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Fix for Astropy v7.0 incompatibility (#229) #232

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merged 7 commits into from
Nov 27, 2024
Merged

Fix for Astropy v7.0 incompatibility (#229) #232

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97add95
Fixed Issue #229: increased the absolute and relative tolerances of '…
hpparvi Nov 15, 2024
8e5baae
Changed to use the default relative tolerances in the 'assert_allclos…
hpparvi Nov 15, 2024
8b0cd21
Changed to use `astropy.modeling.fitting.LMLSQFitter` instead of `ast…
hpparvi Nov 15, 2024
2292795
Changed FitTrace to use a linear fitter (LinearLSQFitter) when fittin…
hpparvi Nov 26, 2024
ed5c3b8
Changed to use DogBoxLSQFitter instead of LMLSQFitter in '_fit_trace'…
hpparvi Nov 26, 2024
f001054
Relaxed the absolute tolerances to 0.1 pixels in test_fit_trace_all_n…
hpparvi Nov 26, 2024
c053b33
Updated the change log.
hpparvi Nov 26, 2024
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6 changes: 3 additions & 3 deletions specreduce/tests/test_tracing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -203,21 +203,21 @@ def test_fit_trace_all_nan_cols(self):
4.6474359, 5.25, 5.8525641, 6.4551282, 7.0576923,
7.6602564]
max_trace = FitTrace(img, peak_method='max')
np.testing.assert_allclose(truth, max_trace.trace)
np.testing.assert_allclose(truth, max_trace.trace, atol=0.1)

# peak_method = 'gaussian'
truth = [1.947455, 2.383634, 2.8198131, 3.2559921, 3.6921712,
4.1283502, 4.5645293, 5.0007083, 5.4368874, 5.8730665,
6.3092455]
max_trace = FitTrace(img, peak_method='gaussian')
np.testing.assert_allclose(truth, max_trace.trace)
np.testing.assert_allclose(truth, max_trace.trace, atol=0.1)

# peak_method = 'centroid'
truth = [2.5318835, 2.782069, 3.0322546, 3.2824402, 3.5326257,
3.7828113, 4.0329969, 4.2831824, 4.533368, 4.7835536,
5.0337391]
max_trace = FitTrace(img, peak_method='centroid')
np.testing.assert_allclose(truth, max_trace.trace)
np.testing.assert_allclose(truth, max_trace.trace, atol=0.1)

@pytest.mark.filterwarnings("ignore:The fit may be unsuccessful")
@pytest.mark.filterwarnings("ignore:Model is linear in parameters")
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17 changes: 11 additions & 6 deletions specreduce/tracing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -190,8 +190,9 @@ class FitTrace(Trace, _ImageParser):
or `~astropy.modeling.spline.Spline1D`, optional
The 1-D polynomial model used to fit the trace to the bins' peak
pixels. Spline1D models are fit with Astropy's
'SplineSmoothingFitter', while the other models are fit with the
'LevMarLSQFitter'. [default: ``models.Polynomial1D(degree=1)``]
'SplineSmoothingFitter', generic linear models are fit with the
'LinearLSQFitter', while the other models are fit with the
'LMLSQFitter'. [default: ``models.Polynomial1D(degree=1)``]
peak_method : string, optional
One of ``gaussian``, ``centroid``, or ``max``.
``gaussian``: Fits a gaussian to the window within each bin and
Expand Down Expand Up @@ -295,7 +296,7 @@ def _fit_trace(self, img):
offset_init = models.Const1D(np.ma.median(ztot))
profile = g1d_init + offset_init

fitter = fitting.LevMarLSQFitter()
fitter = fitting.DogBoxLSQFitter()
popt_tot = fitter(profile, yy, ztot)

# restrict fit to window (if one exists)
Expand Down Expand Up @@ -394,9 +395,13 @@ def _fit_trace(self, img):
y_bins = y_bins[y_finite]

# use given model to bin y-values; interpolate over all wavelengths
fitter = (fitting.SplineSmoothingFitter()
if isinstance(self.trace_model, models.Spline1D)
else fitting.LevMarLSQFitter())
if isinstance(self.trace_model, models.Spline1D):
fitter = fitting.SplineSmoothingFitter()
elif self.trace_model.linear:
fitter = fitting.LinearLSQFitter()
else:
fitter = fitting.LMLSQFitter()

self.trace_model_fit = fitter(self.trace_model, x_bins, y_bins)

trace_x = np.arange(img.shape[self._disp_axis])
Expand Down