     |     |      |      |        |     |
 +----------------------------------------------------------+-----+-----+-----+-----+-----+-----+------+------+--------+-----+
 | :ref:`extract_2d <extract_2d_step>`\ :sup:`1`            | |c| | |c| |     |     |     |     |      | |c|  |  |c|   | |c| |
@@ -172,10 +172,10 @@ abbreviations used in the table are as follows:
 +=======================================+============+==============+=================+==============+
 | :ref:`assign_wcs <assign_wcs_step>`   |   ALL      |     ALL      |       ALL       |       ALL    |
 +---------------------------------------+------------+--------------+-----------------+--------------+
-| :ref:`background <background_step>`   |  NONE      |    NONE      |      NONE       |      NONE    |
-+---------------------------------------+------------+--------------+-----------------+--------------+
 | :ref:`imprint <imprint_step>`         |  NONE      |     IFU      |      NONE       |      NONE    |
 +---------------------------------------+------------+--------------+-----------------+--------------+
+| :ref:`background <background_step>`   |  NONE      |    NONE      |      NONE       |      NONE    |
++---------------------------------------+------------+--------------+-----------------+--------------+
 | :ref:`msaflagopen <msaflagopen_step>` |  MOS, IFU  |   MOS, IFU   |    MOS, IFU     |       MOS    |
 +---------------------------------------+------------+--------------+-----------------+--------------+
 | :ref:`extract_2d <extract_2d_step>`   |  MOS, FS   |   MOS, FS    |    MOS, FS      |       MOS    |

jwst/imprint/imprint_step.py

@@ -18,17 +18,43 @@ class ImprintStep(Step):
 
     def process(self, input, imprint):
 
-        # Open the input data model
-        with datamodels.open(input) as input_model:
-
-            # Open the imprint exposure data model
-            imprint_model = datamodels.open(imprint)
-
-            # Do the imprint exposure subtraction
+        # subtract leakcal (imprint) image
+        # If there is only one imprint image is in the association use for all the data.
+        # If there is more than one imprint image  in the association then select
+        # the imprint  image to subtract based on position number (DataModel.meta.dither.position_number).
+
+        # Open the input data model and get position number of image
+        input_model = datamodels.open(input)
+        pos_no = input_model.meta.dither.position_number
+
+        # find imprint that goes with input image - if there is only 1 imprint image - use it.
+        num_imprint = len(imprint)
+        match = None
+        if num_imprint == 1:
+            match = 0
+        else:
+            i = 0
+            while match is None and i < num_imprint:
+                # open imprint images and read in pos_no to find match
+                imprint_model = datamodels.open(imprint[i])
+                imprint_pos_no = imprint_model.meta.dither.position_number
+                imprint_model.close()
+
+                if pos_no == imprint_pos_no:
+                    match = i
+                i = i + 1
+
+        # Initialize result to be input (just in case no matching imprint image was found)
+        result = input_model.copy()
+
+        if match is not None:
+            imprint_model = datamodels.open(imprint[match])
             result = subtract_images.subtract(input_model, imprint_model)
 
             # Update the step status and close the imprint model
             result.meta.cal_step.imprint = 'COMPLETE'
+            input_model.close()
             imprint_model.close()
-
+        else:
+            self.log.info(f'No imprint image was found for {input}')
         return result

jwst/imprint/tests/test_imprint.py

@@ -12,7 +12,9 @@ def test_step(make_imagemodel):
     """Assert that the results should be all zeros.
     """
     im = make_imagemodel(10, 10)
-    result = ImprintStep.call(im, im)
+    imprint = []
+    imprint.append(im)
+    result = ImprintStep.call(im, imprint)
 
     assert result.meta.cal_step.imprint == 'COMPLETE'
     assert result.data.sum() == 0

jwst/pipeline/calwebb_spec2.py

@@ -209,7 +209,8 @@ def process_exposure_product(
 
             # Decide on what steps can actually be accomplished based on the
             # provided input.
-            self._step_verification(exp_type, members_by_type, multi_int)
+
+            self._step_verification(exp_type, science, members_by_type, multi_int)
 
             # Start processing the individual steps.
             # `assign_wcs` is the critical step. Without it, processing
@@ -237,8 +238,21 @@ def process_exposure_product(
                         raise RuntimeError('Cannot determine WCS.')
 
         # Steps whose order is the same for all types of input.
-        calibrated = self.bkg_subtract(calibrated, members_by_type['background'])
+
+        # Leakcal subtraction (imprint)  occurs before background subtraction on a per-exposure basis.
+        # If there is only one `imprint` member, this imprint exposure is subtracted from all the
+        # science and background exposures.  Otherwise, there will be as many `imprint` members as
+        # there are science plus background members.
+
         calibrated = self.imprint_subtract(calibrated, members_by_type['imprint'])
+
+        # for each background image subtract an associated leak cal
+        for i, bkg_file in enumerate(members_by_type['background']):
+            bkg_imprint_sub = self.imprint_subtract(bkg_file, members_by_type['imprint'])
+            members_by_type['background'][i] = bkg_imprint_sub
+
+        calibrated = self.bkg_subtract(calibrated, members_by_type['background'])
+
         calibrated = self.msa_flagging(calibrated)
 
         # The order of the next few steps is tricky, depending on mode:
@@ -320,7 +334,7 @@ def process_exposure_product(
 
         return calibrated
 
-    def _step_verification(self, exp_type, members_by_type, multi_int):
+    def _step_verification(self, exp_type, input, members_by_type, multi_int):
         """Verify whether requested steps can operate on the given data
 
         Though ideally this would all be controlled through the pipeline
@@ -350,14 +364,15 @@ def _step_verification(self, exp_type, members_by_type, multi_int):
                 self.log.debug('Science data does not allow direct background subtraction. Skipping "bkg_subtract".')
                 self.bkg_subtract.skip = True
 
-        # Check for imprint subtraction
+        # Check for imprint subtraction. If we have a background then we could have an imprint image associated with the
+        # background.
         imprint = members_by_type['imprint']
         if not self.imprint_subtract.skip:
             if len(imprint) > 0 and (exp_type in ['NRS_MSASPEC', 'NRS_IFU']
                                      or is_nrs_ifu_flatlamp(input)):
-                if len(imprint) > 1:
+                if len(imprint) > 1 and (exp_type in ['NRS_MSASPEC'] or is_nrs_ifu_flatlamp(input)):
                     self.log.warning('Wrong number of imprint members')
-                members_by_type['imprint'] = imprint[0]
+                    members_by_type['imprint'] = imprint[0]
             else:
                 self.log.debug('Science data does not allow imprint processing. Skipping "imprint_subtraction".')
                 self.imprint_subtract.skip = True