Resolving issues and suggestions from PR reviews by @melanieclarke and …

…@emolter

docs/jwst/ami_analyze/description.rst

@@ -62,33 +62,33 @@ Examples of how to create ASDF files containing the properly formatted informati
 
 .. code-block:: python
 
-   # Create a F380M filter + A0V source bandpass ASDF file
+   # Create a F480M filter + Vega bandpass ASDF file
 
    import asdf
    from jwst.ami import utils
+   from stdatamodels.jwst import datamodels
+   from synphot import SourceSpectrum
 
-   filt='F380M'
-   src = 'A0V'
+   # F480M throughput reference file from JWST CRDS
+   throughput_file = 'jwst_niriss_throughput_0012.fits'
    nspecbin=19
+   throughput_model = datamodels.open(throughput_file)
 
-   filt_spec = utils.get_filt_spec(filt)
-   src_spec = utils.get_src_spec(src)
-
-   bandpass = utils.combine_src_filt(filt_spec, 
-                                  src_spec, 
-                                  trim=0.01, 
-                                  nlambda=nspecbin)
-
-   # this bandpass has shape (19, 2); each row is [throughput, wavelength]
-
-   asdf_name = 'bandpass_f380m_a0v.asdf'
+   filt_spec = utils.get_filt_spec(throughput_model)
+   src_spec = SourceSpectrum.from_vega()  
+   bandpass = utils.combine_src_filt(filt_spec,
+                                    src_spec,
+                                    trim=0.01,
+                                    nlambda=nspecbin)
 
+   # This bandpass has shape (19, 2); each row is [throughput, wavelength]
+   asdf_name = 'bandpass_f480m_vega.asdf'
    tree = {"bandpass": bandpass}
-
    with open(asdf_name, 'wb') as fh:
         af = asdf.AsdfFile(tree)
         af.write_to(fh)
    af.close()
+   throughput_model.close()
 
 
 .. code-block:: python
@@ -97,13 +97,14 @@ Examples of how to create ASDF files containing the properly formatted informati
 
    import asdf
    tree = {
-   'mx': 1., # dimensionless x-magnification
-   'my': 1., # dimensionless y-magnification
-   'sx': 0., # dimensionless x shear
-   'sy': 0., # dimensionless y shear
-   'xo': 0., # x-offset in pupil space
-   'yo': 0., # y-offset in pupil space
-   'rotradccw': None }
+         'mx': 1., # dimensionless x-magnification
+         'my': 1., # dimensionless y-magnification
+         'sx': 0., # dimensionless x shear
+         'sy': 0., # dimensionless y shear
+         'xo': 0., # x-offset in pupil space
+         'yo': 0., # y-offset in pupil space
+         'rotradccw': None 
+         }
 
    affineasdf = 'affine.asdf'
 

jwst/ami/ami_analyze_step.py

@@ -36,14 +36,19 @@ def save_model(self, model, *args, **kwargs):
             kwargs["suffix"] = ["ami-oi", "amimulti-oi", "amilg"][kwargs.pop("idx")]
         return Step.save_model(self, model, *args, **kwargs)
 
-
     def override_bandpass(self):
         """
-        Read bandpass from asdf file. Expects an array of [effstims, wave_m] 
-        (i.e. np.array((effstims,wave_m)).T) stored as 'bandpass' in asdf file,
-        where effstims are normalized countrates (unitless) and wave_m is wavelengths 
-        across the filter at which to compute the model (meters).
+        Read bandpass from asdf file and use it to override the default.
 
+        Expects an array of [effstims, wave_m] 
+        (i.e. np.array((effstims,wave_m)).T) stored as 'bandpass' in asdf file,
+        where effstims are normalized countrates (unitless) and wave_m are the
+        wavelengths across the filter at which to compute the model (meters).
+        
+        Returns
+        -------
+            bandpass: array
+                Array of [countrates, wavelengths]
         """
 
         try:
@@ -62,15 +67,26 @@ def override_bandpass(self):
             self.bandpass = bandpass 
             return bandpass
 
-        except:
-            message = (f'Could not read bandpass from {self.bandpass}. \
-                See documentation for info on creating a custom bandpass ASDF file.')
+        except FileNotFoundError:
+            message = f'File {self.bandpass} could not be found at the specified location.'
             raise Exception(message)
 
+        except KeyError:
+            message1 = 'ASDF file does not contain the required "bandpass" key. ' 
+            message2 = 'See step documentation for info on creating a custom bandpass ASDF file.'
+            raise Exception((message1 + message2))
+
+        except (IndexError, ValueError):
+            message1 = f'Could not use bandpass from {self.bandpass}. It may have the wrong shape. '
+            message2 = 'See documentation for info on creating a custom bandpass ASDF file.'
+            raise Exception((message1 + message2))
+
     def override_affine2d(self):
         """
-        Read user-input affine transform from ASDF file. Make Affine2d object
-        (see utils.Affine2D class). Input should contain mx,my,sx,sy,xo,yo,rotradccw.
+        Read user-input affine transform from ASDF file. 
+
+        Makes an Affine2d object (see utils.Affine2D class). 
+        Input should contain mx,my,sx,sy,xo,yo,rotradccw.
         """
         try:
             with asdf.open(self.affine2d, lazy_load=False) as af:
@@ -87,10 +103,24 @@ def override_affine2d(self):
             # now self.affine2d updated from string to object
             self.affine2d = affine2d
             return affine2d
-        except:
-            self.log.info(f'Could not read affine transfrom parameters from {self.affine2d}. \
-                See documentation for info on creating a custom affine2d ASDF file.')
-            self.log.info('**** DEFAULTING TO USE IDENTITY TRANSFORM ****')
+
+        except FileNotFoundError:
+            self.log.info(f'File {self.affine2d} could not be found at the specified location.')
+            self.log.info('\t **** DEFAULTING TO USE IDENTITY TRANSFORM ****')
+            affine2d = None
+
+        except KeyError:
+            message1 = 'ASDF file does not contain all of the required keys: mx, my, sx, sy ,xo, yo, rotradccw. ' 
+            message2 = 'See step documentation for info on creating a custom affine2d ASDF file.'
+            self.log.info((message1 + message2))
+            self.log.info('\t **** DEFAULTING TO USE IDENTITY TRANSFORM ****')
+            affine2d = None
+
+        except (IndexError, TypeError, ValueError):
+            message1 = f'Could not use affine2d from {self.affine2d}. '
+            message2 = 'See documentation for info on creating a custom bandpass ASDF file.'
+            self.log.info((message1 + message2))
+            self.log.info('\t **** DEFAULTING TO USE IDENTITY TRANSFORM ****')
             affine2d = None
 
         self.affine2d = affine2d

jwst/ami/instrument_data.py

@@ -184,7 +184,6 @@ def read_data_model(self, input_model):
         self.vparity = input_model.meta.wcsinfo.vparity
         self.v3iyang = input_model.meta.wcsinfo.v3yangle
 
-        self.parangh = self.roll_ref
         self.crpix1 = input_model.meta.wcsinfo.crpix1
         self.crpix2 = input_model.meta.wcsinfo.crpix2
         self.pupil = input_model.meta.instrument.pupil
@@ -333,7 +332,9 @@ def reset_nwav(self, nwav):
 
     def mast2sky(self):
         """
-        Rotate hole center coordinates:
+        Rotate hole center coordinates.
+
+        Rotation of coordinates is:
             Clockwise by the ROLL_REF + V3I_YANG from north in degrees if VPARITY = -1
             Counterclockwise by the ROLL_REF + V3I_YANG from north in degrees if VPARITY = 1
         Hole center coords are in the V2, V3 plane in meters.
@@ -342,7 +343,8 @@ def mast2sky(self):
         -----
             Nov. 2024 email discussion with Tony Sohn, Paul Goudfrooij confirmed V2/V3 coordinate
             rotation back to "North up" equatorial orientation should use ROLL_REF + V3I_YANG
-            (= PA_APER). 
+            (= PA_APER).
+
         Returns
         -------
         ctrs_rot: array
@@ -354,13 +356,13 @@ def mast2sky(self):
         # NOT used for the fringe fitting itself
         mask_ctrs = utils.rotate2dccw(mask_ctrs, np.pi / 2.0)
         vpar = self.vparity  # Relative sense of rotation between Ideal xy and V2V3
-        rot_ang = self.roll_ref + self.v3iyang  # subject to change!
+        rot_ang = self.roll_ref + self.v3iyang
 
         if self.roll_ref == 0.0:
             return mask_ctrs
         else:
             # Using rotate2sccw, which rotates **vectors** CCW in a fixed coordinate system,
-            # so to rotate coord system CW instead of the vector, reverse sign of rotation angle.  Double-check comment
+            # so to rotate coord system CW instead of the vector, reverse sign of rotation angle.
             if vpar == -1:
                 # rotate clockwise  <rotate coords clockwise>
                 ctrs_rot = utils.rotate2dccw(mask_ctrs, np.deg2rad(-rot_ang))

jwst/ami/leastsqnrm.py

@@ -746,8 +746,8 @@ def populate_antisymmphasearray(deltaps, n=7):
     deltaps: 1D float array
         pistons between each pair of holes
 
-    n: integer
-        number of holes
+    n: integer, optional
+        number of holes (default=7)
 
     Returns
     -------
@@ -778,8 +778,8 @@ def populate_symmamparray(amps, n=7):
     amps: 1D float array
         fringe visibility between each pair of holes
 
-    n: integer
-        number of holes
+    n: integer, optional
+        number of holes (default=7)
 
     Returns
     -------
@@ -810,8 +810,8 @@ def t3_amplitudes(amps, n=7):
     amps: 1D float array
         fringe visibility between each pair of holes
 
-    n: integer
-        number of holes
+    n: integer, optional
+        number of holes (default=7)
 
     Returns
     -------
@@ -847,8 +847,8 @@ def redundant_cps(deltaps, n=7):
     deltaps: 1D float array
         pistons between each pair of holes
 
-    n: integer
-        number of holes
+    n: integer, optional
+        number of holes (default=7)
 
     Returns
     -------
@@ -943,8 +943,8 @@ def closure_amplitudes(amps, n=7):
     amps: 1D float array
          fringe amplitudes
 
-    N: integer
-        number of holes
+    n: integer, optional
+        number of holes (default=7)
 
     Returns
     -------
@@ -981,8 +981,8 @@ def q4_phases(deltaps, n=7):
     deltaps: 1D float array
         pistons between each pair of holes
 
-    n: integer
-        number of holes
+    n: integer, optional
+        number of holes (default=7)
 
     Returns
     -------

jwst/ami/nrm_core.py

@@ -234,5 +234,3 @@ def fit_fringes_single_integration(self, slc):
         # model now stored as nrm.modelpsf, also nrm.residual
         self.nrm = nrm # this gets updated with each slice
         return nrm # to fit_fringes_all, where the output model will be created from list of nrm objects
-
-