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Minor bug fixes that seemed necessary to get v2.0 to run #394

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Minor bug fixes that seemed necessary to get v2.0 to run #394

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33f0bd0
Fix: set _speccal before fit_mle_elines needs it
jhennawi Dec 26, 2025
93327a6
bug fixes in sedmodel.py
jhennawi Dec 26, 2025
9662d70
Fix: replaced bitwise not with logical not
jhennawi Dec 26, 2025
172fdb4
Fix: replaced bitwise not with logical not
jhennawi Dec 26, 2025
555ff0a
changed bitwise to logical and
jhennawi Jan 11, 2026
778cd1a
Merge upstream/main into fix-speccal-ordering
jhennawi Jan 29, 2026
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12 changes: 9 additions & 3 deletions prospect/models/sedmodel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -211,7 +211,7 @@ def predict_intrinsic(self, obs_dummy, continuum_only=True, **extras):

# --- add fixed lines if necessary ---
emask = self._fix_eline_pixelmask
if emask.any() & (~continuum_only):
if emask.any() and (not continuum_only):
inds = self._fix_eline & self._valid_eline
espec = self.predict_eline_spec(line_indices=inds,
wave=self._outwave[emask])
Expand All @@ -220,7 +220,7 @@ def predict_intrinsic(self, obs_dummy, continuum_only=True, **extras):

# --- add (previously) fitted lines if necessary ---
emask = self._fit_eline_pixelmask
if emask.any() (~continuum_only):
if emask.any() and (not continuum_only):
inst_spec[emask] += self._fit_eline_spec.sum(axis=1)

return inst_spec
Expand Down Expand Up @@ -313,6 +313,12 @@ def predict_spec(self, obs):
extra_mask=extra_mask,
**self.params)
inst_spec = inst_spec * response
# Set _speccal before fit_mle_elines needs it
# Ensure it's an array (response can be scalar 1.0 when no polynomial calibration)
if np.isscalar(response):
self._speccal = np.ones_like(inst_spec) * response
else:
self._speccal = response

# --- fit and add lines if necessary ---
emask = self._fit_eline_pixelmask
Expand Down Expand Up @@ -713,7 +719,7 @@ def fit_mle_elines(self, obs, calibrated_spec, sigma_spec=None):
# Store fitted emission line luminosities in physical units, including prior
self._eline_lum[idx] = alpha_bar / linecal
# store new Gaussian uncertainties in physical units
self._eline_lum_var[np.ix_(idx, idx)] = sigma_alpha_bar / linecal[:, None] / linecal[None, :]
self._eline_lum_covar[np.ix_(idx, idx)] = sigma_alpha_bar / linecal[:, None] / linecal[None, :]

# return the maximum-likelihood line spectrum for this observation in observed units
self._eline_lum_mle[idx] = alpha_hat / linecal
Expand Down