ruff reformatting, typos, etc

Author: rcooper295

jwst/ami/oifits.py

@@ -462,8 +462,6 @@ def make_oifits(self):
         oim = datamodels.AmiOIModel()
         self.init_oimodel_arrays(oim)
 
-        # for u-v coords: index 0 and 1 reversed to get the good coverage (same fft)
-
         # primary header keywords
         oim.meta.telescope = instrument_data.telname
         oim.meta.origin = "STScI"
@@ -518,6 +516,7 @@ def make_oifits(self):
         oim.vis["VISAMPERR"] = self.e_visamp
         oim.vis["VISPHI"] = self.visphi
         oim.vis["VISPHIERR"] = self.e_visphi
+        # for all u-v coords: index 0 and 1 reversed to get the good coverage (same fft)
         oim.vis["UCOORD"] = self.bls[:, 1]
         oim.vis["VCOORD"] = self.bls[:, 0]
         oim.vis["STA_INDEX"] = self._format_staindex(self.bholes)
@@ -789,14 +788,15 @@ def _format_staindex(self, tab):
             List of arrays of hole baseline indices (of length 2, 3, 4, etc.)
         """
         sta_index = []
-        offset = 1 if np.min(tab) == 0 else 0 # 1-indexed
+        offset = 1 if np.min(tab) == 0 else 0  # 1-indexed
 
         for row in tab:
             line = np.array(row, dtype=int) + offset
             sta_index.append(line)
 
         return sta_index
 
+
 class CalibOifits:
     """
     Produce a final calibrated AmiOIModel.
@@ -856,7 +856,7 @@ def calibrate(self):
         cp_out = self.targoimodel.t3["T3PHI"] - self.caloimodel.t3["T3PHI"]
         sqv_out = self.targoimodel.vis2["VIS2DATA"] / self.caloimodel.vis2["VIS2DATA"]
         va_out = self.targoimodel.vis["VISAMP"] / self.caloimodel.vis["VISAMP"]
-        ca_out = np.log(self.targoimodel.q4["Q4AMP"]/self.caloimodel.q4["Q4AMP"]) # log of ratio
+        ca_out = np.log(self.targoimodel.q4["Q4AMP"] / self.caloimodel.q4["Q4AMP"])  # log of ratio
         # using standard propagation of error for multiplication/division
         # which assumes uncorrelated Gaussian errors (questionable)
         cperr_t = self.targoimodel.t3["T3PHIERR"]
@@ -881,7 +881,7 @@ def calibrate(self):
         caerr_out = np.sqrt(
             (caerr_t / self.targoimodel.q4["Q4AMP"]) ** 2
             + (caerr_c / self.caloimodel.q4["Q4AMP"]) ** 2
-            )
+        )
 
         pistons_t = self.targoimodel.array["PISTONS"]
         pisterr_t = self.targoimodel.array["PIST_ERR"]

jwst/ami/tests/test_ami_normalize.py

@@ -102,61 +102,38 @@ def oi_data(example_model, bandpass):
     oim.vis = np.zeros(n_baselines, dtype=oim.vis.dtype)
     oim.vis["TARGET_ID"] = 1
     oim.vis["TIME"] = 0
-    # oim.vis["MJD"] = 0
-    # oim.vis["INT_TIME"] = 0
     oim.vis["VISAMP"] = visamp
     oim.vis["VISAMPERR"] = visamp * ERR
     oim.vis["VISPHI"] = visphi
     oim.vis["VISPHIERR"] = visphi * ERR
-    # oim.vis["UCOORD"] = ucoord
-    # oim.vis["VCOORD"] = vcoord
-    # oim.vis["STA_INDEX"] = sta_index
     oim.vis["FLAG"] = flag_vis
 
     # oi_vis2 extension data
     oim.vis2 = np.zeros(n_baselines, dtype=oim.vis2.dtype)
     oim.vis2["TARGET_ID"] = 1
     oim.vis2["TIME"] = 0
-    # oim.vis2["MJD"] = observation_date.mjd
-    # oim.vis2["INT_TIME"] = instrument_data.itime
     oim.vis2["VIS2DATA"] = (visamp**2).T
     oim.vis2["VIS2ERR"] = (visamp**2).T * ERR
-    # oim.vis2["UCOORD"] = ucoord
-    # oim.vis2["VCOORD"] = vcoord
-    # oim.vis2["STA_INDEX"] = np.arange(n_holes) + 1
     oim.vis2["FLAG"] = flag_vis
 
     # oi_t3 extension data
     oim.t3 = np.zeros(n_closure_phases, dtype=oim.t3.dtype)
     oim.t3["TARGET_ID"] = 1
     oim.t3["TIME"] = 0
-    # oim.t3["MJD"] = observation_date.mjd
     oim.t3["T3AMP"] = t3amp
     oim.t3["T3AMPERR"] = t3amp * ERR
     oim.t3["T3PHI"] = t3phi
     oim.t3["T3PHIERR"] = t3phi * ERR
-    # oim.t3["U1COORD"] = u1coord
-    # oim.t3["V1COORD"] = v1coord
-    # oim.t3["U2COORD"] = u2coord
-    # oim.t3["V2COORD"] = v2coord
-    # oim.t3["STA_INDEX"] = sta_index
     oim.t3["FLAG"] = flag_t3
 
     # oi_q4 data
     oim.q4 = np.zeros(n_quads, dtype=oim.q4.dtype)
     oim.q4["TARGET_ID"] = 1
     oim.q4["TIME"] = 0
-    # oim.q4["MJD"] = observation_date.mjd
     oim.q4["Q4AMP"] = q4amp
     oim.q4["Q4AMPERR"] = q4amp * ERR
     oim.q4["Q4PHI"] = q4phi
     oim.q4["Q4PHIERR"] = q4phi * ERR
-    # oim.q4["U1COORD"] = u1coord_q4
-    # oim.q4["V1COORD"] = v1coord_q4
-    # oim.q4["U2COORD"] = u2coord_q4
-    # oim.q4["V2COORD"] = v2coord_q4
-    # oim.q4["U3COORD"] = u3coord_q4
-    # oim.q4["V3COORD"] = v3coord_q4
     oim.q4["FLAG"] = flag_q4
 
     # oi_wavelength extension data
@@ -197,5 +174,5 @@ def test_ami_normalize(oi_data, ref_data):
     assert np.allclose(result.vis2["VIS2DATA"], (RAW_AMP / REF_AMP) ** 2)
     assert np.allclose(result.t3["T3AMP"], RAW_AMP)
     assert np.allclose(result.t3["T3PHI"], RAW_PHI - REF_PHI)
-    assert np.allclose(result.q4["Q4_AMP"], np.log(RAW_AMP / REF_AMP))
-    assert np.allclose(result.q4["Q4_PHI"], RAW_PHI)
+    assert np.allclose(result.q4["Q4AMP"], np.log(RAW_AMP / REF_AMP))
+    assert np.allclose(result.q4["Q4PHI"], RAW_PHI)

jwst/ami/tests/test_nrm_core.py

@@ -44,7 +44,7 @@ def test_fringe_fitter(example_model, nrm_model, bandpass, nrm_psf):
         assert len(oimodel.vis) == 21  # number of baselines: 7 holes choose 2
         assert len(oimodel.vis2) == 21
         assert len(oimodel.t3) == 35  # number of triples: 7 holes choose 3
-        assert len(oimodel.q4) == 35 # number of quads: 7 holes choose 4
+        assert len(oimodel.q4) == 35  # number of quads: 7 holes choose 4
         vis_amp = oimodel.vis["VISAMP"]
         vis_amp_err = oimodel.vis["VISAMPERR"]
         vis_phase = oimodel.vis["VISPHI"]
@@ -60,7 +60,6 @@ def test_fringe_fitter(example_model, nrm_model, bandpass, nrm_psf):
         q4_phase = oimodel.q4["Q4PHI"]
         q4_phase_err = oimodel.q4["Q4PHIERR"]
 
-
         for arr in [
             vis_amp,
             vis_amp_err,
@@ -73,7 +72,7 @@ def test_fringe_fitter(example_model, nrm_model, bandpass, nrm_psf):
             t3_phase,
             t3_phase_err,
             q4_phase,
-            q4_phase_err
+            q4_phase_err,
         ]:
             assert arr.dtype == np.float64
             if i == 0: