make sur npix_array is returned

also return covariance

py/rvspecfit/desi/desi_fit.py

@@ -41,7 +41,8 @@ def __str__(self):
     'RV_WARN': 2,  # rv is to close to the edge
     'RVERR_WARN': 4,  # RV error is too large
     'PARAM_WARN': 8,  # parameters are too close to the edge
-    'VSINI_WARN': 16  # vsini is too large
+    'VSINI_WARN': 16,  # vsini is too large
+    'BAD_SPECTRUM': 32  # some issue with the spectrum
 }
 
 
@@ -774,7 +775,6 @@ def get_specdata(waves,
                 medspec = np.nanmedian(np.abs(spec))
         if not np.isfinite(medspec) or medspec == 0:
             # bail out the spectrum is insane
-            # TODO make the logic clearer
             continue
         baddat = ~np.isfinite(spec + curivars)
         if mask_dicroic:
@@ -1042,6 +1042,7 @@ def proc_desi(fname,
     else:
         rr_z = np.zeros(len(seqid_to_fit)) + np.nan
         rr_spectype = np.ma.zeros(len(seqid_to_fit), dtype=str)
+
     subset_ret = subset.copy()
     # returned subset to deal with the fact that
     # I'll skip some spectra

py/rvspecfit/vel_fit.py

@@ -395,6 +395,12 @@ def _minimum_sampler(func,
 
 
 def _uncertainties_from_hessian(hessian):
+    """
+    Take the hessian and return the uncertainties vector and
+    covariance matrix
+    Here I also protect all sorts of failures when encountering
+    bad hessian
+    """
     diag_hessian = np.diag(hessian)
     inv_diag_hessian = 1. / (diag_hessian + (diag_hessian == 0))
     inv_diag_hessian[diag_hessian == 0] = np.inf
@@ -419,7 +425,7 @@ def _uncertainties_from_hessian(hessian):
     diag_err0[sub2] = 0
     diag_err = np.sqrt(diag_err0)
     diag_err[sub2] = np.nan
-    return diag_err
+    return diag_err, hessian_inv
 
 
 def process(specdata,
@@ -630,15 +636,17 @@ def hess_func_wrap(p):
     hess_step = ndf.MaxStepGenerator(base_step=hess_step)
     hessian = ndf.Hessian(hess_func_wrap, step=hess_step)(
         [ret['param'][_] for _ in specParamNames])
-    diag_err = _uncertainties_from_hessian(hessian)
+    diag_err, covar_mat = _uncertainties_from_hessian(hessian)
     ret['param_err'] = dict(zip(specParamNames, diag_err))
+    ret['param_covar'] = covar_mat
     ret['minimize_success'] = minimize_success
 
     ret['yfit'] = outp['models']
     ret['raw_models'] = outp['raw_models']
     ret['chisq'] = outp['chisq']
     ret['logl'] = outp['logl']
     ret['chisq_array'] = outp['chisq_array']
+    ret['npix_array'] = outp['npix_array']
     t6 = time.time()
     logging.debug('Timings process: %.4f %.4f %.4f %.4f, %.4f %.4f' %
                   (t1 - t0, t2 - t1, t3 - t2, t4 - t3, t5 - t4, t6 - t5))