black

diffpy/__init__.py

@@ -19,6 +19,7 @@
 
 
 from pkgutil import extend_path
+
 __path__ = extend_path(__path__, __name__)
 
 

diffpy/pdfmorph/__init__.py

@@ -20,6 +20,6 @@
 __version__ = '0.0.1'
 
 # top-level import
-from diffpy.pdfmorph.pdfmorph_api import (pdfmorph, morph_default_config,
-                                          plot_morph)
+from diffpy.pdfmorph.pdfmorph_api import pdfmorph, morph_default_config, plot_morph
+
 # End of file

diffpy/pdfmorph/log.py

@@ -45,4 +45,5 @@ def setVerbosity(vb):
     plog.info("log level set to %r", level)
     return
 
+
 # End of file

diffpy/pdfmorph/morphs/__init__.py

@@ -31,8 +31,19 @@
 from diffpy.pdfmorph.morphs.morphstretch import MorphStretch
 
 # List of morphs
-morphs = [ MorphRGrid, MorphScale, MorphStretch, MorphXtalPDFtoRDF, MorphSmear,
-        MorphXtalRDFtoPDF, MorphSphere, MorphSpheroid, MorphISphere,
-        MorphISpheroid, MorphResolutionDamping, MorphShift]
+morphs = [
+    MorphRGrid,
+    MorphScale,
+    MorphStretch,
+    MorphXtalPDFtoRDF,
+    MorphSmear,
+    MorphXtalRDFtoPDF,
+    MorphSphere,
+    MorphSpheroid,
+    MorphISphere,
+    MorphISpheroid,
+    MorphResolutionDamping,
+    MorphShift,
+]
 
 # End of file

diffpy/pdfmorph/morphs/morph.py

@@ -18,9 +18,10 @@
 """
 
 
-LABEL_RA = 'r (A)'     # r-grid
-LABEL_GR = 'G (1/A^2)' # PDF G(r)
-LABEL_RR = 'R (1/A)'   # RDF R(r)
+LABEL_RA = 'r (A)'  # r-grid
+LABEL_GR = 'G (1/A^2)'  # PDF G(r)
+LABEL_RR = 'R (1/A)'  # RDF R(r)
+
 
 class Morph(object):
     '''Base class for implementing a morph on an objective given a reference.
@@ -75,17 +76,26 @@ class Morph(object):
 
     # Properties
 
-    xyobjin = property(lambda self: (self.xobjin, self.yobjin),
-            doc='Return a tuple of objective input arrays')
-    xyobjout = property(lambda self: (self.xobjout, self.yobjout),
-            doc='Return a tuple of objective output arrays')
-    xyrefin = property(lambda self: (self.xrefin, self.yrefin),
-            doc='Return a tuple of reference input arrays')
-    xyrefout = property(lambda self: (self.xrefout, self.yrefout),
-            doc='Return a tuple of reference output arrays')
-    xyallout = property(lambda self: 
-            (self.xobjout, self.yobjout, self.xrefout, self.yrefout), 
-            doc='Return a tuple of all output arrays')
+    xyobjin = property(
+        lambda self: (self.xobjin, self.yobjin),
+        doc='Return a tuple of objective input arrays',
+    )
+    xyobjout = property(
+        lambda self: (self.xobjout, self.yobjout),
+        doc='Return a tuple of objective output arrays',
+    )
+    xyrefin = property(
+        lambda self: (self.xrefin, self.yrefin),
+        doc='Return a tuple of reference input arrays',
+    )
+    xyrefout = property(
+        lambda self: (self.xrefout, self.yrefout),
+        doc='Return a tuple of reference output arrays',
+    )
+    xyallout = property(
+        lambda self: (self.xobjout, self.yobjout, self.xrefout, self.yrefout),
+        doc='Return a tuple of all output arrays',
+    )
 
     def __init__(self, config=None):
         '''Create a default Morph instance.
@@ -107,7 +117,6 @@ def __init__(self, config=None):
         self.applyConfig(config)
         return
 
-
     def morph(self, xobj, yobj, xref, yref):
         '''Morph arrays objective or reference.
 
@@ -130,13 +139,10 @@ def morph(self, xobj, yobj, xref, yref):
         self.checkConfig()
         return self.xyallout
 
-
     def __call__(self, xobj, yobj, xref, yref):
-        '''Alias for morph.
-        '''
+        '''Alias for morph.'''
         return self.morph(xobj, yobj, xref, yref)
 
-
     def applyConfig(self, config):
         '''Process any configuration data from a dictionary.
 
@@ -147,15 +153,13 @@ def applyConfig(self, config):
         self.config = config
         return
 
-
     def checkConfig(self):
         '''Verify data in self.config.  No action by default.
 
         To be overridden in a derived class.
         '''
         return
 
-
     def plotInputs(self, xylabels=True):
         '''Plot input arrays using matplotlib.pyplot
 
@@ -164,14 +168,14 @@ def plotInputs(self, xylabels=True):
         Return a list of matplotlib line objects.
         '''
         from matplotlib.pyplot import plot, xlabel, ylabel
-        rv = plot(self.xrefin, self.yrefin, label = "reference")
-        rv = plot(self.xobjin, self.yobjin, label = "objective")
+
+        rv = plot(self.xrefin, self.yrefin, label="reference")
+        rv = plot(self.xobjin, self.yobjin, label="objective")
         if xylabels:
             xlabel(self.xinlabel)
             ylabel(self.yinlabel)
         return rv
 
-
     def plotOutputs(self, xylabels=True, **plotargs):
         '''Plot output arrays using matplotlib.pyplot
 
@@ -182,16 +186,16 @@ def plotOutputs(self, xylabels=True, **plotargs):
         Return a list of matplotlib line objects.
         '''
         from matplotlib.pyplot import plot, xlabel, ylabel
+
         pargs = dict(plotargs)
         pargs.pop("label", None)
-        rv = plot(self.xrefout, self.yrefout, label = "reference", **pargs)
-        rv = plot(self.xobjout, self.yobjout, label = "objective", **pargs)
+        rv = plot(self.xrefout, self.yrefout, label="reference", **pargs)
+        rv = plot(self.xobjout, self.yobjout, label="objective", **pargs)
         if xylabels:
             xlabel(self.xoutlabel)
             ylabel(self.youtlabel)
         return rv
 
-
     def __getattr__(self, name):
         '''Obtain the value from self.config, when normal lookup fails.
 
@@ -206,7 +210,6 @@ def __getattr__(self, name):
             emsg = 'Object has no attribute %r' % name
             raise AttributeError(emsg)
 
-
     def __setattr__(self, name, val):
         '''Set configuration variables to config.
 
@@ -220,5 +223,5 @@ def __setattr__(self, name, val):
             object.__setattr__(self, name, val)
         return
 
-# End class Morph
 
+# End class Morph

diffpy/pdfmorph/morphs/morphchain.py

@@ -52,49 +52,39 @@ class MorphChain(list):
 
     '''
 
-    xobjin = property(
-            lambda self: None if len(self) == 0 else self[0].xobjin)
-    yobjin = property(
-            lambda self: None if len(self) == 0 else self[0].yobjin)
-    xrefin = property(
-            lambda self: None if len(self) == 0 else self[0].xrefin)
-    yrefin = property(
-            lambda self: None if len(self) == 0 else self[0].yrefin)
-    xobjout = property(
-            lambda self: None if len(self) == 0 else self[-1].xobjout)
-    yobjout = property(
-            lambda self: None if len(self) == 0 else self[-1].yobjout)
-    xrefout = property(
-            lambda self: None if len(self) == 0 else self[-1].xrefout)
-    yrefout = property(
-            lambda self: None if len(self) == 0 else self[-1].yrefout)
-    xyobjin = property(
-            lambda self: (None, None) if len(self) == 0 else self[0].xyobjin)
+    xobjin = property(lambda self: None if len(self) == 0 else self[0].xobjin)
+    yobjin = property(lambda self: None if len(self) == 0 else self[0].yobjin)
+    xrefin = property(lambda self: None if len(self) == 0 else self[0].xrefin)
+    yrefin = property(lambda self: None if len(self) == 0 else self[0].yrefin)
+    xobjout = property(lambda self: None if len(self) == 0 else self[-1].xobjout)
+    yobjout = property(lambda self: None if len(self) == 0 else self[-1].yobjout)
+    xrefout = property(lambda self: None if len(self) == 0 else self[-1].xrefout)
+    yrefout = property(lambda self: None if len(self) == 0 else self[-1].yrefout)
+    xyobjin = property(lambda self: (None, None) if len(self) == 0 else self[0].xyobjin)
     xyobjout = property(
-            lambda self: (None, None) if len(self) == 0 else self[-1].xyobjout)
-    xyrefin = property(
-            lambda self: (None, None) if len(self) == 0 else self[0].xyrefin)
+        lambda self: (None, None) if len(self) == 0 else self[-1].xyobjout
+    )
+    xyrefin = property(lambda self: (None, None) if len(self) == 0 else self[0].xyrefin)
     xyrefout = property(
-            lambda self: (None, None) if len(self) == 0 else self[-1].xyrefout)
+        lambda self: (None, None) if len(self) == 0 else self[-1].xyrefout
+    )
     xyallout = property(
-            lambda self: (None, None, None, None) if len(self) == 0 \
-                    else self[-1].xyallout)
+        lambda self: (None, None, None, None) if len(self) == 0 else self[-1].xyallout
+    )
     parnames = property(lambda self: set(p for m in self for p in m.parnames))
 
-
     def __init__(self, config, *args):
         """Initialize the configuration.
 
         config      --  Configuration dictionary.
-        
+
         Additional arguments are morphs that will extend the queue of morphs.
 
         """
         self.config = config
         self.extend(args)
         return
 
-
     def morph(self, xobj, yobj, xref, yref):
         '''Apply the chain of morphs to the input data.
 
@@ -112,13 +102,10 @@ def morph(self, xobj, yobj, xref, yref):
             xyall = morph(*xyall)
         return xyall
 
-
     def __call__(self, xobj, yobj, xref, yref):
-        '''Alias for morph.
-        '''
+        '''Alias for morph.'''
         return self.morph(xobj, yobj, xref, yref)
 
-
     def __getattr__(self, name):
         '''Obtain the value from self.config, when normal lookup fails.
 
@@ -133,7 +120,6 @@ def __getattr__(self, name):
             emsg = 'Object has no attribute %r' % name
             raise AttributeError(emsg)
 
-
     def __setattr__(self, name, val):
         '''Set configuration variables to config.
 
@@ -149,4 +135,3 @@ def __setattr__(self, name, val):
 
 
 # End class MorphChain
-

diffpy/pdfmorph/morphs/morphishape.py

@@ -22,6 +22,7 @@ class MorphISpheroid -- apply inverse spheroidal shape function
 from diffpy.pdfmorph.morphs.morph import *
 from diffpy.pdfmorph.morphs.morphshape import _sphericalCF, _spheroidalCF
 
+
 class MorphISphere(Morph):
     '''Apply inverse spherical characteristic function to the objective
 
@@ -47,8 +48,10 @@ def morph(self, xobj, yobj, xref, yref):
         self.yobjout[f == 0] = 0
         return self.xyallout
 
+
 # End of class MorphISphere
 
+
 class MorphISpheroid(Morph):
     '''Apply inverse spherical characteristic function to the objective
 
@@ -75,4 +78,5 @@ def morph(self, xobj, yobj, xref, yref):
         self.yobjout[f == 0] == 0
         return self.xyallout
 
+
 # End of class MorphSpheroid

diffpy/pdfmorph/morphs/morphpdftordf.py

@@ -20,6 +20,7 @@
 
 from diffpy.pdfmorph.morphs.morph import *
 
+
 class MorphXtalPDFtoRDF(Morph):
     '''Morph crystal PDFs to RDFs.
 
@@ -53,4 +54,5 @@ def morph(self, xobj, yobj, xref, yref):
         self.yrefout = self.xrefin * (self.yrefin - refbaseline)
         return self.xyallout
 
+
 # End of class MorphXtalPDFtoRDF

diffpy/pdfmorph/morphs/morphrdftopdf.py

@@ -50,12 +50,13 @@ def morph(self, xobj, yobj, xref, yref):
         Morph.morph(self, xobj, yobj, xref, yref)
         objbaseline = self.baselineslope * self.xobjin
         refbaseline = self.baselineslope * self.xrefin
-        self.yrefout =  self.yrefin / self.xrefin + refbaseline
+        self.yrefout = self.yrefin / self.xrefin + refbaseline
         if self.xrefin[0] == 0:
             self.yrefout[0] = 0
-        self.yobjout =  self.yobjin / self.xobjin + objbaseline
+        self.yobjout = self.yobjin / self.xobjin + objbaseline
         if self.xobjin[0] == 0:
             self.yobjout[0] = 0
         return self.xyallout
 
+
 # End of class MorphScale

diffpy/pdfmorph/morphs/morphresolution.py

@@ -22,6 +22,7 @@
 
 from diffpy.pdfmorph.morphs.morph import *
 
+
 class MorphResolutionDamping(Morph):
     '''Apply resolution damping and broadening to the objective.
 
@@ -44,9 +45,9 @@ class MorphResolutionDamping(Morph):
     def morph(self, xobj, yobj, xref, yref):
         """Apply a resolution damping."""
         Morph.morph(self, xobj, yobj, xref, yref)
-        b = numpy.exp(-0.5 * (self.xobjin*self.qdamp)**2)
+        b = numpy.exp(-0.5 * (self.xobjin * self.qdamp) ** 2)
         self.yobjout *= b
         return self.xyallout
 
-# End of class MorphResolutionDamping
 
+# End of class MorphResolutionDamping

diffpy/pdfmorph/morphs/morphrgrid.py

@@ -24,6 +24,7 @@
 # roundoff tolerance for selecting bounds on arrays.
 epsilon = 1e-8
 
+
 class MorphRGrid(Morph):
     '''Resample to specified r-grid.
 
@@ -40,7 +41,7 @@ class MorphRGrid(Morph):
     If any of these is not defined or outside the bounds of the input arrays,
     then it will be taken to be the most inclusive value from the input arrays.
     These modified values will be stored as the above attributes.
-    
+
     '''
 
     # Define input output types
@@ -72,4 +73,5 @@ def morph(self, xobj, yobj, xref, yref):
         self.yrefout = numpy.interp(self.xrefout, self.xrefin, self.yrefin)
         return self.xyallout
 
+
 # End of class MorphRGrid

diffpy/pdfmorph/morphs/morphscale.py

@@ -20,6 +20,7 @@
 
 from diffpy.pdfmorph.morphs.morph import *
 
+
 class MorphScale(Morph):
     '''Scale the objective.
 
@@ -45,4 +46,5 @@ def morph(self, xobj, yobj, xref, yref):
         self.yobjout *= self.scale
         return self.xyallout
 
+
 # End of class MorphScale