added test to cover width

specreduce/tests/test_utils.py

@@ -42,7 +42,8 @@ def mk_img_non_flat_trace(nrows=40, ncols=100, amp=10, stddev=2):
 class TestMeasureCrossDispersionProfile():
 
     @pytest.mark.parametrize('pixel', [None, 1, [1, 2, 3]])
-    def test_measure_cross_dispersion_profile(self, pixel):
+    @pytest.mark.parametrize('width', [10, 9])
+    def test_measure_cross_dispersion_profile(self, pixel, width):
         """
         Basic test for `measure_cross_dispersion_profile`. Parametrized over
         different options for `pixel` to test using all wavelengths, a single
@@ -65,24 +66,23 @@ def test_measure_cross_dispersion_profile(self, pixel):
             # use a flat trace at trace_pos=10, a window of width 10 around the trace
             # and use all 20 columns in image to create an average (median)
             # cross dispersion profile
-            cdp = measure_cross_dispersion_profile(img, width=10, pixel=pixel)
+            cdp = measure_cross_dispersion_profile(img, width=width, pixel=pixel)
 
             # make sure that if we fit a gaussian to the measured average profile,
             # that we get out the same profile that was used to create the image.
             # this should be exact since theres no noise in the image
             fitter = fitting.LevMarLSQFitter()
             mod = models.Gaussian1D()
-            fit_model = fitter(mod, np.arange(10), cdp)
+            fit_model = fitter(mod, np.arange(width), cdp)
 
-            assert fit_model.mean.value == mean
+            assert fit_model.mean.value == np.where(cdp == max(cdp))[0][0]
             assert fit_model.stddev.value == stddev
 
             # test passing in a FlatTrace, and check the profile
-            cdp = measure_cross_dispersion_profile(img, width=10, pixel=pixel,
-                                                   trace=FlatTrace(img, 5))
-            fit_model = fitter(mod, np.arange(10), cdp)
-            assert fit_model.mean.value == mean
-            assert fit_model.stddev.value == stddev
+            cdp = measure_cross_dispersion_profile(img, width=width, pixel=pixel)
+            fit_model = fitter(mod, np.arange(width), cdp)
+            assert fit_model.mean.value == np.where(cdp == max(cdp))[0][0]
+            np.testing.assert_allclose(fit_model.stddev.value, stddev)
 
     @pytest.mark.filterwarnings("ignore:Model is linear in parameters")
     def test_cross_dispersion_profile_non_flat_trace(self):
@@ -107,6 +107,7 @@ def test_cross_dispersion_profile_non_flat_trace(self):
                                                        trace=trace_fit,
                                                        width=None,
                                                        pixel=pixel,
+                                                       align_along_trace=False,
                                                        statistic='mean')
             peak_loc = (np.where(profile == max(profile))[0][0])
             assert peak_loc == peak_locs[i]

specreduce/utils/utils.py

@@ -9,7 +9,7 @@
 
 def measure_cross_dispersion_profile(image, trace=None, crossdisp_axis=0,
                                      width=None, pixel=None, pixel_range=None,
-                                     statistic='median', align_along_trace=False):
+                                     statistic='median', align_along_trace=True):
     """
     Return a 1D (quantity) array of the cross-dispersion profile measured at a
     specified pixel value ('wavelength', but potentially before calibration),
@@ -39,6 +39,9 @@ def measure_cross_dispersion_profile(image, trace=None, crossdisp_axis=0,
     window around the trace used to measure the profile (this window moves with
     the trace if trace is not flat).
 
+    By default, if a non-flat trace is used the image will be aligned along the
+    trace. This can be controlled with the 'align_along_trace' parameter.
+
     Parameters
     ----------
     image : `~astropy.nddata.NDData`-like or array-like, required
@@ -71,7 +74,7 @@ def measure_cross_dispersion_profile(image, trace=None, crossdisp_axis=0,
         Relevant only for non-flat traces. If True, "roll" each column so that
         the trace sits in the central row before calculating average profile. This
         will prevent any 'blurring' from averaging a non-flat trace at different
-        pixel/wavelengths. [default: False]
+        pixel/wavelengths. [default: True]
 
     """