Merge pull request #827 from HEXRD/wppf-sanitize-material-names

Sanitize material names in WPPF

Author: psavery

hexrd/wppf/phase.py

@@ -86,7 +86,7 @@ def _readHDF(self, fhdf, xtal):
             confusion later on
         """
         self.lparms = list(gid.get('LatticeParameters'))
-        self.name = name
+        self.name = name.replace('-', '_')
         fid.close()
 
     def _init_from_materials(self, material_obj):
@@ -98,7 +98,7 @@ def _init_from_materials(self, material_obj):
         O7/01/2021 SS ADDED DIRECT AND RECIPROCAL STRUCTURE MATRIX AS
         FIELDS IN THE CLASS
         """
-        self.name = material_obj.name
+        self.name = material_obj.name.replace('-', '_')
         self.dmin = material_obj.dmin.getVal('nm')
         self.sgnum = material_obj.unitcell.sgnum
         self.sgsetting = material_obj.sgsetting
@@ -346,7 +346,7 @@ def CalcStar(self, v, space, applyLaue=False):
 
     def removeinversion(self, ksym):
         """
-        this function chooses a subset from a list 
+        this function chooses a subset from a list
         of symmetrically equivalent reflections such
         that there are no g and -g present.
         """
@@ -541,12 +541,17 @@ def __str__(self):
         return resstr
 
     def __getitem__(self, key):
+        # Always sanitize the material name since lmfit won't accept '-'
+        key = key.replace('-', '_')
+
         if(key in self.phase_dict.keys()):
             return self.phase_dict[key]
         else:
             raise ValueError('phase with name not found')
 
     def __setitem__(self, key, mat_cls):
+        # Always sanitize the material name since lmfit won't accept '-'
+        key = key.replace('-', '_')
 
         if(key in self.phase_dict.keys()):
             warnings.warn('phase already in parameter \
@@ -589,7 +594,7 @@ def add_many(self, material_file, material_keys):
             self[k].pf = 1.0/len(self)
 
         self.material_file = material_file
-        self.material_keys = material_keys
+        self.material_keys = [k.replace('-', '_') for k in material_keys]
 
     def load(self, fname):
         """
@@ -737,7 +742,7 @@ def _init_from_materials(self, material_obj):
 
         """
         # name
-        self.name = material_obj.name
+        self.name = material_obj.name.replace('-', '_')
 
         # inverse of absorption length
         self.abs_fact = 1e-4 * (1./material_obj.absorption_length)
@@ -860,7 +865,7 @@ def _readHDF(self, fhdf, xtal):
         # read atom types (by atomic number, Z)
         self.atom_type = np.array(gid.get('Atomtypes'), dtype=np.int32)
         self.atom_ntype = self.atom_type.shape[0]
-        self.name = name
+        self.name = name.replace('-', '_')
 
         fid.close()
 
@@ -1461,12 +1466,17 @@ def __str__(self):
         return resstr
 
     def __getitem__(self, key):
+        # Always sanitize the material name since lmfit won't accept '-'
+        key = key.replace('-', '_')
+
         if(key in self.phase_dict.keys()):
             return self.phase_dict[key]
         else:
             raise ValueError('phase with name not found')
 
     def __setitem__(self, key, mat_cls):
+        # Always sanitize the material name since lmfit won't accept '-'
+        key = key.replace('-', '_')
 
         if(key in self.phase_dict.keys()):
             warnings.warn('phase already in parameter list. overwriting ...')
@@ -1524,7 +1534,7 @@ def add_many(self, material_file, material_keys):
                 self[k][l].pf = 1.0/self.num_phases
 
         self.material_file = material_file
-        self.material_keys = material_keys
+        self.material_keys = [k.replace('-', '_') for k in material_keys]
 
     def load(self, fname):
         """

hexrd/wppf/wppfsupport.py

@@ -32,6 +32,9 @@
 classes are put here to minimize code duplication. Some examples
 include initialize background, generate_default_parameter list etc.
 """
+import copy
+import warnings
+
 from hexrd.material.symbols import pstr_spacegroup
 from hexrd.wppf.parameters import Parameters
 from lmfit import Parameters as Parameters_lmfit
@@ -41,7 +44,6 @@
 import hexrd
 import numpy as np
 from hexrd import constants
-import warnings
 
 def _generate_default_parameters_pseudovoight(params):
     """
@@ -461,6 +463,9 @@ def _generate_default_parameters_LeBail(mat,
     @details: generate a default parameter class given a list/dict/
     single instance of material class
     """
+    # Sanitize the material names
+    mat = _sanitize_material_names(mat)
+
     if ptype == "wppf":
         params = Parameters()
     elif ptype == "lmfit":
@@ -659,6 +664,8 @@ def _generate_default_parameters_Rietveld(mat,
     @details: generate a default parameter class given a list/dict/
     single instance of material class
     """
+    mat = _sanitize_material_names(mat)
+
     params = _generate_default_parameters_LeBail(mat,
                                                  peakshape,
                                                  bkgmethod,
@@ -932,6 +939,27 @@ def _add_intensity_parameters(params,hkls,Icalc,prefix):
                 [params.add(name=pname[i],
                     value=Icalc[p][k][i],
                     min=0.0) for i in range(shape)]
+
+
+def _sanitize_material_names(mats):
+    if isinstance(mats, Material):
+        if '-' in mats.name:
+            mats = copy.deepcopy(mats)
+            mats.name = mats.name.replace('-', '_')
+    elif isinstance(mats, (list, dict)):
+        mats = copy.deepcopy(mats)
+        if isinstance(mats, list):
+            mats_iter = mats
+        else:
+            mats_iter = mats.values()
+
+        for mat in mats_iter:
+            if '-' in mat.name:
+                mat.name = mat.name.replace('-', '_')
+
+    return mats
+
+
 background_methods = {
     'spline': None,