JP-3790: MIRI MRS models to hold residual fringe correction (#377)

Co-authored-by: jemorrison <[email protected]>

changes/377.feature.rst

@@ -0,0 +1 @@
+Add new spectral models for MIRI MRS data, including new table columns for residual fringe corrected flux, surface brightness, and background.

src/stdatamodels/jwst/datamodels/__init__.py

@@ -40,7 +40,7 @@
 from .multiexposure import MultiExposureModel
 from .multiextract1d import MultiExtract1dImageModel
 from .multislit import MultiSlitModel
-from .multispec import MultiSpecModel
+from .multispec import MultiSpecModel, MRSMultiSpecModel
 from .nirspec_flat import NirspecFlatModel, NirspecQuadFlatModel
 from .nrm import NRMModel
 from .outlierpars import OutlierParsModel
@@ -69,7 +69,7 @@
 from .pastasossmodel import PastasossModel
 from .sossextractmodel import SossExtractModel
 from .sosswavegrid import SossWaveGridModel
-from .spec import SpecModel
+from .spec import SpecModel, MRSSpecModel
 from .speckernel import SpecKernelModel
 from .specprofile import SpecProfileModel, SpecProfileSingleModel
 from .specpsf import SpecPsfModel
@@ -123,7 +123,7 @@
     'LinearityModel', 'MaskModel', 'MSAModel',
     'MultiCombinedSpecModel', 'MultiExposureModel',
     'MultiExtract1dImageModel', 'MultiSlitModel',
-    'MultiSpecModel',
+    'MultiSpecModel', 'MRSMultiSpecModel',
     'NIRCAMGrismModel', 'NIRISSGrismModel',
     'OTEModel',
     'OutlierParsModel','OutlierIFUOutputModel',
@@ -142,7 +142,7 @@
     'ReferenceFileModel', 'ReferenceCubeModel', 'ReferenceImageModel', 'ReferenceQuadModel',
     'RegionsModel', 'ResetModel',
     'ResolutionModel', 'MiriResolutionModel',
-    'RSCDModel', 'SaturationModel', 'SIRSKernelModel', 'SlitDataModel', 'SlitModel', 'SpecModel',
+    'RSCDModel', 'SaturationModel', 'SIRSKernelModel', 'SlitDataModel', 'SlitModel', 'SpecModel','MRSSpecModel',
     'SegmentationMapModel',
     'SossExtractModel',
     'SossWaveGridModel',

src/stdatamodels/jwst/datamodels/multispec.py

@@ -1,8 +1,8 @@
 from .model_base import JwstDataModel
-from .spec import SpecModel
+from .spec import SpecModel, MRSSpecModel
 
 
-__all__ = ['MultiSpecModel']
+__all__ = ['MultiSpecModel', 'MRSMultiSpecModel']
 
 
 class MultiSpecModel(JwstDataModel):
@@ -57,3 +57,25 @@ def __init__(self, init=None, **kwargs):
             return
 
         super(MultiSpecModel, self).__init__(init=init, **kwargs)
+
+
+class MRSMultiSpecModel(JwstDataModel):
+    """
+    A data model for MIRI MRS multi-spec images.
+
+    This model has a special member `spec` that can be used to
+    deal with an entire spectrum at a time.  It behaves identically
+    to `MultiSpecModel`, except that the spectra have additional columns
+    for the MIRI MRS mode, containing residual fringe corrected values.
+    """
+    schema_url = "http://stsci.edu/schemas/jwst_datamodel/mrs_multispec.schema"
+
+    def __init__(self, init=None, **kwargs):
+
+        if isinstance(init, MRSSpecModel):
+            super(MRSMultiSpecModel, self).__init__(init=None, **kwargs)
+            self.spec.append(self.spec.item())
+            self.spec[0].spec_table = init.spec_table
+            return
+
+        super(MRSMultiSpecModel, self).__init__(init=init, **kwargs)

src/stdatamodels/jwst/datamodels/schemas/mrs_multispec.schema.yaml

@@ -0,0 +1,19 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/fits-schema/fits-schema"
+id: "http://stsci.edu/schemas/jwst_datamodel/mrs_multispec.schema"
+allOf:
+- $ref: core.schema
+- $ref: int_times.schema
+- type: object
+  properties:
+    spec:
+      type: array
+      title: An array of spectra
+      items:
+        allOf:
+          - type: object
+            properties:
+              spec_table:
+                $ref: mrs_spectable.schema
+          - $ref: specmeta.schema

src/stdatamodels/jwst/datamodels/schemas/mrs_spec.schema.yaml

@@ -0,0 +1,11 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/fits-schema/fits-schema"
+id: "http://stsci.edu/schemas/jwst_datamodel/mrs_spec.schema"
+title: Spectrum data model with residual fringe correction for MIRI MRS
+allOf:
+- $ref: core.schema
+- type: object
+  properties:
+    spec_table:
+      $ref: mrs_spectable.schema

src/stdatamodels/jwst/datamodels/schemas/mrs_spectable.schema.yaml

@@ -0,0 +1,49 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/fits-schema/fits-schema"
+id: "http://stsci.edu/schemas/jwst_datamodel/mrs_spectable.schema"
+title: Extracted spectral data table with residual fringe correction for MIRI MRS
+fits_hdu: EXTRACT1D
+datatype:
+- name: WAVELENGTH
+  datatype: float64
+- name: FLUX
+  datatype: float64
+- name: FLUX_ERROR
+  datatype: float64
+- name: FLUX_VAR_POISSON
+  datatype: float64
+- name: FLUX_VAR_RNOISE
+  datatype: float64
+- name: FLUX_VAR_FLAT
+  datatype: float64
+- name: SURF_BRIGHT
+  datatype: float64
+- name: SB_ERROR
+  datatype: float64
+- name: SB_VAR_POISSON
+  datatype: float64
+- name: SB_VAR_RNOISE
+  datatype: float64
+- name: SB_VAR_FLAT
+  datatype: float64
+- name: DQ
+  datatype: uint32
+- name: BACKGROUND
+  datatype: float64
+- name: BKGD_ERROR
+  datatype: float64
+- name: BKGD_VAR_POISSON
+  datatype: float64
+- name: BKGD_VAR_RNOISE
+  datatype: float64
+- name: BKGD_VAR_FLAT
+  datatype: float64
+- name: NPIXELS
+  datatype: float64
+- name: RF_FLUX
+  datatype: float64
+- name: RF_SURF_BRIGHT
+  datatype: float64
+- name: RF_BACKGROUND
+  datatype: float64

src/stdatamodels/jwst/datamodels/schemas/multispec.schema.yaml

@@ -11,172 +11,9 @@ allOf:
       type: array
       title: An array of spectra
       items:
-        type: object
-        properties:
-          spec_table:
-            $ref: spectable.schema
-          name:
-            title: Slit name
-            type: string
-            fits_keyword: SLTNAME
-            fits_hdu: EXTRACT1D
-          slitlet_id:
-            title: Slitlet ID
-            type: integer
-            default: 0
-            fits_keyword: SLITID
-            fits_hdu: EXTRACT1D
-          source_id:
-            title: Source ID number
-            type: integer
-            default: 0
-            fits_keyword: SOURCEID
-            fits_hdu: EXTRACT1D
-          source_name:
-            title: Source name
-            type: string
-            fits_keyword: SRCNAME
-            fits_hdu: EXTRACT1D
-          source_alias:
-            title: Source alias
-            type: string
-            fits_keyword: SRCALIAS
-            fits_hdu: EXTRACT1D
-          stellarity:
-            title: Source stellarity
-            type: number
-            fits_keyword: STLARITY
-            fits_hdu: EXTRACT1D
-          source_type:
-            title: Source type used for calibration
-            type: string
-            fits_keyword: SRCTYPE
-            fits_hdu: EXTRACT1D
-          source_xpos:
-            title: Source position in slit (x-axis)
-            type: number
-            default: 0.0
-            fits_keyword: SRCXPOS
-            fits_hdu: EXTRACT1D
-          source_ypos:
-            title: Source position in slit (y-axis)
-            type: number
-            default: 0.0
-            fits_keyword: SRCYPOS
-            fits_hdu: EXTRACT1D
-          source_ra:
-            title: Right Ascension of the source
-            type: number
-            fits_keyword: SRCRA
-            fits_hdu: EXTRACT1D
-          source_dec:
-            title: Declination of the source
-            type: number
-            fits_keyword: SRCDEC
-            fits_hdu: EXTRACT1D
-          extraction_x:
-            title: X center of extraction region
-            type: number
-            fits_keyword: EXTR_X
-            fits_hdu: EXTRACT1D
-          extraction_y:
-            title: Y center of extraction region
-            type: number
-            fits_keyword: EXTR_Y
-            fits_hdu: EXTRACT1D
-          extraction_xstart:
-            title: X axis start of extraction region
-            type: number
-            fits_keyword: EXTRXSTR
-            fits_hdu: EXTRACT1D
-          extraction_xstop:
-            title: X axis end of extraction region
-            type: number
-            fits_keyword: EXTRXSTP
-            fits_hdu: EXTRACT1D
-          extraction_ystart:
-            title: Y axis start of extraction region
-            type: number
-            fits_keyword: EXTRYSTR
-            fits_hdu: EXTRACT1D
-          extraction_ystop:
-            title: Y axis end of extraction region
-            type: number
-            fits_keyword: EXTRYSTP
-            fits_hdu: EXTRACT1D
-          shutter_state:
-            title: All (open and close) shutters in a slit
-            type: string
-            default: ""
-            fits_keyword: SHUTSTA
-            fits_hdu: EXTRACT1D
-          slit_ra:
-            title: "[deg] Right Ascension at middle of slit"
-            type: number
-            default: 0.0
-            fits_keyword: SLIT_RA
-            fits_hdu: EXTRACT1D
-          slit_dec:
-            title: "[deg] Declination at middle of slit"
-            type: number
-            default: 0.0
-            fits_keyword: SLIT_DEC
-            fits_hdu: EXTRACT1D
-          spectral_order:
-            title: Spectral order number
-            type: integer
-            default: 1
-            fits_keyword: SPORDER
-            fits_hdu: EXTRACT1D
-          dispersion_direction:
-            title: Dispersion direction
-            type: integer
-            fits_keyword: DISPAXIS
-            fits_hdu: EXTRACT1D
-          int_num:
-            title: Integration number
-            type: integer
-            fits_keyword: INT_NUM
-            fits_hdu: EXTRACT1D
-          time_sys:
-            title: "principal time system for time-related keywords"
-            type: string
-            default: "UTC"
-            fits_keyword: TIMESYS
-            fits_hdu: EXTRACT1D
-          time_unit:
-            title: Default unit applicable to all time values
-            type: string
-            default: 's'
-            fits_keyword: TIMEUNIT
-            fits_hdu: EXTRACT1D
-          start_time_mjd:
-            title: "[d] integration start time in MJD"
-            type: number
-            fits_keyword: MJD-BEG
-            fits_hdu: EXTRACT1D
-          mid_time_mjd:
-            title: "[d] integration mid-point in MJD"
-            type: number
-            fits_keyword: MJD-AVG
-            fits_hdu: EXTRACT1D
-          end_time_mjd:
-            title: "[d] integration end time in MJD"
-            type: number
-            fits_keyword: MJD-END
-            fits_hdu: EXTRACT1D
-          start_tdb:
-            title: "TDB at start of integration [MJD]"
-            type: number
-            fits_keyword: TDB-BEG
-            fits_hdu: EXTRACT1D
-          mid_tdb:
-            title: "TDB at middle of integration [MJD]"
-            type: number
-            fits_keyword: TDB-MID
-            fits_hdu: EXTRACT1D
-          end_tdb:
-            title: "TDB at end of integration [MJD]"
-            type: number
-            fits_keyword: TDB-END
-            fits_hdu: EXTRACT1D
+        allOf:
+          - type: object
+            properties:
+              spec_table:
+                $ref: spectable.schema
+          - $ref: specmeta.schema