ami3 pipeline and ami average docs updates

docs/jwst/ami_average/description.rst

@@ -3,6 +3,15 @@ Description
 
 :Class: `jwst.ami.AmiAverageStep`
 :Alias: ami_average
+
+.. Attention:: 
+	The ``ami_average`` step has been removed from the default ami3 pipeline
+	until the effects of averaging multiple exposures has been more thoroughly examined.
+	It may be updated in the future; until then the legacy code is left in place. It
+	does not use the OIFITS-format (`~jwst.datamodels.AmiOIModel`) input that the current 
+	``ami_analayze`` step produces. It uses the deprecated `~jwst.datamodels.AmiLgModel`
+	for both input and output.
+
 
 The ``ami_average`` step is one of the AMI-specific steps in the ``ami``
 sub-package and is part of Stage 3 :ref:`calwebb_ami3 <calwebb_ami3>` processing.

docs/jwst/pipeline/calwebb_ami3.rst

@@ -17,8 +17,6 @@ The steps applied by the ``calwebb_ami3`` pipeline are shown below.
 +==========================================+
 | :ref:`ami_analyze <ami_analyze_step>`    |
 +------------------------------------------+
-| :ref:`ami_average <ami_average_step>`    |
-+------------------------------------------+
 | :ref:`ami_normalize <ami_normalize_step>`|
 +------------------------------------------+
 
@@ -27,37 +25,28 @@ exposures, the pipeline will:
 
  - apply the :ref:`ami_analyze <ami_analyze_step>` step to each input exposure
    independently, computing fringe parameters for each
- - apply the :ref:`ami_average <ami_average_step>` step to compute the average of the
-   :ref:`ami_analyze <ami_analyze_step>` results for all of the science target exposures,
-   and the average for all of the reference PSF results (if present)
- - apply the :ref:`ami_normalize <ami_normalize_step>` step to correct the average science
-   target results using the average reference PSF results (if present)
+ - apply the :ref:`ami_normalize <ami_normalize_step>` step to correct the science
+   target results using the reference PSF results (if present)
 
 If no reference PSF target exposures are present in the input ASN file, the ``ami_normalize``
 step is skipped.
 
 Arguments
 ---------
-The ``calwebb_ami3`` pipeline has one optional argument::
-
-  --save_averages  boolean  default=False
-
-If set to ``True``, the results of the :ref:`ami_average <ami_average_step>` step will be saved
-to a file. If not, the results of the :ref:`ami_average <ami_average_step>` step are passed
-along in memory to the :ref:`ami_normalize <ami_normalize_step>` step.
+The ``calwebb_ami3`` pipeline does not currently use any optional arguments.
 
 Inputs
 ------
 
-2D calibrated images
+3D calibrated images
 ^^^^^^^^^^^^^^^^^^^^
 
-:Data model: `~jwst.datamodels.ImageModel`
-:File suffix: _cal
+:Data model: `~jwst.datamodels.DataModel`
+:File suffix: _calints
 
 The inputs to ``calwebb_ami3`` need to be in the form of an ASN file that lists
 multiple science target exposures, and optionally reference PSF exposures as well.
-The individual exposures must be in the form of calibrated ("_cal") products from
+The individual exposures must be in the form of 3D calibrated ("_calints") products from
 :ref:`calwebb_image2 <calwebb_image2>` processing.
 
 An example ASN file containing 2 science target and 2 reference PSF target exposures is
@@ -67,24 +56,18 @@ as indicated by the "exptype" values for each.
 ::
 
  {"asn_type": "ami3",
-  "asn_rule": "discover_Asn_AMI",
+  "asn_rule": DMS_Level3_Base",
   "program": "10005",
   "asn_id": "a3001",
   "target": "t001",
   "asn_pool": "jw10005_001_01_pool",
   "products": [
       {"name": "jw10005-a3001_t001_niriss_f277w-nrm",
        "members": [
-           {"expname": "jw10005007001_02102_00001_nis_cal.fits",
+           {"expname": "jw10005007001_02102_00001_nis_calints.fits",
             "exptype": "psf"
            },
-           {"expname": "jw10005027001_02102_00001_nis_cal.fits",
-            "exptype": "psf"
-           },
-           {"expname": "jw10005004001_02102_00001_nis_cal.fits",
-            "exptype": "science"
-           },
-           {"expname": "jw10005001001_02102_00001_nis_cal.fits",
+           {"expname": "jw10005004001_02102_00001_nis_calints.fits",
             "exptype": "science"
            }
        ]
@@ -95,41 +78,27 @@ as indicated by the "exptype" values for each.
 Outputs
 -------
 
-Fringe parameter tables
-^^^^^^^^^^^^^^^^^^^^^^^
+Interferometric observables
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+:Data model: `~jwst.datamodels.AmiOIModel`
+:File suffix: _ami.oifits
 
-:Data model: `~jwst.datamodels.AmiLgModel`
-:File suffix: _ami
 
 For every input exposure, the fringe parameters and closure phases calculated
-by the :ref:`ami_analyze <ami_analyze_step>` step are saved to an "_ami" product file, which
-is a FITS table containing the fringe parameters and closure phases. Product names
-use the input "_cal" exposure-based file name, with the association candidate ID
-included and the product type changed to "_ami", e.g.
-"jw93210001001_03101_00001_nis_a0003_ami.fits."
-
-Averaged fringe parameters table
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-:Data model: `~jwst.datamodels.AmiLgModel`
-:File suffix: _amiavg or _psf-amiavg
-
-If multiple target or reference PSF exposures are used as input and the
-"--save_averages" parameter is set to ``True``, the :ref:`ami_average <ami_average_step>` step
-will save averaged results for the target in an "_amiavg" product and for the
-reference PSF in a "_psf-amiavg" product. The file name root will use the
-source-based output product name given in the ASN file. These files are the
-same FITS table format as the "_ami" products.
-
-Normalized fringe parameters table
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-:Data model: `~jwst.datamodels.AmiLgModel`
-:File suffix: _aminorm
-
-If reference PSF exposures are included in the input ASN, the averaged AMI results
-for the target will be normalized by the averaged AMI results for the reference PSF,
-via the :ref:`ami_normalize <ami_normalize_step>` step, and will be saved to an "_aminorm"
-product file. This file has the same FITS table format as the "_ami" products.
+by the :ref:`ami_analyze <ami_analyze_step>` step are saved to "_ami.oifits" product file,
+which is a kind of FITS table of median observables over all integrations of the input file.
+Product names use the input "_calints" exposure-based file name, with the association candidate ID
+included and the product type changed to "_ami.oifits", e.g.
+"jw93210001001_03101_00001_nis_a0003_ami.oifits."
+
+Normalized Interferometric Observables
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+:Data model: `~jwst.datamodels.AmiOIModel`
+:File suffix: _aminorm.oifits
+
+If reference PSF exposures are included in the input ASN, the AMI results
+for the target will be normalized by the AMI results for the reference PSF,
+via the :ref:`ami_normalize <ami_normalize_step>` step, and will be saved to an "_aminorm.oifits"
+product file. This file has the same FITS table format as the "_ami.oifits" products.
 The file name root uses the source-based output product name given in the ASN file,
-e.g. "jw93210-a0003_t001_niriss_f480m-nrm_aminorm.fits."
+e.g. "jw93210-a0003_t001_niriss_f480m-nrm_aminorm.oifits."

jwst/pipeline/calwebb_ami3.py

@@ -22,15 +22,11 @@ class Ami3Pipeline(Pipeline):
     Ami3Pipeline: Apply all level-3 calibration steps to an
     association of level-2b AMI exposures. Included steps are:
     ami_analyze (fringe detection)
-    # ami_average (average results of fringe detection)
     ami_normalize (normalize results by reference target)
     """
 
     class_alias = "calwebb_ami3"
 
-    spec = """
-        save_averages = boolean(default=True)
-    """
 
     # Define aliases to steps
     step_defs = {'ami_analyze': ami_analyze_step.AmiAnalyzeStep,
@@ -120,8 +116,8 @@ def process(self, input):
                 # blendmeta.blendmodels(result, inputs=[targ, psf])
                 self.save_model(result, suffix='aminorm')
                 result.close()
-                del psf_lg
-                del targ_lg
+            del psf_lg
+            del targ_lg
 
 
         # We're done