Added 'other_parameters' keyword in _get_scan.

This allows to set or modify any option right before runing
Phagen and Spec. Mostly for debug purposes.

src/msspec/calculator.py

@@ -615,7 +615,7 @@ class _PED(_MSCALCULATOR):
     def _get_scan(self, scan_type='theta', phi=0,
                   theta=np.linspace(-70, 70, 141), level=None,
                   kinetic_energy=None, data=None,
-                  malloc={}):
+                  malloc={}, other_parameters={}):
         LOGGER.info("Computting the %s scan...", scan_type)
         if data:
             self.iodata = data
@@ -650,6 +650,13 @@ class _PED(_MSCALCULATOR):
 
         self.spectroscopy_parameters.set_parameter('level', level)
 
+        # It is still possible to modify any option right before runing phagen
+        # and spec
+        for k, v in other_parameters.items():
+            grp_str, param_str = k.split('.')
+            grp = getattr(self, grp_str)
+            grp.set_parameter(param_str, v, force=True)
+
         self.get_tmatrix()
         self.run_spec(malloc)
 
@@ -851,7 +858,7 @@ class _PED(_MSCALCULATOR):
         return self.iodata
 
     def get_scattering_factors(self, level='1s', kinetic_energy=None,
-                               data=None):
+                               data=None, **kwargs):
         """Computes the scattering factors of all prototypical atoms in the
         cluster.
 
@@ -870,11 +877,11 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='scatf', level=level, data=data,
-                              kinetic_energy=kinetic_energy)
+                              kinetic_energy=kinetic_energy, **kwargs)
         return data
 
     def get_theta_scan(self, phi=0, theta=np.linspace(-70, 70, 141),
-                       level=None, kinetic_energy=None, data=None):
+                       level=None, kinetic_energy=None, data=None, **kwargs):
         """Computes a polar scan of the emitted photoelectrons.
 
         :param phi: The azimuthal angle in degrees. See
@@ -891,11 +898,12 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='theta', level=level, theta=theta,
-                              phi=phi, kinetic_energy=kinetic_energy, data=data)
+                              phi=phi, kinetic_energy=kinetic_energy,
+                              data=data, **kwargs)
         return data
 
     def get_phi_scan(self, phi=np.linspace(0, 359, 359), theta=0,
-                     level=None, kinetic_energy=None, data=None):
+                     level=None, kinetic_energy=None, data=None, **kwargs):
         """Computes an azimuthal scan of the emitted photoelectrons.
 
         :param phi: All the values of the azimuthal angle to be computed. See
@@ -912,12 +920,13 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='phi', level=level, theta=theta,
-                              phi=phi, kinetic_energy=kinetic_energy, data=data)
+                              phi=phi, kinetic_energy=kinetic_energy,
+                              data=data, **kwargs)
         return data
 
     def get_theta_phi_scan(self, phi=np.linspace(0, 360),
                            theta=np.linspace(0, 90, 45), level=None,
-                           kinetic_energy=None, data=None):
+                           kinetic_energy=None, data=None, **kwargs):
         """Computes a stereographic scan of the emitted photoelectrons.
 
         The azimuth ranges from 0 to 360° and the polar angle ranges from 0 to
@@ -934,11 +943,11 @@ class _PED(_MSCALCULATOR):
         """
         data = self._get_scan(scan_type='theta_phi', level=level, theta=theta,
                               phi=phi, kinetic_energy=kinetic_energy, data=data,
-                              malloc={'NPH_M': 8000})
+                              malloc={'NPH_M': 8000}, **kwargs)
         return data
 
     def get_energy_scan(self, phi=0, theta=0,
-                        level=None, kinetic_energy=None, data=None):
+                        level=None, kinetic_energy=None, data=None, **kwargs):
         """Computes an energy scan of the emitted photoelectrons.
 
         :param phi: All the values of the azimuthal angle to be computed. See
@@ -955,7 +964,8 @@ class _PED(_MSCALCULATOR):
 
         """
         data = self._get_scan(scan_type='energy', level=level, theta=theta,
-                              phi=phi, kinetic_energy=kinetic_energy, data=data)
+                              phi=phi, kinetic_energy=kinetic_energy,
+                              data=data, **kwargs)
         return data