Fix Update Linelist and line parameter fitting

src/pysme/sme_synth.py

@@ -178,7 +178,9 @@ def UpdateLineList(self, atomic, species, index):
         index : array(int) of size (nlines,)
             indices of the lines to update relative to the overall linelist
         """
-        atomic = atomic.T
+        index = np.asarray(index, dtype=np.int16)
+        species = species[index].astype("S8")
+        atomic = atomic[index].T
 
         _smelib.UpdateLineList(
             species,

src/pysme/smelib/_smelib.cpp

@@ -287,7 +287,8 @@ static PyObject *smelib_UpdateLineList(PyObject *self, PyObject *args)
     const int n = 4;
     const char *result = NULL;
     void *args_c[n];
-    int nlines, nchar;
+    short nlines;
+    int nchar;
     double *linelist = NULL;
     IDL_STRING *species = NULL;
     short *index = NULL;

src/pysme/solve.py

@@ -719,8 +719,16 @@ def solve(self, sme, param_names=None, segments="all", bounds=None):
         self.update_linelist = False
         for name in self.parameter_names:
             if name[:8] == "linelist":
-                self.update_linelist = True
-                break
+                if self.update_linelist is False:
+                    self.update_linelist = []
+                try:
+                    idx = int(name.split()[1])
+                except IndexError:
+                    raise ValueError(
+                        f"Could not parse fit parameter {name}, expected a "
+                        "linelist parameter like 'linelist n gflog'"
+                    )
+                self.update_linelist += [idx]
 
         # Create appropiate bounds
         if bounds is None:
@@ -746,14 +754,13 @@ def solve(self, sme, param_names=None, segments="all", bounds=None):
         spec = sme.spec[segments][mask]
         uncs = sme.uncs[segments][mask]
 
+        # Divide the uncertainties by the spectrum, to improve the fit in the continuum
+        # Just as in IDL SME, this increases the relative error for points inside lines
+        uncs /= np.sqrt(np.abs(spec))
+
         # This is the expected range of the uncertainty
         # if the residuals are larger, they are dampened by log(1 + z)
         self.f_scale = 0.2 * np.nanmean(spec.ravel()) / np.nanmean(uncs.ravel())
-        # self.f_scale = VariableNumber(self.f_scale)
-
-        # Divide the uncertainties by the spectrum, to improve the fit in the continuum
-        # Just as in IDL SME, this increases the relative error for points inside lines
-        # uncs /= spec
 
         logger.info("Fitting Spectrum with Parameters: %s", ",".join(param_names))
         logger.debug("Initial values: %s", p0)

src/pysme/synthesize.py

@@ -554,7 +554,7 @@ def synthesize_spectrum(
             dll.InputLineList(sme.linelist)
         if updateLineList:
             # TODO Currently Updates the whole linelist, could be improved to only change affected lines
-            dll.UpdateLineList(sme.atomic, sme.species, np.arange(len(sme.linelist)))
+            dll.UpdateLineList(sme.atomic, sme.species, updateLineList)
         if passAtmosphere:
             sme = self.get_atmosphere(sme)
             dll.InputModel(sme.teff, sme.logg, sme.vmic, sme.atmo)