Merge pull request #823 from HEXRD/wppf-amorphous-fixes

Implement a few various fixes for WPPF amorphous

Author: psavery

hexrd/wppf/WPPF.py

@@ -996,7 +996,8 @@ def peakshape(self, val):
         """
         if hasattr(self, "params"):
             params = wppfsupport._generate_default_parameters_LeBail(
-                self.phases, self.peakshape, self.bkgmethod
+                self.phases, self.peakshape, self.bkgmethod,
+                amorphous_model=self.amorphous_model,
             )
             for p in params:
                 if p in self.params:
@@ -1343,7 +1344,7 @@ def params(self, param_info):
                 self.peakshape,
                 self.bkgmethod,
                 init_val=self.cheb_init_coef,
-                amorphous_model=self.amorphous_model
+                amorphous_model=self.amorphous_model,
             )
             self._params = params
 
@@ -1577,7 +1578,7 @@ def DOC(self):
         if self.amorphous_model is None:
             return 1.
         else:
-            tth, intensity   = self.spectrum_expt.data
+            tth, intensity   = self.spectrum_sim.data
             _, background    = self.background.data
             total_intensity = intensity-background
             amorphous_area = \
@@ -2569,7 +2570,7 @@ def params(self, param_info):
                 self.peakshape,
                 self.bkgmethod,
                 init_val=self.cheb_init_coef,
-                amorphous_model=self.amorphous_model
+                amorphous_model=self.amorphous_model,
             )
             self._params = params
 
@@ -2957,7 +2958,8 @@ def peakshape(self, val):
                 self.phases,
                 self.peakshape,
                 self.bkgmethod,
-                init_val=self.cheb_init_coef
+                init_val=self.cheb_init_coef,
+                amorphous_model=self.amorphous_model,
             )
             for p in params:
                 if p in self.params:

hexrd/wppf/amorphous.py

@@ -6,6 +6,14 @@
     _split_unit_gaussian as sp_gauss,
     _split_unit_pv as sp_pv)
 
+
+AMORPHOUS_MODEL_TYPES = {
+    'Split Gaussian': 'split_gaussian',
+    'Split Pseudo-Voigt': 'split_pv',
+    'Experimental': 'experimental',
+}
+
+
 class Amorphous:
     '''
     >> @AUTHOR:     Saransh Singh,
@@ -112,7 +120,12 @@ def __init__(self,
             center = {'c1': 30.}
 
         if fwhm is None:
-            fwhm = {'c1': np.array([5, 5])}
+            if model_type == 'split_pv':
+                array = np.array([5, 5, 5, 5])
+            else:
+                array = np.array([5, 5])
+
+            fwhm = {'c1': array}
 
         self.tth_list = tth_list
 
@@ -147,7 +160,10 @@ def tth_list(self):
 
     @tth_list.setter
     def tth_list(self, val):
-        if isinstance(val, np.ndarray):
+        if isinstance(val, np.ma.MaskedArray):
+            print('here')
+            self._tth_list = val.filled()
+        elif isinstance(val, np.ndarray):
             self._tth_list = val
         elif isinstance(val, (list, tuple)):
             self._tth_list = np.array(val)
@@ -300,6 +316,7 @@ def amorphous_lineout(self):
             for key in self.center:
                 p = np.hstack((self.center[key],
                            self.fwhm[key]))
+
                 lo += self.scale[key]*self.peak_model(p, self.tth_list)
 
         return lo

hexrd/wppf/wppfsupport.py

@@ -406,15 +406,13 @@ def convert(**kwargs):
 
         if amorphous_model.model_type == "split_gaussian":
             params.add(f'{key}_amorphous_fwhm_l', **convert(
-                nn,
                 value=amorphous_model.fwhm[key][0],
                 min=0,
                 max=np.inf,
                 vary=False,
             ))
 
             params.add(f'{key}_amorphous_fwhm_r', **convert(
-                nn,
                 value=amorphous_model.fwhm[key][1],
                 min=0,
                 max=np.inf,