Some features to enable ScatteringSystem reconstruction

TODO.md

@@ -25,11 +25,12 @@ TODO list before 1.0 release
   * As a description of a T-matrix / particle metadata.
 - Nice CLI for all general enough utilities.
 - Remove legacy code.
-- Split qpms_c.pyx.
+- Split `qpms_c.pyx`.
 - Reduce compiler warnings.
+- Serialisation (saving, loading) of `ScatteringSystem` and other structures.
 - Python exceptions instead of hard crashes in the C library where possible.
 - Scatsystem init sometimes fail due to rounding errors and hardcoded absolute tolerance 
-  in the qpms_tmatrix_isclose() call.
+  in the `qpms_tmatrix_isclose()` call.
 - Prefix all identifiers. Maybe think about a different prefix than qpms?
 - Consistent indentation and style overall.
 - Rewrite the parallelized translation matrix, mode problem matrix generators

misc/finiterectlat-modes.py

@@ -95,7 +95,12 @@ results['inside_contour'] = inside_ellipse((results['eigval'].real, results['eig
 results['refractive_index_internal'] = [medium(om).n for om in results['eigval']]
 
 outfile = defaultprefix + (('_ir%s_%s.npz' % (str(iri), irname)) if iri is not None else '.npz') if a.output is None else a.output
-np.savez(outfile, meta=vars(a), **results)
+np.savez(outfile, meta=vars(a),
+        ss_positions=ss.positions, ss_fullvec_poffsets=ss.fullvec_poffsets, 
+        ss_fullvec_psizes=ss.fullvec_psizes,
+        ss_bspecs_flat = np.concatenate(ss.bspecs),
+        ss_lattice_basis=ss.lattice_basis, ss_reciprocal_basis = ss.reciprocal_basis,
+        **results)
 logging.info("Saved to %s" % outfile)
 
 exit(0)

misc/lat2d_modes.py

@@ -112,7 +112,12 @@ res['inside_contour'] = inside_ellipse((res['eigval'].real, res['eigval'].imag),
 #del res['omega']  If contour points are not needed...
 #del res['ImTW'] # not if dbg=false anyway
 outfile = defaultprefix + ".npz" if a.output is None else a.output
-np.savez(outfile, meta=vars(a), empty_freqs=np.array(empty_freqs), **res)
+np.savez(outfile, meta=vars(a), empty_freqs=np.array(empty_freqs), 
+        ss_positions=ss.positions, ss_fullvec_poffsets=ss.fullvec_poffsets, 
+        ss_fullvec_psizes=ss.fullvec_psizes,
+        ss_bspecs_flat = np.concatenate(ss.bspecs),
+        ss_lattice_basis=ss.lattice_basis, ss_reciprocal_basis = ss.reciprocal_basis,
+        **res)
 logging.info("Saved to %s" % outfile)
 
 

qpms/argproc.py

@@ -189,7 +189,7 @@ def material_spec(string):
         except ValueError:
             try: lemat = complex(string)
             except ValueError as ve:
-                raise argpares.ArgumentTypeError("Material specification must be a supported material name %s, or a number" % (str(lorentz_drude.keys()),)) from ve
+                raise argparse.ArgumentTypeError("Material specification must be a supported material name %s, or a number" % (str(lorentz_drude.keys()),)) from ve
         return lemat
 
 class ArgParser:

qpms/cymaterials.pyx

@@ -185,8 +185,23 @@ cdef qpms_epsmu_t python_epsmu_generator(cdouble omega, const void *params):
     em.eps, em.mu = fun(omega)
     return em
 
+
+
 cdef class EpsMuGenerator:
     def __init__(self, what):
+        if isinstance(what, str):
+            if what in lorentz_drude.keys():
+                what = lorentz_drude[what]
+            else:
+                try: what = float(what)
+                except ValueError:
+                    try: what = complex(what)
+                    except ValueError as ve:
+                        raise ValueError("Trying to create EpsMuGenerator from a string that can't be parsed as a number (constant refractive index) nor supported lorentz-drude key") from ve
+        if isinstance(what, int):
+            what = float(what)
+        if isinstance(what, (float, complex)):
+            what = EpsMu(what**2)
         if isinstance(what, EpsMu):
             self.holder = what
             self.g.function = qpms_epsmu_const_g
@@ -212,7 +227,7 @@ cdef class EpsMuGenerator:
             self.g.function = python_epsmu_generator
             self.g.params = <const void *> what
         else:
-            raise ValueError("Must be constructed from EpsMu, LorentzDrudeModel or MaterialInterpolator, or a python callable object that returns an (epsilon, mu) tuple.")
+            raise ValueError("Must be constructed from a number (refractive index), EpsMu, LorentzDrudeModel or MaterialInterpolator, or a python callable object that returns an (epsilon, mu) tuple.")
 
     property typ:
         def __get__(self):