From 2bff4fe6017f0e247bfcbfa451121e187ad160a5 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Tue, 5 Nov 2024 16:57:38 -0500
Subject: [PATCH 01/23] f2f 0.8 m, print rotation search to log

---
 jwst/ami/ami_analyze.py      | 13 +++++++++----
 jwst/ami/mask_definitions.py |  2 +-
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/jwst/ami/ami_analyze.py b/jwst/ami/ami_analyze.py
index 631c780004..45379d594a 100644
--- a/jwst/ami/ami_analyze.py
+++ b/jwst/ami/ami_analyze.py
@@ -126,15 +126,17 @@ def apply_LG_plus(
     # Throughput (combined filter and source spectrum) calculated here
     bandpass = utils.handle_bandpass(bandpass, throughput_model)
 
-    rotsearch_d = np.append(
+    
+
+    if affine2d is None:
+        rotsearch_d = np.append(
         np.arange(
             rotsearch_parameters[0], rotsearch_parameters[1], rotsearch_parameters[2]
         ),
         rotsearch_parameters[1],
-    )
+        )
 
-    log.info(f"Initial values to use for rotation search: {rotsearch_d}")
-    if affine2d is None:
+        log.info(f"Initial values to use for rotation search: {rotsearch_d}")
         # affine2d object, can be overridden by user input affine.
         # do rotation search on uncropped median image (assuming rotation constant over exposure)
         # replace remaining NaNs in median image with median of surrounding 8 (non-NaN) pixels
@@ -173,6 +175,9 @@ def apply_LG_plus(
             oversample,
             holeshape,
         )
+        log.info(f'Found rotation: {affine2d.rotradccw:.4f} rad ({np.rad2deg(affine2d.rotradccw):.4f} deg)')
+        # the affine2d returned here has only rotation...
+        # to use rotation and scaling/shear, do some matrix multiplication here??
 
     niriss = instrument_data.NIRISS(filt,
                                     nrm_model,
diff --git a/jwst/ami/mask_definitions.py b/jwst/ami/mask_definitions.py
index edf6936531..d761f90c34 100755
--- a/jwst/ami/mask_definitions.py
+++ b/jwst/ami/mask_definitions.py
@@ -175,5 +175,5 @@ def jwst_g7s6c(chooseholes=None):
 
     """
 
-    f2f = 0.82 * m  # m flat to flat
+    f2f = 0.8 * m  # m flat to flat
     return f2f, jwst_g7s6_centers_asbuilt(chooseholes=chooseholes)

From f1a2bd9969594bb0cfbe1bcd72aebc0791800cfc Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Mon, 11 Nov 2024 10:27:02 -0500
Subject: [PATCH 02/23] option to use affine from commissioning by passing
 affine2d='commissioning'. Not yet default behavior.

---
 jwst/ami/ami_analyze_step.py | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/jwst/ami/ami_analyze_step.py b/jwst/ami/ami_analyze_step.py
index 3330e6aa25..2284ef9902 100755
--- a/jwst/ami/ami_analyze_step.py
+++ b/jwst/ami/ami_analyze_step.py
@@ -182,9 +182,17 @@ def process(self, input):
                 bandpass = self.override_bandpass()
 
             if affine2d is not None:
-                # if it is None, handled in apply_LG_plus
-                affine2d = self.override_affine2d()
-
+                if affine2d == 'commissioning':
+                    affine2d = utils.Affine2d(mx= 9.92820e-01,
+                        my=9.98540e-01,
+                        sx=6.18605e-03,
+                        sy=-7.27008e-03,
+                        xo=0,
+                        yo=0,
+                        name='commisioning')
+                else:
+                    affine2d = self.override_affine2d()
+            # and if it is None, rotation search done in apply_LG_plus
 
             # Get the name of the NRM reference file to use
             nrm_reffile = self.get_reference_file(input_model, 'nrm')

From 2027c36f71ff86657c10f7bf4507e2f7bf33d59d Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Mon, 18 Nov 2024 11:26:06 -0500
Subject: [PATCH 03/23] Mask definitions read in from NRM reference file in
 place of hardcoded values in mask_definitions.py. Removed references to other
 NRMs.

---
 jwst/ami/mask_definition_ami.py | 130 ++++++++++++++++++++++++++++++++
 1 file changed, 130 insertions(+)
 create mode 100644 jwst/ami/mask_definition_ami.py

diff --git a/jwst/ami/mask_definition_ami.py b/jwst/ami/mask_definition_ami.py
new file mode 100644
index 0000000000..d4986537ae
--- /dev/null
+++ b/jwst/ami/mask_definition_ami.py
@@ -0,0 +1,130 @@
+#
+#  Module for defining mask geometry in pupil space
+#  Replace old mask_definitions by reading info in nrm_model into a similar object.
+#
+
+import numpy as np
+import math
+
+from .utils import rotate2dccw
+
+m = 1.0
+mm = 1.0e-3 * m
+um = 1.0e-6 * m
+
+
+class NRM_definitions():
+
+    def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None):
+        """
+        Set attributes of NRM_mask_definitions class.
+
+        Parameters
+        ----------
+        nrm_model: NRMModel
+        	datamodel containing NRM reference file data
+        
+        rotdeg: list of floats
+            range of rotations to search (degrees)
+
+        chooseholes: list
+            None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
+
+        Returns
+        -------
+        None
+        """
+        if maskname not in ['jwst_ami','jwst_g7s6c']:
+        	raise ValueError("Mask name not supported")
+
+        self.maskname = maskname # there's only one mask but this is used in oifits
+
+        self.read_nrm_model(nrm_model, chooseholes=chooseholes)
+
+        if rotdeg is not None:
+            self.rotdeg = rotdeg
+
+    def read_nrm_model(self, nrm_model, chooseholes=None):
+    	"""
+
+	    Calculate hole centers with appropriate rotation,
+	    set these and other mask geometry details from NRMModel as
+	    attributes.
+
+	    Parameters
+	    ----------
+	    nrm_model: NRMModel
+        	datamodel containing NRM reference file data 
+	    chooseholes: list
+	        None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
+
+	    Returns
+	    -------
+	    f2f: float
+	        flat-to-flat distance of mask holes
+	    ctrs_asbuilt: array
+	        Actual hole centers [meters]
+	    """
+
+    	ctrs_asdesigned = [[nrm_model.x_a1, nrm_model.y_a1],        # B4 -> B4
+		    				[nrm_model.x_a2, nrm_model.y_a2],       # C5 -> C2
+						    [nrm_model.x_a3, nrm_model.y_a3],       # B3 -> B5
+						    [nrm_model.x_a4, nrm_model.y_a4],       # B6 -> B2
+						    [nrm_model.x_a5, nrm_model.y_a5],       # C6 -> C1
+						   	[nrm_model.x_a6, nrm_model.y_a6],        # B2 -> B6
+						    [nrm_model.x_a7, nrm_model.y_a7]]        # C1 -> C6
+
+		self.hdia = nrm_model.flat_to_flat
+		self.activeD = nrm_model.diameter
+		self.OD = nrm_model.pupil_circumscribed
+
+    	holedict = {}  # as_built names, C2 open, C5 closed, but as designed coordinates
+	    # Assemble holes by actual open segment names (as_built).  Either the full mask or the
+	    # subset-of-holes mask will be V2-reversed after the as_designed centers are defined
+	    # Debug orientations with b4,c6,[c2]
+	    allholes = ('b4', 'c2', 'b5', 'b2', 'c1', 'b6', 'c6')
+
+	    for hole, coords in zip(allholes,ctrs_asdesigned):
+	    	holedict[hole] = coords
+
+	    if chooseholes:  # holes B4 B5 C6 asbuilt for orientation testing
+	        holelist = []
+	        for h in allholes:
+	            if h in chooseholes:
+	                holelist.append(holedict[h])
+	        ctrs_asdesigned = np.array(holelist)
+
+	    ctrs_asbuilt = ctrs_asdesigned.copy()
+
+	    # create 'live' hole centers in an ideal, orthogonal undistorted xy pupil space,
+	    # eg maps open hole C5 in as_designed to C2 as_built, eg C4 unaffected....
+	    ctrs_asbuilt[:, 0] *= -1
+
+	    # LG++ rotate hole centers by 90 deg to match MAST o/p DMS PSF with
+	    # no affine2d transformations 8/2018 AS
+	    # LG++ The above aligns the hole pattern with the hex analytic FT,
+	    # flat top & bottom as seen in DMS data. 8/2018 AS
+	    ctrs_asbuilt = rotate2dccw(ctrs_asbuilt, np.pi / 2.0)  # overwrites attributes
+
+	    # create 'live' hole centers in an ideal, orthogonal undistorted xy pupil space,
+	    self.ctrs = ctrs_asbuilt
+
+    def showmask(self):
+        """
+        Calculate the diameter of the smallest centered circle (D)
+        enclosing the live mask area
+
+        Parameters
+        ----------
+
+        Returns
+        -------
+        Diameter of the smallest centered circle
+
+        """
+        radii = []
+        for ctr in self.ctrs:
+            radii.append(math.sqrt(ctr[0] * ctr[0] + ctr[1] * ctr[1]))
+
+        return 2.0 * (max(radii) + 0.5 * self.hdia)
+

From fff610400ba11d45ed822b2f6555bfec554c904e Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Mon, 18 Nov 2024 15:34:54 -0500
Subject: [PATCH 04/23] use updated mask_definition_ami

---
 jwst/ami/instrument_data.py     | 11 +++++------
 jwst/ami/lg_model.py            | 23 ++++++++++-------------
 jwst/ami/mask_definition_ami.py |  4 ++--
 3 files changed, 17 insertions(+), 21 deletions(-)

diff --git a/jwst/ami/instrument_data.py b/jwst/ami/instrument_data.py
index 26d4f73d08..d5ef938cfd 100755
--- a/jwst/ami/instrument_data.py
+++ b/jwst/ami/instrument_data.py
@@ -6,7 +6,7 @@
 import logging
 import numpy as np
 
-from .mask_definitions import NRM_mask_definitions
+from .mask_definition_ami import NRM_definition
 from . import utils
 from . import bp_fix
 from stdatamodels.jwst.datamodels import dqflags
@@ -91,12 +91,11 @@ def __init__(self,
         # only one NRM on JWST:
         self.telname = "JWST"
         self.instrument = "NIRISS"
-        self.arrname = "jwst_g7s6c"
-        self.holeshape = "hex"
-        self.mask = NRM_mask_definitions(
+        self.arrname = "jwst_ami"
+        self.mask = NRM_definition(
+            nrm_model,
             maskname=self.arrname,
-            chooseholes=self.chooseholes,
-            holeshape=self.holeshape,
+            chooseholes=self.chooseholes
         )
 
         # save affine deformation of pupil object or create a no-deformation object.
diff --git a/jwst/ami/lg_model.py b/jwst/ami/lg_model.py
index 2981baaa8a..44d94a6194 100755
--- a/jwst/ami/lg_model.py
+++ b/jwst/ami/lg_model.py
@@ -6,7 +6,7 @@
 from . import leastsqnrm as leastsqnrm
 from . import analyticnrm2
 from . import utils
-from . import mask_definitions
+from . import mask_definition_ami
 
 log = logging.getLogger(__name__)
 log.addHandler(logging.NullHandler())
@@ -22,7 +22,7 @@
 class NrmModel:
     """
     A class for conveniently dealing with an "NRM object" This should be able
-    to take an NRM_mask_definitions object for mask geometry.
+    to take an NRM_definition object for mask geometry.
     Defines mask geometry and detector-scale parameters.
     Simulates PSF (broadband or monochromatic)
     Builds a fringe model - either by user definition, or automated to data
@@ -35,7 +35,7 @@ class NrmModel:
     def __init__(
         self,
         mask=None,
-        holeshape="circ",
+        holeshape="hex",
         pixscale=None,
         over=1,
         pixweight=None,
@@ -91,19 +91,16 @@ def __init__(
         self.over = over
         self.pixweight = pixweight
 
-        # mask = "jwst"
-        # self.maskname = mask
-
-        # get these from mask_definitions instead
+        # get these from mask_definition_ami instead
         if mask is None:
-            log.info("No mask name specified for model, using jwst_g7s6c")
-            mask = mask_definitions.NRM_mask_definitions(
-                maskname="jwst_g7s6c", chooseholes=chooseholes, holeshape="hex"
+            log.info("Using JWST AMI mask geometry from NrmModel")
+            mask = mask_definition_ami.NRM_definition(
+                maskname="jwst_ami", chooseholes=chooseholes
             )
         elif isinstance(mask, str):
-            mask = mask_definitions.NRM_mask_definitions(
-                maskname=mask, chooseholes=chooseholes, holeshape="hex"
-            )
+            mask = mask_definition_ami.NRM_definition(
+                maskname=mask, chooseholes=chooseholes
+            ) # retain ability to possibly  use other named masks, for now
         self.ctrs = mask.ctrs
         self.d = mask.hdia
         self.D = mask.activeD
diff --git a/jwst/ami/mask_definition_ami.py b/jwst/ami/mask_definition_ami.py
index d4986537ae..3a4b8c14fb 100644
--- a/jwst/ami/mask_definition_ami.py
+++ b/jwst/ami/mask_definition_ami.py
@@ -13,11 +13,11 @@
 um = 1.0e-6 * m
 
 
-class NRM_definitions():
+class NRM_definition():
 
     def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None):
         """
-        Set attributes of NRM_mask_definitions class.
+        Set attributes of NRM_definition class.
 
         Parameters
         ----------

From 5a3fd3e6bcc0098406b940abe2150411a1f3edb0 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Mon, 18 Nov 2024 16:02:37 -0500
Subject: [PATCH 05/23] Keep holeshape for model, converted spaces to tabs

---
 jwst/ami/instrument_data.py     |   1 +
 jwst/ami/mask_definition_ami.py | 192 ++++++++++++++++----------------
 2 files changed, 97 insertions(+), 96 deletions(-)

diff --git a/jwst/ami/instrument_data.py b/jwst/ami/instrument_data.py
index d5ef938cfd..08d30bdc6e 100755
--- a/jwst/ami/instrument_data.py
+++ b/jwst/ami/instrument_data.py
@@ -92,6 +92,7 @@ def __init__(self,
         self.telname = "JWST"
         self.instrument = "NIRISS"
         self.arrname = "jwst_ami"
+        self.holeshape = 'hex'
         self.mask = NRM_definition(
             nrm_model,
             maskname=self.arrname,
diff --git a/jwst/ami/mask_definition_ami.py b/jwst/ami/mask_definition_ami.py
index 3a4b8c14fb..04cfe730f7 100644
--- a/jwst/ami/mask_definition_ami.py
+++ b/jwst/ami/mask_definition_ami.py
@@ -15,116 +15,116 @@
 
 class NRM_definition():
 
-    def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None):
-        """
-        Set attributes of NRM_definition class.
-
-        Parameters
-        ----------
-        nrm_model: NRMModel
-        	datamodel containing NRM reference file data
-        
-        rotdeg: list of floats
-            range of rotations to search (degrees)
-
-        chooseholes: list
-            None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
-
-        Returns
-        -------
-        None
-        """
-        if maskname not in ['jwst_ami','jwst_g7s6c']:
-        	raise ValueError("Mask name not supported")
-
-        self.maskname = maskname # there's only one mask but this is used in oifits
-
-        self.read_nrm_model(nrm_model, chooseholes=chooseholes)
-
-        if rotdeg is not None:
-            self.rotdeg = rotdeg
-
-    def read_nrm_model(self, nrm_model, chooseholes=None):
-    	"""
-
-	    Calculate hole centers with appropriate rotation,
-	    set these and other mask geometry details from NRMModel as
-	    attributes.
-
-	    Parameters
-	    ----------
-	    nrm_model: NRMModel
-        	datamodel containing NRM reference file data 
-	    chooseholes: list
-	        None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
-
-	    Returns
-	    -------
-	    f2f: float
-	        flat-to-flat distance of mask holes
-	    ctrs_asbuilt: array
-	        Actual hole centers [meters]
-	    """
-
-    	ctrs_asdesigned = [[nrm_model.x_a1, nrm_model.y_a1],        # B4 -> B4
-		    				[nrm_model.x_a2, nrm_model.y_a2],       # C5 -> C2
-						    [nrm_model.x_a3, nrm_model.y_a3],       # B3 -> B5
-						    [nrm_model.x_a4, nrm_model.y_a4],       # B6 -> B2
-						    [nrm_model.x_a5, nrm_model.y_a5],       # C6 -> C1
-						   	[nrm_model.x_a6, nrm_model.y_a6],        # B2 -> B6
-						    [nrm_model.x_a7, nrm_model.y_a7]]        # C1 -> C6
+	def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None):
+		"""
+		Set attributes of NRM_definition class.
+
+		Parameters
+		----------
+		nrm_model: NRMModel
+			datamodel containing NRM reference file data
+		
+		rotdeg: list of floats
+			range of rotations to search (degrees)
+
+		chooseholes: list
+			None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
+
+		Returns
+		-------
+		None
+		"""
+		if maskname not in ['jwst_ami','jwst_g7s6c']:
+			raise ValueError("Mask name not supported")
+
+		self.maskname = maskname # there's only one mask but this is used in oifits
+
+		self.read_nrm_model(nrm_model, chooseholes=chooseholes)
+
+		if rotdeg is not None:
+			self.rotdeg = rotdeg
+
+	def read_nrm_model(self, nrm_model, chooseholes=None):
+		"""
+
+		Calculate hole centers with appropriate rotation,
+		set these and other mask geometry details from NRMModel as
+		attributes.
+
+		Parameters
+		----------
+		nrm_model: NRMModel
+			datamodel containing NRM reference file data 
+		chooseholes: list
+			None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
+
+		Returns
+		-------
+		f2f: float
+			flat-to-flat distance of mask holes
+		ctrs_asbuilt: array
+			Actual hole centers [meters]
+		"""
+
+		ctrs_asdesigned = np.array([[nrm_model.x_a1, nrm_model.y_a1],        # B4 -> B4
+							[nrm_model.x_a2, nrm_model.y_a2],       # C5 -> C2
+							[nrm_model.x_a3, nrm_model.y_a3],       # B3 -> B5
+							[nrm_model.x_a4, nrm_model.y_a4],       # B6 -> B2
+							[nrm_model.x_a5, nrm_model.y_a5],       # C6 -> C1
+							[nrm_model.x_a6, nrm_model.y_a6],        # B2 -> B6
+							[nrm_model.x_a7, nrm_model.y_a7]])        # C1 -> C6
 
 		self.hdia = nrm_model.flat_to_flat
 		self.activeD = nrm_model.diameter
 		self.OD = nrm_model.pupil_circumscribed
 
-    	holedict = {}  # as_built names, C2 open, C5 closed, but as designed coordinates
-	    # Assemble holes by actual open segment names (as_built).  Either the full mask or the
-	    # subset-of-holes mask will be V2-reversed after the as_designed centers are defined
-	    # Debug orientations with b4,c6,[c2]
-	    allholes = ('b4', 'c2', 'b5', 'b2', 'c1', 'b6', 'c6')
+		holedict = {}  # as_built names, C2 open, C5 closed, but as designed coordinates
+		# Assemble holes by actual open segment names (as_built).  Either the full mask or the
+		# subset-of-holes mask will be V2-reversed after the as_designed centers are defined
+		# Debug orientations with b4,c6,[c2]
+		allholes = ('b4', 'c2', 'b5', 'b2', 'c1', 'b6', 'c6')
 
-	    for hole, coords in zip(allholes,ctrs_asdesigned):
-	    	holedict[hole] = coords
+		for hole, coords in zip(allholes,ctrs_asdesigned):
+			holedict[hole] = coords
 
-	    if chooseholes:  # holes B4 B5 C6 asbuilt for orientation testing
-	        holelist = []
-	        for h in allholes:
-	            if h in chooseholes:
-	                holelist.append(holedict[h])
-	        ctrs_asdesigned = np.array(holelist)
+		if chooseholes:  # holes B4 B5 C6 asbuilt for orientation testing
+			holelist = []
+			for h in allholes:
+				if h in chooseholes:
+					holelist.append(holedict[h])
+			ctrs_asdesigned = np.array(holelist)
 
-	    ctrs_asbuilt = ctrs_asdesigned.copy()
+		ctrs_asbuilt = ctrs_asdesigned.copy()
 
-	    # create 'live' hole centers in an ideal, orthogonal undistorted xy pupil space,
-	    # eg maps open hole C5 in as_designed to C2 as_built, eg C4 unaffected....
-	    ctrs_asbuilt[:, 0] *= -1
+		# create 'live' hole centers in an ideal, orthogonal undistorted xy pupil space,
+		# eg maps open hole C5 in as_designed to C2 as_built, eg C4 unaffected....
+		ctrs_asbuilt[:, 0] *= -1
 
-	    # LG++ rotate hole centers by 90 deg to match MAST o/p DMS PSF with
-	    # no affine2d transformations 8/2018 AS
-	    # LG++ The above aligns the hole pattern with the hex analytic FT,
-	    # flat top & bottom as seen in DMS data. 8/2018 AS
-	    ctrs_asbuilt = rotate2dccw(ctrs_asbuilt, np.pi / 2.0)  # overwrites attributes
+		# LG++ rotate hole centers by 90 deg to match MAST o/p DMS PSF with
+		# no affine2d transformations 8/2018 AS
+		# LG++ The above aligns the hole pattern with the hex analytic FT,
+		# flat top & bottom as seen in DMS data. 8/2018 AS
+		ctrs_asbuilt = rotate2dccw(ctrs_asbuilt, np.pi / 2.0)  # overwrites attributes
 
-	    # create 'live' hole centers in an ideal, orthogonal undistorted xy pupil space,
-	    self.ctrs = ctrs_asbuilt
+		# create 'live' hole centers in an ideal, orthogonal undistorted xy pupil space,
+		self.ctrs = ctrs_asbuilt
 
-    def showmask(self):
-        """
-        Calculate the diameter of the smallest centered circle (D)
-        enclosing the live mask area
+	def showmask(self):
+		"""
+		Calculate the diameter of the smallest centered circle (D)
+		enclosing the live mask area
 
-        Parameters
-        ----------
+		Parameters
+		----------
 
-        Returns
-        -------
-        Diameter of the smallest centered circle
+		Returns
+		-------
+		Diameter of the smallest centered circle
 
-        """
-        radii = []
-        for ctr in self.ctrs:
-            radii.append(math.sqrt(ctr[0] * ctr[0] + ctr[1] * ctr[1]))
+		"""
+		radii = []
+		for ctr in self.ctrs:
+			radii.append(math.sqrt(ctr[0] * ctr[0] + ctr[1] * ctr[1]))
 
-        return 2.0 * (max(radii) + 0.5 * self.hdia)
+		return 2.0 * (max(radii) + 0.5 * self.hdia)
 

From 40f1e7247c308edd0d66c27781c14d497e87e508 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Wed, 20 Nov 2024 13:55:09 -0500
Subject: [PATCH 06/23] Clean up, add log messages about affine

---
 jwst/ami/ami_analyze.py      | 5 +++++
 jwst/ami/ami_analyze_step.py | 6 +++---
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/jwst/ami/ami_analyze.py b/jwst/ami/ami_analyze.py
index 45379d594a..31659179c9 100644
--- a/jwst/ami/ami_analyze.py
+++ b/jwst/ami/ami_analyze.py
@@ -179,6 +179,11 @@ def apply_LG_plus(
         # the affine2d returned here has only rotation...
         # to use rotation and scaling/shear, do some matrix multiplication here??
 
+    log.info('Using affine transform with parameters:')
+    log.info(f'\tmx={affine2d.mx}\tmy={affine2d.my}')
+    log.info(f'\tsx={affine2d.sx}\tsy={affine2d.sy}')
+    log.info(f'\txo={affine2d.xo}\tyo={affine2d.yo}')
+
     niriss = instrument_data.NIRISS(filt,
                                     nrm_model,
                                     bandpass=bandpass,
diff --git a/jwst/ami/ami_analyze_step.py b/jwst/ami/ami_analyze_step.py
index 2284ef9902..ec334aa890 100755
--- a/jwst/ami/ami_analyze_step.py
+++ b/jwst/ami/ami_analyze_step.py
@@ -180,16 +180,16 @@ def process(self, input):
             # If there's a user-defined bandpass or affine, handle it
             if bandpass is not None:
                 bandpass = self.override_bandpass()
-
             if affine2d is not None:
                 if affine2d == 'commissioning':
-                    affine2d = utils.Affine2d(mx= 9.92820e-01,
+                    affine2d = utils.Affine2d(mx=9.92820e-01,
                         my=9.98540e-01,
                         sx=6.18605e-03,
                         sy=-7.27008e-03,
                         xo=0,
                         yo=0,
-                        name='commisioning')
+                        name='commissioning')
+                    self.log.info("Using affine parameters from commissioning.")
                 else:
                     affine2d = self.override_affine2d()
             # and if it is None, rotation search done in apply_LG_plus

From 8cbbfc0cf9b1a9e422fe6dd23530c14ab5ef46e3 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Wed, 20 Nov 2024 17:20:03 -0500
Subject: [PATCH 07/23] Rename lg_model.NrmModel to lg_model.LgModel to avoid
 confusion with stdatamodels NRMModel

---
 jwst/ami/find_affine2d_parameters.py |  2 +-
 jwst/ami/lg_model.py                 | 10 +++++-----
 jwst/ami/nrm_core.py                 |  4 ++--
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/jwst/ami/find_affine2d_parameters.py b/jwst/ami/find_affine2d_parameters.py
index f21609e92e..6bdc74e826 100644
--- a/jwst/ami/find_affine2d_parameters.py
+++ b/jwst/ami/find_affine2d_parameters.py
@@ -98,7 +98,7 @@ def find_rotation(imagedata, psf_offset, rotdegs, mx, my, sx, sy, xo, yo,
     crosscorr_rots = []
 
     for (rot, aff) in zip(rotdegs, affine2d_list):
-        jw = lg_model.NrmModel(mask='jwst_g7s6c', holeshape=holeshape, over=over, affine2d=aff)
+        jw = lg_model.LgModel(mask='jwst_ami', holeshape=holeshape, over=over, affine2d=aff)
 
         jw.set_pixelscale(pixel)
         # psf_offset in data coords & pixels.  Does it get rotated?  Second order errors poss.
diff --git a/jwst/ami/lg_model.py b/jwst/ami/lg_model.py
index 44d94a6194..b52e0f8285 100755
--- a/jwst/ami/lg_model.py
+++ b/jwst/ami/lg_model.py
@@ -19,7 +19,7 @@
 mas = 1.0e-3 / (60 * 60 * 180 / np.pi)  # in radians
 
 
-class NrmModel:
+class LgModel:
     """
     A class for conveniently dealing with an "NRM object" This should be able
     to take an NRM_definition object for mask geometry.
@@ -47,7 +47,7 @@ def __init__(
         **kwargs,
     ):
         """
-        Set attributes of NrmModel class.
+        Set attributes of LgModel class.
 
         Parameters
         ----------
@@ -93,7 +93,7 @@ def __init__(
 
         # get these from mask_definition_ami instead
         if mask is None:
-            log.info("Using JWST AMI mask geometry from NrmModel")
+            log.info("Using JWST AMI mask geometry from LgModel")
             mask = mask_definition_ami.NRM_definition(
                 maskname="jwst_ami", chooseholes=chooseholes
             )
@@ -122,7 +122,7 @@ def __init__(
 
         self.chooseholes = chooseholes
 
-        # affine2d property not to be changed in NrmModel - create a new
+        # affine2d property not to be changed in LgModel - create a new
         #     instance instead
         # Save affine deformation of pupil object or create a no-deformation
         #     object.
@@ -400,7 +400,7 @@ def fit_image(
     def create_modelpsf(self):
         """
         Make an image from the object's model and fit solutions, by setting the
-        NrmModel object's modelpsf attribute
+        LgModel object's modelpsf attribute
 
         Parameters
         ----------
diff --git a/jwst/ami/nrm_core.py b/jwst/ami/nrm_core.py
index e8e54b68f7..8ae1fdc58b 100755
--- a/jwst/ami/nrm_core.py
+++ b/jwst/ami/nrm_core.py
@@ -170,7 +170,7 @@ def fit_fringes_single_integration(self, slc):
 
         Returns
         -------
-        nrm: NrmModel object
+        nrm: LgModel object
             Model with best fit results
         
         Notes
@@ -190,7 +190,7 @@ def fit_fringes_single_integration(self, slc):
         
         """
 
-        nrm = lg_model.NrmModel(mask=self.instrument_data.mask,
+        nrm = lg_model.LgModel(mask=self.instrument_data.mask,
                                 pixscale=self.instrument_data.pscale_rad,
                                 holeshape=self.instrument_data.holeshape,
                                 affine2d=self.instrument_data.affine2d,

From a7d7d4fa9dad56243b4b6834deece414218c4693 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Wed, 20 Nov 2024 17:35:48 -0500
Subject: [PATCH 08/23] default affine2d updated to 'commissioning' (special
 case)

---
 jwst/ami/ami_analyze_step.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jwst/ami/ami_analyze_step.py b/jwst/ami/ami_analyze_step.py
index ec334aa890..b35ea00970 100755
--- a/jwst/ami/ami_analyze_step.py
+++ b/jwst/ami/ami_analyze_step.py
@@ -24,7 +24,7 @@ class AmiAnalyzeStep(Step):
         usebp = boolean(default=True) # If True, exclude pixels marked DO_NOT_USE from fringe fitting
         firstfew = integer(default=None) # If not None, process only the first few integrations
         chooseholes = string(default=None) # If not None, fit only certain fringes e.g. ['B4','B5','B6','C2']
-        affine2d = string(default=None) # ASDF file containing user-defined affine parameters
+        affine2d = string(default='commissioning') # ASDF file containing user-defined affine parameters OR 'commssioning'
         run_bpfix = boolean(default=True) # Run Fourier bad pixel fix on cropped data
     """
 

From 1f296f17da18b6257e1719ce8fa585a39831c361 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Tue, 26 Nov 2024 16:33:35 -0500
Subject: [PATCH 09/23] change log

---
 changes/8974.ami.rst | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 changes/8974.ami.rst

diff --git a/changes/8974.ami.rst b/changes/8974.ami.rst
new file mode 100644
index 0000000000..ea39be8806
--- /dev/null
+++ b/changes/8974.ami.rst
@@ -0,0 +1 @@
+Use mask and pupil geometry constants from NRM reference file, and apply affine distortion from commissioning to LG model as default.
\ No newline at end of file

From c432d0a71141381b03091120e712831673bcc639 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Fri, 6 Dec 2024 16:24:21 -0500
Subject: [PATCH 10/23] removed old mask_definitions.py

---
 jwst/ami/mask_definitions.py | 179 -----------------------------------
 1 file changed, 179 deletions(-)
 delete mode 100755 jwst/ami/mask_definitions.py

diff --git a/jwst/ami/mask_definitions.py b/jwst/ami/mask_definitions.py
deleted file mode 100755
index d761f90c34..0000000000
--- a/jwst/ami/mask_definitions.py
+++ /dev/null
@@ -1,179 +0,0 @@
-#
-#  Module for defining mask geometry in pupil space
-#
-
-import numpy as np
-import math
-
-from .utils import rotate2dccw
-
-m = 1.0
-mm = 1.0e-3 * m
-um = 1.0e-6 * m
-
-
-class NRM_mask_definitions():
-
-    def __init__(self, maskname=None, rotdeg=None, holeshape="circ", rescale=False,
-                 chooseholes=None):
-        """
-        Set attributes of NRM_mask_definitions class.
-
-        Parameters
-        ----------
-        maskname: string
-            name of mask
-
-        rotdeg: list of floats
-            range of rotations to search (degrees)
-
-        holeshape: string
-            shape of apertures
-
-        rescale: float
-            multiplicative factor to adjust hole sizes and centers in entrance pupil
-
-        chooseholes: list
-            None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
-
-        Returns
-        -------
-        None
-        """
-
-        if maskname not in ["gpi_g10s40", "jwst_g7s6", "jwst_g7s6c", "visir_sam",
-                            "p1640", "keck_nirc2", "pharo", "NIRC2_9NRM"]:
-            raise ValueError("mask not supported")
-        if holeshape is None:
-            holeshape = 'circ'
-
-        if holeshape not in ["circ", "hex", ]:
-            raise ValueError("Unsupported mask holeshape" + maskname)
-        self.maskname = maskname
-
-        if self.maskname == "jwst_g7s6c":
-            # activeD and D taken from webbpsf-data/NIRISS/coronagraph/MASK_NRM.fits
-
-            self.hdia, self.ctrs = jwst_g7s6c(chooseholes=chooseholes)
-            self.activeD = 6.559 * m  # webbpsf kwd DIAM  - not a 'circle including all holes'
-            self.OD = 6.610645669291339 * m  # Full pupil file size, incl padding, webbpsf kwd PUPLDIAM
-            if rotdeg is not None:
-                self.rotdeg = rotdeg
-
-        elif self.maskname == "jwst_g7s6":
-            pass  # not finished
-
-    def showmask(self):
-        """
-        Calculate the diameter of the smallest centered circle (D)
-        enclosing the live mask area
-
-        Parameters
-        ----------
-
-        Returns
-        -------
-        Diameter of the smallest centered circle
-
-        """
-        radii = []
-        for ctr in self.ctrs:
-            radii.append(math.sqrt(ctr[0] * ctr[0] + ctr[1] * ctr[1]))
-
-        return 2.0 * (max(radii) + 0.5 * self.hdia)
-
-
-def jwst_g7s6_centers_asbuilt(chooseholes=None):  # was jwst_g7s6_centers_asdesigned
-    """
-    Calculate hole centers with appropriate rotation
-
-    Parameters
-    ----------
-    chooseholes: list
-        None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
-
-    Returns
-    -------
-    ctrs_asbuilt: array
-        Actual hole centers [meters]
-    """
-
-    holedict = {}  # as_built names, C2 open, C5 closed, but as designed coordinates
-    # Assemble holes by actual open segment names (as_built).  Either the full mask or the
-    # subset-of-holes mask will be V2-reversed after the as_designed centers  are defined
-    # Debug orientations with b4,c6,[c2]
-    allholes = ('b4', 'c2', 'b5', 'b2', 'c1', 'b6', 'c6')
-
-    #                                             design  built
-    holedict['b4'] = [0.00000000, -2.640000]       # B4 -> B4
-    holedict['c2'] = [-2.2863100, 0.0000000]       # C5 -> C2
-    holedict['b5'] = [2.2863100, -1.3200001]       # B3 -> B5
-    holedict['b2'] = [-2.2863100, 1.3200001]       # B6 -> B2
-    holedict['c1'] = [-1.1431500, 1.9800000]       # C6 -> C1
-    holedict['b6'] = [2.2863100, 1.3200001]        # B2 -> B6
-    holedict['c6'] = [1.1431500, 1.9800000]        # C1 -> C6
-
-    # as designed MB coordinates (Mathilde Beaulieu, Peter, Anand).
-    # as designed: segments C5 open, C2 closed, meters V2V3 per Paul Lightsey def
-    # as built C5 closed, C2 open
-    #
-    # undistorted pupil coords on PM.  These numbers are considered immutable.
-    # as designed seg -> as built seg in comments each ctr entry (no distortion)
-    if chooseholes:  # holes B4 B5 C6 asbuilt for orientation testing
-        holelist = []
-        for h in allholes:
-            if h in chooseholes:
-                holelist.append(holedict[h])
-        ctrs_asdesigned = np.array(holelist)
-    else:
-        # the REAL THING - as_designed 7 hole, m in PM space, no distortion
-        # ... shape (7,2)
-        ctrs_asdesigned = np.array([
-            [0.00000000, -2.640000],     # B4 -> B4  as-designed -> as-built mapping
-            [-2.2863100, 0.0000000],     # C5 -> C2
-            [2.2863100, -1.3200001],     # B3 -> B5
-            [-2.2863100, 1.3200001],     # B6 -> B2
-            [-1.1431500, 1.9800000],     # C6 -> C1
-            [2.2863100, 1.3200001],      # B2 -> B6
-            [1.1431500, 1.9800000]])     # C1 -> C6
-
-    # Preserve ctrs.as-designed (treat as immutable)
-    # Reverse V2 axis coordinates to close C5 open C2, and others follow suit...
-    # preserve cts.as_built  (treat as immutable)
-    ctrs_asbuilt = ctrs_asdesigned.copy()
-
-    # create 'live' hole centers in an ideal, orthogonal undistorted xy pupil space,
-    # eg maps open hole C5 in as_designed to C2 as_built, eg C4 unaffected....
-    ctrs_asbuilt[:, 0] *= -1
-
-    # LG++ rotate hole centers by 90 deg to match MAST o/p DMS PSF with
-    # no affine2d transformations 8/2018 AS
-    # LG++ The above aligns the hole pattern with the hex analytic FT,
-    # flat top & bottom as seen in DMS data. 8/2018 AS
-    ctrs_asbuilt = rotate2dccw(ctrs_asbuilt, np.pi / 2.0)  # overwrites attributes
-
-    # create 'live' hole centers in an ideal, orthogonal undistorted xy pupil space,
-    return ctrs_asbuilt * m
-
-
-def jwst_g7s6c(chooseholes=None):
-    """
-
-    Calculate hole centers with appropriate rotation
-
-    Parameters
-    ----------
-    chooseholes: list
-        None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
-
-    Returns
-    -------
-    f2f: float
-        flat-to-flat distance of mask holes
-    ctrs_asbuilt: array
-        Actual hole centers [meters]
-
-    """
-
-    f2f = 0.8 * m  # m flat to flat
-    return f2f, jwst_g7s6_centers_asbuilt(chooseholes=chooseholes)

From 0b435a3a44626ec430df39711daf9d6681ab2937 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Mon, 9 Dec 2024 13:35:01 -0500
Subject: [PATCH 11/23] Add special affine2d default 'commissioning' to
 documentation

---
 docs/jwst/ami_analyze/description.rst | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/docs/jwst/ami_analyze/description.rst b/docs/jwst/ami_analyze/description.rst
index 26b2f597ff..36e9b6622c 100644
--- a/docs/jwst/ami_analyze/description.rst
+++ b/docs/jwst/ami_analyze/description.rst
@@ -47,11 +47,14 @@ other options:
 :--chooseholes: If not None, fit only certain fringes e.g. ['B4','B5','B6','C2']
                 (default=None)
 
-:--affine2d: ASDF file containing user-defined affine parameters (default=None)
+:--affine2d: ASDF file containing user-defined affine parameters (default='commissioning')
 
 :--run_bpfix: Run Fourier bad pixel fix on cropped data (default=True)
 
 
+Note that the `affine2d` default argument is a special case; 'commissioning' is currently the only string other than an ASDF filename that is accepted.
+
+
 Creating ASDF files
 ^^^^^^^^^^^^^^^^^^^
 The optional arguments `bandpass` and `affine2d` must be written to `ASDF <https://asdf-standard.readthedocs.io/>`_ 

From ac8915ffdd191ecd70e70a4e8ac92a4499878ec3 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Mon, 9 Dec 2024 14:28:04 -0500
Subject: [PATCH 12/23] docstring updates, update test to use correct datamodel
 meta structure

---
 jwst/ami/mask_definition_ami.py      | 16 +++++-----------
 jwst/ami/tests/test_ami_interface.py |  4 ++--
 2 files changed, 7 insertions(+), 13 deletions(-)

diff --git a/jwst/ami/mask_definition_ami.py b/jwst/ami/mask_definition_ami.py
index 04cfe730f7..59a33c44a0 100644
--- a/jwst/ami/mask_definition_ami.py
+++ b/jwst/ami/mask_definition_ami.py
@@ -23,17 +23,14 @@ def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None
 		----------
 		nrm_model: NRMModel
 			datamodel containing NRM reference file data
-		
+		maskname: string
+			Identifier for mask geometry; default 'jwst_ami', optional
 		rotdeg: list of floats
-			range of rotations to search (degrees)
-
+			range of rotations to search (degrees), optional
 		chooseholes: list
-			None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
-
-		Returns
-		-------
-		None
+			None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask, optional
 		"""
+
 		if maskname not in ['jwst_ami','jwst_g7s6c']:
 			raise ValueError("Mask name not supported")
 
@@ -114,9 +111,6 @@ def showmask(self):
 		Calculate the diameter of the smallest centered circle (D)
 		enclosing the live mask area
 
-		Parameters
-		----------
-
 		Returns
 		-------
 		Diameter of the smallest centered circle
diff --git a/jwst/ami/tests/test_ami_interface.py b/jwst/ami/tests/test_ami_interface.py
index 23e765a343..1b64801d25 100644
--- a/jwst/ami/tests/test_ami_interface.py
+++ b/jwst/ami/tests/test_ami_interface.py
@@ -48,8 +48,8 @@ def example_model(mock_nrm_reference_file):
     model.meta.program.pi_name = "someone"
     model.meta.target.catalog_name = ""
     model.meta.visit.start_time = "2022-06-05 12:15:41.5020000"
-    model.meta.wcsinfo.roll_ref = 171.8779402866089
-    model.meta.wcsinfo.v3yangle = 0.56126717
+    model.meta.ami.roll_ref = 171.8779402866089
+    model.meta.ami.v3yangle = 0.56126717
     model.meta.filename = "test_calints.fits"
     model.meta.instrument.pupil = "NRM"
     model.meta.exposure.type = "NIS_AMI"

From 22656e69e3fb4633f04c8588f60e3119ce057828 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Mon, 9 Dec 2024 14:59:53 -0500
Subject: [PATCH 13/23] undo wrong 'fix' to test

---
 jwst/ami/tests/test_ami_interface.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/jwst/ami/tests/test_ami_interface.py b/jwst/ami/tests/test_ami_interface.py
index 1b64801d25..23e765a343 100644
--- a/jwst/ami/tests/test_ami_interface.py
+++ b/jwst/ami/tests/test_ami_interface.py
@@ -48,8 +48,8 @@ def example_model(mock_nrm_reference_file):
     model.meta.program.pi_name = "someone"
     model.meta.target.catalog_name = ""
     model.meta.visit.start_time = "2022-06-05 12:15:41.5020000"
-    model.meta.ami.roll_ref = 171.8779402866089
-    model.meta.ami.v3yangle = 0.56126717
+    model.meta.wcsinfo.roll_ref = 171.8779402866089
+    model.meta.wcsinfo.v3yangle = 0.56126717
     model.meta.filename = "test_calints.fits"
     model.meta.instrument.pupil = "NRM"
     model.meta.exposure.type = "NIS_AMI"

From a472b26335e40a55acdca61d4079951e0f16ff94 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Mon, 9 Dec 2024 15:53:21 -0500
Subject: [PATCH 14/23] Remove use of mock_nrm_reference_file since it exists
 on crds ops now

---
 jwst/ami/tests/test_ami_interface.py | 25 +------------------------
 1 file changed, 1 insertion(+), 24 deletions(-)

diff --git a/jwst/ami/tests/test_ami_interface.py b/jwst/ami/tests/test_ami_interface.py
index 23e765a343..4e9f9675b5 100644
--- a/jwst/ami/tests/test_ami_interface.py
+++ b/jwst/ami/tests/test_ami_interface.py
@@ -10,30 +10,7 @@
 
 
 @pytest.fixture()
-def mock_nrm_reference_file(tmp_path, monkeypatch):
-    """
-    At the moment nrm only exists on CRDS-TEST so this
-    fixture will mock fetching any 'nrm' reference file
-    """
-    fn = tmp_path / "nrm.fits"
-
-    # make a fake nrm file
-    m = datamodels.NRMModel()
-    m.nrm = np.zeros((1024, 1024), dtype='f4')
-    m.save(fn)
-
-    original_get_reference_file = crds_client.get_reference_file
-
-    def mock_get_reference_file(dataset, reference_file_type, observatory):
-        if reference_file_type == 'nrm':
-            return str(fn)
-        return original_get_reference_file(dataset, reference_file_type, observatory)
-
-    monkeypatch.setattr(crds_client, "get_reference_file", mock_get_reference_file)
-
-
-@pytest.fixture()
-def example_model(mock_nrm_reference_file):
+def example_model():
     model = datamodels.CubeModel((2, 80, 80))
     # some non-zero data is required as this step will center
     # the image and find the centroid (both fail with all zeros)

From 3d4fb46e967cd08489f5ccf7e0f08eb9e9572a80 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Mon, 9 Dec 2024 17:02:31 -0500
Subject: [PATCH 15/23] fix FutureWarning in linalg.lstsq

---
 jwst/ami/leastsqnrm.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jwst/ami/leastsqnrm.py b/jwst/ami/leastsqnrm.py
index 79983d34e7..ec31a48680 100644
--- a/jwst/ami/leastsqnrm.py
+++ b/jwst/ami/leastsqnrm.py
@@ -490,7 +490,7 @@ def weighted_operations(img, model, dqm=None):
     Aw = flatmodel * weights[:, np.newaxis]
     bw = flatimg * weights
     # resids are pixel value residuals, flattened to 1d vector
-    x, rss, rank, singvals = np.linalg.lstsq(Aw, bw)
+    x, rss, rank, singvals = np.linalg.lstsq(Aw, bw, rcond=None)
 
     # actual residuals in image:
     res = flatimg - np.dot(flatmodel, x)

From 761e18296822814891651a42b0479b1b44f98c9f Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Tue, 10 Dec 2024 17:53:27 -0500
Subject: [PATCH 16/23] pass NRMModel to lg_model.LgModel so that
 find_affine2d_parameters.find_rotation() has mask info it needs when affine2d
 input is None. Could probably be cleaned up a bit

---
 jwst/ami/ami_analyze.py              | 11 ++++++-----
 jwst/ami/find_affine2d_parameters.py |  7 +++++--
 jwst/ami/instrument_data.py          |  5 ++++-
 jwst/ami/lg_model.py                 | 12 ++++++++----
 jwst/ami/nrm_core.py                 |  3 ++-
 5 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/jwst/ami/ami_analyze.py b/jwst/ami/ami_analyze.py
index 31659179c9..4277bac9a8 100644
--- a/jwst/ami/ami_analyze.py
+++ b/jwst/ami/ami_analyze.py
@@ -126,9 +126,8 @@ def apply_LG_plus(
     # Throughput (combined filter and source spectrum) calculated here
     bandpass = utils.handle_bandpass(bandpass, throughput_model)
 
-    
-
     if affine2d is None:
+        log.info("Searching for best-fit affine transform")
         rotsearch_d = np.append(
         np.arange(
             rotsearch_parameters[0], rotsearch_parameters[1], rotsearch_parameters[2]
@@ -161,6 +160,7 @@ def apply_LG_plus(
 
         affine2d = find_rotation(
             meddata,
+            nrm_model,
             psf_offset,
             rotsearch_d,
             mx,
@@ -180,9 +180,10 @@ def apply_LG_plus(
         # to use rotation and scaling/shear, do some matrix multiplication here??
 
     log.info('Using affine transform with parameters:')
-    log.info(f'\tmx={affine2d.mx}\tmy={affine2d.my}')
-    log.info(f'\tsx={affine2d.sx}\tsy={affine2d.sy}')
-    log.info(f'\txo={affine2d.xo}\tyo={affine2d.yo}')
+    log.info(f'\tmx={affine2d.mx:.6f}\tmy={affine2d.my:.6f}')
+    log.info(f'\tsx={affine2d.sx:.6f}\tsy={affine2d.sy:.6f}')
+    log.info(f'\txo={affine2d.xo:.6f}\tyo={affine2d.yo:.6f}')
+    log.info(f'\trotradccw={affine2d.rotradccw:.4f}')
 
     niriss = instrument_data.NIRISS(filt,
                                     nrm_model,
diff --git a/jwst/ami/find_affine2d_parameters.py b/jwst/ami/find_affine2d_parameters.py
index 6bdc74e826..0ba18090ab 100644
--- a/jwst/ami/find_affine2d_parameters.py
+++ b/jwst/ami/find_affine2d_parameters.py
@@ -35,7 +35,7 @@ def create_afflist_rot(rotdegs):
     return alist
 
 
-def find_rotation(imagedata, psf_offset, rotdegs, mx, my, sx, sy, xo, yo,
+def find_rotation(imagedata, nrm_model, psf_offset, rotdegs, mx, my, sx, sy, xo, yo,
                   pixel, npix, bandpass, over, holeshape):
     """
     Create an affine2d object using the known rotation and scale.
@@ -45,6 +45,9 @@ def find_rotation(imagedata, psf_offset, rotdegs, mx, my, sx, sy, xo, yo,
     imagedata: 2D float array
         image data
 
+    nrm_model: NRMModel datamodel
+        datamodel containing mask geometry information
+
     psf_offset: 2D float array
         offset from image center in detector pixels
 
@@ -98,7 +101,7 @@ def find_rotation(imagedata, psf_offset, rotdegs, mx, my, sx, sy, xo, yo,
     crosscorr_rots = []
 
     for (rot, aff) in zip(rotdegs, affine2d_list):
-        jw = lg_model.LgModel(mask='jwst_ami', holeshape=holeshape, over=over, affine2d=aff)
+        jw = lg_model.LgModel(nrm_model, mask='jwst_ami', holeshape=holeshape, over=over, affine2d=aff)
 
         jw.set_pixelscale(pixel)
         # psf_offset in data coords & pixels.  Does it get rotated?  Second order errors poss.
diff --git a/jwst/ami/instrument_data.py b/jwst/ami/instrument_data.py
index 08d30bdc6e..f2c41cff86 100755
--- a/jwst/ami/instrument_data.py
+++ b/jwst/ami/instrument_data.py
@@ -38,6 +38,9 @@ def __init__(self,
         ----------
         filt: string
             filter name
+        
+        nrm_model: NRMModel datamodel
+            datamodel containing mask geometry information
 
         chooseholes: list
             None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
@@ -94,7 +97,7 @@ def __init__(self,
         self.arrname = "jwst_ami"
         self.holeshape = 'hex'
         self.mask = NRM_definition(
-            nrm_model,
+            self.nrm_model,
             maskname=self.arrname,
             chooseholes=self.chooseholes
         )
diff --git a/jwst/ami/lg_model.py b/jwst/ami/lg_model.py
index b52e0f8285..598df552ca 100755
--- a/jwst/ami/lg_model.py
+++ b/jwst/ami/lg_model.py
@@ -27,13 +27,14 @@ class LgModel:
     Simulates PSF (broadband or monochromatic)
     Builds a fringe model - either by user definition, or automated to data
     Fits model to data by least squares
-    Masks: gpi_g10s40, jwst, visir
+    Masks: jwst_ami (formerly jwst_g7s6c)
     Algorithm documented in Greenbaum, A. Z., Pueyo, L. P., Sivaramakrishnan,
     A., and Lacour, S., Astrophysical Journal vol. 798, Jan 2015.
     """
 
     def __init__(
         self,
+        nrm_model,
         mask=None,
         holeshape="hex",
         pixscale=None,
@@ -51,6 +52,9 @@ def __init__(
 
         Parameters
         ----------
+        nrm_model: NRMModel datamodel
+            datamodel containing mask geometry information
+
         mask: string
             keyword for built-in values
 
@@ -85,7 +89,7 @@ def __init__(
             self.debug = kwargs["debug"]
         else:
             self.debug = False
-
+            
         self.holeshape = holeshape
         self.pixel = pixscale  # det pix in rad (square)
         self.over = over
@@ -94,11 +98,11 @@ def __init__(
         # get these from mask_definition_ami instead
         if mask is None:
             log.info("Using JWST AMI mask geometry from LgModel")
-            mask = mask_definition_ami.NRM_definition(
+            mask = mask_definition_ami.NRM_definition(nrm_model,
                 maskname="jwst_ami", chooseholes=chooseholes
             )
         elif isinstance(mask, str):
-            mask = mask_definition_ami.NRM_definition(
+            mask = mask_definition_ami.NRM_definition(nrm_model,
                 maskname=mask, chooseholes=chooseholes
             ) # retain ability to possibly  use other named masks, for now
         self.ctrs = mask.ctrs
diff --git a/jwst/ami/nrm_core.py b/jwst/ami/nrm_core.py
index 8ae1fdc58b..e03c911895 100755
--- a/jwst/ami/nrm_core.py
+++ b/jwst/ami/nrm_core.py
@@ -190,7 +190,8 @@ def fit_fringes_single_integration(self, slc):
         
         """
 
-        nrm = lg_model.LgModel(mask=self.instrument_data.mask,
+        nrm = lg_model.LgModel(self.instrument_data.nrm_model,
+                                mask=self.instrument_data.mask,
                                 pixscale=self.instrument_data.pscale_rad,
                                 holeshape=self.instrument_data.holeshape,
                                 affine2d=self.instrument_data.affine2d,

From 77bfec6510f7ef0c18825dbe3479347ce8e1568e Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Tue, 10 Dec 2024 18:00:39 -0500
Subject: [PATCH 17/23] a little cleanup of lgmodel inputs

---
 jwst/ami/lg_model.py | 22 ++++++----------------
 1 file changed, 6 insertions(+), 16 deletions(-)

diff --git a/jwst/ami/lg_model.py b/jwst/ami/lg_model.py
index 598df552ca..c80e5f65ca 100755
--- a/jwst/ami/lg_model.py
+++ b/jwst/ami/lg_model.py
@@ -40,10 +40,8 @@ def __init__(
         pixscale=None,
         over=1,
         pixweight=None,
-        datapath="",
         phi=None,
-        refdir="",
-        chooseholes=False,
+        chooseholes=None,
         affine2d=None,
         **kwargs,
     ):
@@ -59,7 +57,7 @@ def __init__(
             keyword for built-in values
 
         holeshape: string
-           shape of apertures
+           shape of apertures, default="hex"
 
         pixscale: float
            initial estimate of pixel scale in radians
@@ -70,17 +68,11 @@ def __init__(
         pixweight: 2D float array, default is None
             weighting array
 
-        datapath: string
-            directory for output (will remove for final)
-
         phi: float 1D array
             distance of fringe from hole center in units of waves
 
-        refdir: string
-            directory containing ref files (will remove for final)
-
-        chooseholes: list ?
-            holes ...?
+        chooseholes: list of strings
+            None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
 
         affine2d: Affine2d object
             Affine2d object
@@ -89,7 +81,7 @@ def __init__(
             self.debug = kwargs["debug"]
         else:
             self.debug = False
-            
+
         self.holeshape = holeshape
         self.pixel = pixscale  # det pix in rad (square)
         self.over = over
@@ -110,11 +102,9 @@ def __init__(
         self.D = mask.activeD
 
         self.N = len(self.ctrs)
-        self.datapath = datapath
-        self.refdir = refdir
         self.fmt = "%10.4e"
 
-        # get latest OPD from WebbPSF?
+        # get closest in time OPD from WebbPSF?
 
         if phi:  # meters of OPD at central wavelength
             if phi == "perfect":

From 07998646c0ac4d0e52954f837d1214a2b043436c Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Tue, 10 Dec 2024 18:23:32 -0500
Subject: [PATCH 18/23] remove now-unused imports

---
 jwst/ami/tests/test_ami_interface.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/jwst/ami/tests/test_ami_interface.py b/jwst/ami/tests/test_ami_interface.py
index 4e9f9675b5..b4ccd7c081 100644
--- a/jwst/ami/tests/test_ami_interface.py
+++ b/jwst/ami/tests/test_ami_interface.py
@@ -1,8 +1,6 @@
-import numpy as np
 import pytest
 
 import stpipe
-from stpipe import crds_client
 
 from stdatamodels.jwst import datamodels
 

From cd3524f644f9d70da03ff9fac154d0f7e388b562 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Wed, 11 Dec 2024 12:03:07 -0500
Subject: [PATCH 19/23] try to handle None input interpreted as string

---
 jwst/ami/ami_analyze_step.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/jwst/ami/ami_analyze_step.py b/jwst/ami/ami_analyze_step.py
index b35ea00970..3dc95529bc 100755
--- a/jwst/ami/ami_analyze_step.py
+++ b/jwst/ami/ami_analyze_step.py
@@ -157,6 +157,11 @@ def process(self, input):
         # pull out parameters that are strings and change to floats
         psf_offset = [float(a) for a in self.psf_offset.split()]
         rotsearch_parameters = [float(a) for a in self.rotation_search.split()]
+        # handle command-line None input interpreted as string
+        if affine2d in ["None", "none"]:
+            affine2d = None
+        if bandpass in ["None", "none"]:
+            bandpass = None
 
         self.log.info(f"Oversampling factor = {oversample}")
         self.log.info(f"Initial rotation guess = {rotate} deg")

From 85ad403b88c734c4fe3d461bc9fd606675666ed3 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Wed, 11 Dec 2024 14:33:54 -0500
Subject: [PATCH 20/23] Fix break caused by log statement

---
 jwst/ami/ami_analyze_step.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/jwst/ami/ami_analyze_step.py b/jwst/ami/ami_analyze_step.py
index 3dc95529bc..dd57ce894d 100755
--- a/jwst/ami/ami_analyze_step.py
+++ b/jwst/ami/ami_analyze_step.py
@@ -193,6 +193,7 @@ def process(self, input):
                         sy=-7.27008e-03,
                         xo=0,
                         yo=0,
+                        rotradccw=0,
                         name='commissioning')
                     self.log.info("Using affine parameters from commissioning.")
                 else:

From bc48f11cfe0ab55b24292e4bdb482ca17b4b001b Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Thu, 12 Dec 2024 14:26:11 -0500
Subject: [PATCH 21/23] Style and doctring updates following review

---
 docs/jwst/ami_analyze/description.rst |  2 +-
 jwst/ami/ami_analyze_step.py          |  5 ++---
 jwst/ami/instrument_data.py           |  4 ++--
 jwst/ami/lg_model.py                  | 13 +++++++------
 jwst/ami/mask_definition_ami.py       | 21 ++++++++++++---------
 5 files changed, 24 insertions(+), 21 deletions(-)

diff --git a/docs/jwst/ami_analyze/description.rst b/docs/jwst/ami_analyze/description.rst
index 36e9b6622c..2e4ec08636 100644
--- a/docs/jwst/ami_analyze/description.rst
+++ b/docs/jwst/ami_analyze/description.rst
@@ -52,7 +52,7 @@ other options:
 :--run_bpfix: Run Fourier bad pixel fix on cropped data (default=True)
 
 
-Note that the `affine2d` default argument is a special case; 'commissioning' is currently the only string other than an ASDF filename that is accepted.
+Note that the `affine2d` default argument is a special case; 'commissioning' is currently the only string other than an ASDF filename that is accepted. If `None` is passed, it will perform a rotation search (least-squares fit to a PSF model) and use that for the affine transform.
 
 
 Creating ASDF files
diff --git a/jwst/ami/ami_analyze_step.py b/jwst/ami/ami_analyze_step.py
index dd57ce894d..d5c009db7e 100755
--- a/jwst/ami/ami_analyze_step.py
+++ b/jwst/ami/ami_analyze_step.py
@@ -157,11 +157,10 @@ def process(self, input):
         # pull out parameters that are strings and change to floats
         psf_offset = [float(a) for a in self.psf_offset.split()]
         rotsearch_parameters = [float(a) for a in self.rotation_search.split()]
+
         # handle command-line None input interpreted as string
-        if affine2d in ["None", "none"]:
+        if str(affine2d).lower() == 'none':
             affine2d = None
-        if bandpass in ["None", "none"]:
-            bandpass = None
 
         self.log.info(f"Oversampling factor = {oversample}")
         self.log.info(f"Initial rotation guess = {rotate} deg")
diff --git a/jwst/ami/instrument_data.py b/jwst/ami/instrument_data.py
index f2c41cff86..cbc253eabf 100755
--- a/jwst/ami/instrument_data.py
+++ b/jwst/ami/instrument_data.py
@@ -6,7 +6,7 @@
 import logging
 import numpy as np
 
-from .mask_definition_ami import NRM_definition
+from .mask_definition_ami import NRMDefinition
 from . import utils
 from . import bp_fix
 from stdatamodels.jwst.datamodels import dqflags
@@ -96,7 +96,7 @@ def __init__(self,
         self.instrument = "NIRISS"
         self.arrname = "jwst_ami"
         self.holeshape = 'hex'
-        self.mask = NRM_definition(
+        self.mask = NRMDefinition(
             self.nrm_model,
             maskname=self.arrname,
             chooseholes=self.chooseholes
diff --git a/jwst/ami/lg_model.py b/jwst/ami/lg_model.py
index c80e5f65ca..29170738dd 100755
--- a/jwst/ami/lg_model.py
+++ b/jwst/ami/lg_model.py
@@ -22,7 +22,7 @@
 class LgModel:
     """
     A class for conveniently dealing with an "NRM object" This should be able
-    to take an NRM_definition object for mask geometry.
+    to take an NRMDefinition object for mask geometry.
     Defines mask geometry and detector-scale parameters.
     Simulates PSF (broadband or monochromatic)
     Builds a fringe model - either by user definition, or automated to data
@@ -65,14 +65,15 @@ def __init__(
         over: integer
            oversampling factor
 
-        pixweight: 2D float array, default is None
+        pixweight: 2D float array, default None
             weighting array
 
         phi: float 1D array
             distance of fringe from hole center in units of waves
 
-        chooseholes: list of strings
-            None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
+        chooseholes: list of strings, default None
+            E.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask
+            If None, use the real seven-hole mask.
 
         affine2d: Affine2d object
             Affine2d object
@@ -90,11 +91,11 @@ def __init__(
         # get these from mask_definition_ami instead
         if mask is None:
             log.info("Using JWST AMI mask geometry from LgModel")
-            mask = mask_definition_ami.NRM_definition(nrm_model,
+            mask = mask_definition_ami.NRMDefinition(nrm_model,
                 maskname="jwst_ami", chooseholes=chooseholes
             )
         elif isinstance(mask, str):
-            mask = mask_definition_ami.NRM_definition(nrm_model,
+            mask = mask_definition_ami.NRMDefinition(nrm_model,
                 maskname=mask, chooseholes=chooseholes
             ) # retain ability to possibly  use other named masks, for now
         self.ctrs = mask.ctrs
diff --git a/jwst/ami/mask_definition_ami.py b/jwst/ami/mask_definition_ami.py
index 59a33c44a0..140dc539af 100644
--- a/jwst/ami/mask_definition_ami.py
+++ b/jwst/ami/mask_definition_ami.py
@@ -13,11 +13,14 @@
 um = 1.0e-6 * m
 
 
-class NRM_definition():
+class NRMDefinition():
 
 	def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None):
 		"""
-		Set attributes of NRM_definition class.
+		Set attributes of NRMDefinition class. 
+
+		Get hole centers and other mask geometry details from NRMModel, apply rotations/flips 
+		as necessary and set them as attributes.
 
 		Parameters
 		----------
@@ -29,12 +32,17 @@ def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None
 			range of rotations to search (degrees), optional
 		chooseholes: list
 			None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask, optional
+			If None, use real seven-hole mask
 		"""
 
 		if maskname not in ['jwst_ami','jwst_g7s6c']:
 			raise ValueError("Mask name not supported")
 
 		self.maskname = maskname # there's only one mask but this is used in oifits
+		self.hdia = nrm_model.flat_to_flat
+		self.activeD = nrm_model.diameter
+		self.OD = nrm_model.pupil_circumscribed
+		self.ctrs = []
 
 		self.read_nrm_model(nrm_model, chooseholes=chooseholes)
 
@@ -43,10 +51,7 @@ def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None
 
 	def read_nrm_model(self, nrm_model, chooseholes=None):
 		"""
-
-		Calculate hole centers with appropriate rotation,
-		set these and other mask geometry details from NRMModel as
-		attributes.
+		Calculate hole centers with appropriate rotation.
 
 		Parameters
 		----------
@@ -71,9 +76,7 @@ def read_nrm_model(self, nrm_model, chooseholes=None):
 							[nrm_model.x_a6, nrm_model.y_a6],        # B2 -> B6
 							[nrm_model.x_a7, nrm_model.y_a7]])        # C1 -> C6
 
-		self.hdia = nrm_model.flat_to_flat
-		self.activeD = nrm_model.diameter
-		self.OD = nrm_model.pupil_circumscribed
+
 
 		holedict = {}  # as_built names, C2 open, C5 closed, but as designed coordinates
 		# Assemble holes by actual open segment names (as_built).  Either the full mask or the

From 9254e6711d80c20228c8f92193fba82097b3a939 Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Thu, 12 Dec 2024 14:39:32 -0500
Subject: [PATCH 22/23] Fixed use of affine rotradccw, log statement  with
 commissioning default

---
 jwst/ami/ami_analyze.py      | 2 +-
 jwst/ami/ami_analyze_step.py | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/jwst/ami/ami_analyze.py b/jwst/ami/ami_analyze.py
index 4277bac9a8..adb78e94eb 100644
--- a/jwst/ami/ami_analyze.py
+++ b/jwst/ami/ami_analyze.py
@@ -183,7 +183,7 @@ def apply_LG_plus(
     log.info(f'\tmx={affine2d.mx:.6f}\tmy={affine2d.my:.6f}')
     log.info(f'\tsx={affine2d.sx:.6f}\tsy={affine2d.sy:.6f}')
     log.info(f'\txo={affine2d.xo:.6f}\tyo={affine2d.yo:.6f}')
-    log.info(f'\trotradccw={affine2d.rotradccw:.4f}')
+    log.info(f'\trotradccw={affine2d.rotradccw}')
 
     niriss = instrument_data.NIRISS(filt,
                                     nrm_model,
diff --git a/jwst/ami/ami_analyze_step.py b/jwst/ami/ami_analyze_step.py
index d5c009db7e..19cf0791be 100755
--- a/jwst/ami/ami_analyze_step.py
+++ b/jwst/ami/ami_analyze_step.py
@@ -192,7 +192,6 @@ def process(self, input):
                         sy=-7.27008e-03,
                         xo=0,
                         yo=0,
-                        rotradccw=0,
                         name='commissioning')
                     self.log.info("Using affine parameters from commissioning.")
                 else:

From 1cc5a6c0fc05c5bee50b115251398757dbd8fa2d Mon Sep 17 00:00:00 2001
From: Rachel Cooper <rcooper@stsci.edu>
Date: Fri, 13 Dec 2024 11:30:34 -0500
Subject: [PATCH 23/23] Style updates from second review

---
 jwst/ami/ami_analyze.py              |  3 +--
 jwst/ami/ami_analyze_step.py         | 19 +++++++++++------
 jwst/ami/find_affine2d_parameters.py |  9 +++-----
 jwst/ami/instrument_data.py          | 10 ++++-----
 jwst/ami/lg_model.py                 | 32 +++++++++++++++++-----------
 jwst/ami/mask_definition_ami.py      | 17 +--------------
 jwst/ami/nrm_core.py                 | 11 ++++------
 jwst/ami/oifits.py                   | 21 +++++++++---------
 8 files changed, 57 insertions(+), 65 deletions(-)

diff --git a/jwst/ami/ami_analyze.py b/jwst/ami/ami_analyze.py
index adb78e94eb..b872f52951 100644
--- a/jwst/ami/ami_analyze.py
+++ b/jwst/ami/ami_analyze.py
@@ -1,4 +1,3 @@
-#  Module for applying the LG-PLUS algorithm to an AMI exposure
 import logging
 import numpy as np
 import copy
@@ -30,7 +29,7 @@ def apply_LG_plus(
     run_bpfix,
 ):
     """
-    Applies the image plane algorithm to an AMI image
+    Applies the image plane algorithm (LG-PLUS) to an AMI exposure
 
     Parameters
     ----------
diff --git a/jwst/ami/ami_analyze_step.py b/jwst/ami/ami_analyze_step.py
index 19cf0791be..52a8ca9b93 100755
--- a/jwst/ami/ami_analyze_step.py
+++ b/jwst/ami/ami_analyze_step.py
@@ -9,6 +9,13 @@
 
 __all__ = ["AmiAnalyzeStep"]
 
+# Affine parameters from commissioning
+MX_COMM = 9.92820e-01
+MY_COMM = 9.98540e-01
+SX_COMM = 6.18605e-03
+SY_COMM = -7.27008e-03
+XO_COMM = 0.
+YO_COMM = 0.
 
 class AmiAnalyzeStep(Step):
     """Performs analysis of an AMI mode exposure by applying the LG algorithm."""
@@ -186,12 +193,12 @@ def process(self, input):
                 bandpass = self.override_bandpass()
             if affine2d is not None:
                 if affine2d == 'commissioning':
-                    affine2d = utils.Affine2d(mx=9.92820e-01,
-                        my=9.98540e-01,
-                        sx=6.18605e-03,
-                        sy=-7.27008e-03,
-                        xo=0,
-                        yo=0,
+                    affine2d = utils.Affine2d(mx=MX_COMM,
+                        my=MY_COMM,
+                        sx=SX_COMM,
+                        sy=SY_COMM,
+                        xo=XO_COMM,
+                        yo=YO_COMM,
                         name='commissioning')
                     self.log.info("Using affine parameters from commissioning.")
                 else:
diff --git a/jwst/ami/find_affine2d_parameters.py b/jwst/ami/find_affine2d_parameters.py
index 0ba18090ab..b554e7d336 100644
--- a/jwst/ami/find_affine2d_parameters.py
+++ b/jwst/ami/find_affine2d_parameters.py
@@ -1,7 +1,3 @@
-#
-#  Module for calculation of the optimal rotation for an image plane
-#
-
 import logging
 import numpy as np
 
@@ -14,8 +10,9 @@
 
 def create_afflist_rot(rotdegs):
     """
-    Create a list of affine objects with various rotations to use in order to
-    go through and find which fits an image plane data best.
+    Create a list of affine objects with various rotations.
+
+    Find which affine rotation fits an image plane data best.
 
     Parameters
     ----------
diff --git a/jwst/ami/instrument_data.py b/jwst/ami/instrument_data.py
index cbc253eabf..3d317a7e7b 100755
--- a/jwst/ami/instrument_data.py
+++ b/jwst/ami/instrument_data.py
@@ -1,8 +1,3 @@
-#
-#  Module for defining data format, wavelength info, an mask geometry for these
-#   instrument: NIRISS AMI
-#
-
 import logging
 import numpy as np
 
@@ -32,7 +27,10 @@ def __init__(self,
                  run_bpfix=True
                  ):
         """
-        Initialize NIRISS class
+        Initialize NIRISS class for NIRISS/AMI instrument.
+
+        Module for defining all instrument characteristics including data format, 
+        wavelength info, and mask geometry.
 
         Parameters
         ----------
diff --git a/jwst/ami/lg_model.py b/jwst/ami/lg_model.py
index 29170738dd..466fa6323c 100755
--- a/jwst/ami/lg_model.py
+++ b/jwst/ami/lg_model.py
@@ -1,5 +1,3 @@
-# A module for conveniently manipulating an 'NRM object' using the
-# Lacour-Greenbaum algorithm. First written by Alexandra Greenbaum in 2014.
 import logging
 import numpy as np
 
@@ -21,8 +19,9 @@
 
 class LgModel:
     """
-    A class for conveniently dealing with an "NRM object" This should be able
-    to take an NRMDefinition object for mask geometry.
+    A class for conveniently dealing with an "NRM object." 
+    
+    This should be able to take an NRMDefinition object for mask geometry.
     Defines mask geometry and detector-scale parameters.
     Simulates PSF (broadband or monochromatic)
     Builds a fringe model - either by user definition, or automated to data
@@ -30,6 +29,7 @@ class LgModel:
     Masks: jwst_ami (formerly jwst_g7s6c)
     Algorithm documented in Greenbaum, A. Z., Pueyo, L. P., Sivaramakrishnan,
     A., and Lacour, S., Astrophysical Journal vol. 798, Jan 2015.
+    First written by Alexandra Greenbaum in 2014.
     """
 
     def __init__(
@@ -132,8 +132,10 @@ def __init__(
 
     def simulate(self, fov=None, bandpass=None, over=None, psf_offset=(0, 0)):
         """
-        Simulate a detector-scale psf using parameters input from the call and
-        already stored in the object,and generate a simulation fits header
+        Simulate a detector-scale psf.
+
+        Use parameters input from the call and
+        already stored in the object, and generate a simulation fits header
         storing all of the  parameters used to generate that psf.  If the input
         bandpass is one number it will calculate a monochromatic psf.
 
@@ -191,9 +193,11 @@ def make_model(
         self, fov=None, bandpass=None, over=1, psf_offset=(0, 0), pixscale=None
     ):
         """
-        Generates the fringe model with the attributes of the object using a
-        bandpass that is either a single wavelength or a list of tuples of the
-        form [(weight1, wavl1), (weight2, wavl2),...].  The model is
+        Generates the fringe model.
+
+        Use the attributes of the object with a bandpass that is either a single 
+        wavelength or a list of tuples of the form 
+        [(weight1, wavl1), (weight2, wavl2),...].  The model is
         a collection of fringe intensities, where nholes = 7 means the model
         has a @D slice for each of 21 cosines, 21 sines, a DC-like, and a flux
         slice for a toal of 44 2D slices.
@@ -294,8 +298,10 @@ def fit_image(
         weighted=False,
     ):
         """
-        Run a least-squares fit on an input image; find the appropriate
-        wavelength scale and rotation. If a model is not specified then this
+        Run a least-squares fit on an input image.
+
+        Find the appropriate wavelength scale and rotation. 
+        If a model is not specified then this
         method will find the appropriate wavelength scale, rotation (and
         hopefully centering as well -- This is not written into the object yet,
         but should be soon).  Without specifying a model, fit_image can take a
@@ -419,7 +425,9 @@ def improve_scaling(
         self, img, scaleguess=None, rotstart=0.0, centering="PIXELCENTERED"
     ):
         """
-        Determine the scale and rotation that best fits the data.  Correlations
+        Determine the scale and rotation that best fits the data.  
+
+        Correlations
         are calculated in the image plane, in anticipation of data with many
         bad pixels.
 
diff --git a/jwst/ami/mask_definition_ami.py b/jwst/ami/mask_definition_ami.py
index 140dc539af..332c7abc46 100644
--- a/jwst/ami/mask_definition_ami.py
+++ b/jwst/ami/mask_definition_ami.py
@@ -1,21 +1,11 @@
-#
-#  Module for defining mask geometry in pupil space
-#  Replace old mask_definitions by reading info in nrm_model into a similar object.
-#
-
 import numpy as np
 import math
 
 from .utils import rotate2dccw
 
-m = 1.0
-mm = 1.0e-3 * m
-um = 1.0e-6 * m
-
-
 class NRMDefinition():
 
-	def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None):
+	def __init__(self, nrm_model, maskname='jwst_ami', chooseholes=None):
 		"""
 		Set attributes of NRMDefinition class. 
 
@@ -28,8 +18,6 @@ def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None
 			datamodel containing NRM reference file data
 		maskname: string
 			Identifier for mask geometry; default 'jwst_ami', optional
-		rotdeg: list of floats
-			range of rotations to search (degrees), optional
 		chooseholes: list
 			None, or e.g. ['B2', 'B4', 'B5', 'B6'] for a four-hole mask, optional
 			If None, use real seven-hole mask
@@ -46,9 +34,6 @@ def __init__(self, nrm_model, maskname='jwst_ami', rotdeg=None, chooseholes=None
 
 		self.read_nrm_model(nrm_model, chooseholes=chooseholes)
 
-		if rotdeg is not None:
-			self.rotdeg = rotdeg
-
 	def read_nrm_model(self, nrm_model, chooseholes=None):
 		"""
 		Calculate hole centers with appropriate rotation.
diff --git a/jwst/ami/nrm_core.py b/jwst/ami/nrm_core.py
index e03c911895..055e37a205 100755
--- a/jwst/ami/nrm_core.py
+++ b/jwst/ami/nrm_core.py
@@ -1,8 +1,3 @@
-#! /usr/bin/env python
-
-# Module for fringe fitting class
-# Original python was by A. Greenbaum & A. Sivaramakrishnan
-
 import logging
 import numpy as np
 from . import lg_model
@@ -18,8 +13,11 @@
 class FringeFitter:
     def __init__(self, instrument_data, **kwargs):
         """
+        Fit fringes to get interferometric observables for the data.
+
         For the given information on the instrument and mask, calculate the
         fringe observables (visibilities and closure phases in the image plane.
+        Original python was by A. Greenbaum & A. Sivaramakrishnan
 
         Parameters
         ----------
@@ -160,8 +158,7 @@ def make_lgfitmodel(self):
 
     def fit_fringes_single_integration(self, slc):
         """
-        Generate the best model to
-        match a single slice
+        Generate the best model to match a single slice.
 
         Parameters
         ----------
diff --git a/jwst/ami/oifits.py b/jwst/ami/oifits.py
index b373babd24..52616089bc 100644
--- a/jwst/ami/oifits.py
+++ b/jwst/ami/oifits.py
@@ -1,12 +1,5 @@
 #! /usr/bin/env python
-"""
-RawOifits class: takes fringefitter class, which contains nrm_list and instrument_data attributes,
-all info needed to write oifits.
-populate structure needed to write out oifits files according to schema.
-averaged and multi-integration versions, sigma-clipped stats over ints
-
-CalibOifits class: takes two AmiOIModel datamodels and produces a final calibrated datamodel.
-"""
+
 import numpy as np
 from scipy.special import comb
 from astropy.stats import sigma_clipped_stats
@@ -23,8 +16,14 @@
 class RawOifits:
     def __init__(self, fringefitter, method="mean"):
         """
-        Class to store AMI data in the format required to write out to OIFITS files
-        Angular quantities of input are in radians from fringe fitting; converted to degrees for saving.
+        Class to store AMI data in the format required to write out to OIFITS files.
+
+        Takes fringefitter class, which contains nrm_list and instrument_data attributes,
+        all info needed to write oifits. Angular quantities of input are in radians from 
+        fringe fitting; converted to degrees for saving. Populate the structure needed to 
+        write out oifits files according to schema.
+        Produces averaged and multi-integration versions, with sigma-clipped stats over
+        integrations.
 
         Parameters
         ----------
@@ -729,6 +728,8 @@ def _format_STAINDEX_V2(self, tab):
 class CalibOifits:
     def __init__(self, targoimodel, caloimodel):
         """
+        Produce a final calibrated AmiOIModel.
+
         Calibrate (normalize) an AMI observation by subtracting closure phases
         of a reference star from those of a target and dividing visibility amplitudes
         of the target by those of the reference star.