extract1d for IFU data version 2- JP 1736

CHANGES.rst

@@ -56,6 +56,11 @@ datamodels
 
 extract_1d
 ----------
+- For IFU data (NIRSpec and MIRI) the extraction radius is now a varying size 
+  based on wavelength. The apcorr correction if a function of wavelength and
+  radius size. Fixes a bug in units conversion for applying the apcorr correction.
+  The units are now correctly converted from arcseconds to pixels. Added an
+  new method to apply the apcorr correction for IFU data. 
 
 - Fixed bug involving the determination of source RA/Dec for resampled Slit
   data. [#5353]

jwst/datamodels/__init__.py

@@ -9,7 +9,7 @@
 from .apcorr import NrcImgApcorrModel, NisImgApcorrModel
 from .apcorr import MirLrsApcorrModel, MirMrsApcorrModel
 from .apcorr import NrcWfssApcorrModel, NisWfssApcorrModel
-from .apcorr import NrsMosApcorrModel, NrsFsApcorrModel
+from .apcorr import NrsMosApcorrModel, NrsIfuApcorrModel, NrsFsApcorrModel
 from .asn import AsnModel
 from .barshadow import BarshadowModel
 from .combinedspec import CombinedSpecModel
@@ -21,6 +21,7 @@
 from .drizpars import DrizParsModel
 from .drizproduct import DrizProductModel
 from .extract1dimage import Extract1dImageModel
+from .extract1d_spec import IFUExtract1dModel
 from .flat import FlatModel
 from .fringe import FringeModel
 from .gain import GainModel
@@ -90,7 +91,7 @@
     'AmiLgModel',
     'FgsImgApcorrModel', 'MirImgApcorrModel', 'NrcImgApcorrModel', 'NisImgApcorrModel',
     'MirLrsApcorrModel', 'MirMrsApcorrModel', 'NrcWfssApcorrModel', 'NisWfssApcorrModel',
-    'NrsMosApcorrModel', 'NrsFsApcorrModel',
+    'NrsMosApcorrModel', 'NrsFsApcorrModel','NrsIfuApcorrModel',
     'AsnModel',
     'BarshadowModel', 'CameraModel', 'CollimatorModel',
     'CombinedSpecModel', 'ContrastModel', 'CubeModel',
@@ -99,6 +100,7 @@
     'DrizParsModel',
     'DrizProductModel',
     'Extract1dImageModel',
+    'IFUExtract1dModel',
     'FilteroffsetModel',
     'FlatModel', 'NirspecFlatModel', 'NirspecQuadFlatModel',
     'FOREModel', 'FPAModel',

jwst/datamodels/apcorr.py

@@ -4,7 +4,7 @@
            'NrcImgApcorrModel', 'NisImgApcorrModel',
            'MirLrsApcorrModel', 'MirMrsApcorrModel',
            'NrcWfssApcorrModel', 'NisWfssApcorrModel',
-           'NrsMosApcorrModel', 'NrsFsApcorrModel']
+           'NrsMosApcorrModel', 'NrsIfuApcorrModel','NrsFsApcorrModel']
 
 
 class FgsImgApcorrModel(ReferenceFileModel):
@@ -90,14 +90,9 @@ class MirMrsApcorrModel(ReferenceFileModel):
         factors associated with those modes.
 
         - wavelength: float32 1D array
-        - nelem_wl: int16
-        - radius: float32 1D array
-        - apcorr: float32 1D array
-        - apcorr_err: float32 1D array
-        - inner_bkg: float32 1D array
-        - outer_bkg: float32 1D array
-        - axis_ratio: float32 1D array
-        - axis_pa: float32 1D array
+        - radius: float32 2D array
+        - apcorr: float32 2D array
+        - apcorr_err: float32 2D array
 
     """
     schema_url = "http://stsci.edu/schemas/jwst_datamodel/mirmrs_apcorr.schema"
@@ -203,7 +198,7 @@ class NisWfssApcorrModel(ReferenceFileModel):
 
 class NrsMosApcorrModel(ReferenceFileModel):
     """
-    A data model for NIRSpec MOS and IFU apcorr reference files.
+    A data model for NIRSpec MOS apcorr reference files.
 
     Parameters
     __________
@@ -227,6 +222,29 @@ class NrsMosApcorrModel(ReferenceFileModel):
     schema_url = "http://stsci.edu/schemas/jwst_datamodel/nrsmos_apcorr.schema"
 
 
+class NrsIfuApcorrModel(ReferenceFileModel):
+    """
+    A data model for NIRSpec IFU apcorr reference files.
+
+    Parameters
+    __________
+    apcorr_table : numpy table
+        Aperture correction factors table
+        A table-like object containing row selection criteria made up
+        of instrument mode parameters and aperture correction
+        factors associated with those modes.
+
+        - filter: str[12]
+        - grating: str[15]
+        - wavelength: float32 1D array
+        - radius: float32 3D array
+        - apcorr: float32 3D array
+        - apcorr_err: float32 3D array
+
+    """
+    schema_url = "http://stsci.edu/schemas/jwst_datamodel/nrsifu_apcorr.schema"
+
+
 class NrsFsApcorrModel(ReferenceFileModel):
     """
     A data model for NIRSpec Fixed-Slit apcorr reference files.

jwst/datamodels/extract1d_spec.py

@@ -0,0 +1,30 @@
+from .reference import ReferenceFileModel
+
+__all__ = ['IFUExtract1dModel']
+
+
+class IFUExtract1dModel(ReferenceFileModel):
+    """
+    A data model for IFU MIRI and NIRSpec extract 1d reference files.
+
+    Parameters
+    __________
+    extract1d_params : numpy table
+        Basic extract 1D parameters
+        - region_type: ascii
+        - subtract_background: bool
+        - method: ascii
+        - subpixels: int16
+    extract1d_table : numpy table
+        extract1d parameters for varying wavelengths
+        A table-like object containing extract 1d parameters
+        based on wavelength
+        - wavelength: float32 1D array
+        - radius: float32 1D array
+        - inner_bkg: float32 1D array
+        - outer_bkg: float32 1D array
+        - axis_ratio: float32 1D array
+        - axis_pa: float32 1D array
+
+    """
+    schema_url = "http://stsci.edu/schemas/jwst_datamodel/ifuextract1d.schema"

jwst/datamodels/schemas/ifuextract1d.schema.yaml

@@ -0,0 +1,48 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/asdf/asdf-schema-1.0.0"
+id: "http://stsci.edu/schemas/jwst_datamodel/ifuextract1d.schema"
+title: Default IFU Data extract 1d data model
+allOf:
+- $ref: referencefile.schema
+- $ref: keyword_exptype.schema
+- $ref: keyword_pexptype.schema
+- type: object
+  properties:
+    meta:
+      type: object
+      properties:
+        region_type:
+          type: string
+        subtract_background:
+          type: boolean
+        method:
+          type: string
+        subpixels:
+          type: integer
+  properties:
+    data:
+      type: object
+      properties:
+        wavelength:
+          datatype: float32
+        wavelength_units:
+          type: string
+        radius:
+          datatype: float32
+        radius_units:
+          type: string
+        inner_bkg:
+          datatype: float32
+        inner_bkg_units:
+          type: string
+        outer_bkg:
+          datatype: float32
+        outer_bkg_units:
+          type: string
+        axis_ratio:
+          datatype: float32
+        axis_pa:
+          datatype: float32
+        axis_pa_units:
+          type: string

jwst/datamodels/schemas/mirmrs_apcorr.schema.yaml

@@ -1,6 +1,6 @@
 %YAML 1.1
 ---
-$schema: "http://stsci.edu/schemas/fits-schema/fits-schema"
+$schema: "http://stsci.edu/schemas/asdf/asdf-schema-1.0.0"
 id: "http://stsci.edu/schemas/jwst_datamodel/mirmrs_apcorr.schema"
 title: MIRI MRS aperture correction data model
 allOf:
@@ -10,36 +10,21 @@ allOf:
 - type: object
   properties:
     apcorr_table:
-      title: Aperture correction factors table
-      fits_hdu: APCORR
-      datatype:
-      - name: wavelength
-        datatype: float32
-        ndim: 1
-      - name: nelem_wl
-        datatype: int16
-      - name: radius
-        datatype: float32
-        ndim: 1
-      - name: apcorr
-        datatype: float32
-        ndim: 1
-      - name: apcorr_err
-        datatype: float32
-        ndim: 1
-      - name: inner_bkg
-        datatype: float32
-        ndim: 1
-      - name: outer_bkg
-        datatype: float32
-        ndim: 1
-      - name: axis_ratio
-        datatype: float32
-        ndim: 1
-      - name: axis_pa
-        datatype: float32
-        ndim: 1
-    sizeunit:
-      title: Units for the SIZE or RADIUS column in the APCORR table
-      fits_hdu: APCORR
-      fits_keyword: SIZEUNIT
+      type: object
+      properties:
+          channel:
+            type: string
+          band:
+            type: string
+          wavelength:
+            datatype: float32
+          wavelength_units:
+            type: string
+          radius:
+            datatype: float32
+          radius_units: 
+            type: string
+          apcorr:
+            datatype: float32
+          apcorr_err:
+            datatype: float32

jwst/datamodels/schemas/mirmrs_extract1d.schema.yaml

@@ -0,0 +1,41 @@
+%YAML 1.1
+---
+$schema: "http://stsci.edu/schemas/fits-schema/fits-schema"
+id: "http://stsci.edu/schemas/jwst_datamodel/mirmrs_extract1d.schema"
+title: Default MIRI MRS extract 1d data model
+allOf:
+- $ref: referencefile.schema
+- type: object
+  properties:
+    extract1d_params:
+      title: default MIRI extract 1d parameters
+      fits_hdu: PARAMS
+      datatype:
+      - name: id
+        datatype: [ascii,10]
+      - name: region_type
+        datatype: [ascii,10]
+      - name: subtract_background
+        datatype: uint8
+      - name: method
+        datatype: [ascii,10]
+      - name: subpixels
+        datatype: int16
+    extract1d_table:
+      title: wavelength varying extraction parameters
+      fits_hdu: X1D
+      datatype:
+      - name: wavelength
+        datatype: float32
+      - name: nelem_wl
+        datatype: int16
+      - name: radius
+        datatype: float32
+      - name: inner_bkg
+        datatype: float32
+      - name: outer_bkg
+        datatype: float32
+      - name: axis_ratio
+        datatype: float32
+      - name: axis_pa
+        datatype: float32