Style and doctring updates following review

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

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")

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

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

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