Adding inverse shape functions, cleaning up code

Author: cfarrow

diffpy/pdfmorph/log.py

@@ -0,0 +1,50 @@
+##############################################################################
+#
+# diffpy.pdfmorph   by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2010 Trustees of the Columbia University
+#                   in the City of New York.  All rights reserved.
+#
+# File coded by:    Pavol Juhas, Chris Farrow
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+"""Configuration of loggers used in this package.
+
+Logger instances:
+
+plog -- logger instance for normal operation
+"""
+
+# module version
+__id__ = "$Id$"
+
+import logging
+
+# logging configuration
+plog = logging.getLogger('diffpy.pdfmorph')
+
+
+def setVerbosity(vb):
+    '''Set verbosity of the pdfmorph logger.
+
+    vb   -- integer or one of ('debug', 'info', 'warning', 'error') strings
+
+    No return value.
+    '''
+    try:
+        if type(vb) is str:
+            level = int(getattr(logging, vb.upper(), vb))
+        else:
+            level = int(vb)
+    except (TypeError, AttributeError):
+        emsg = "invalid value of verbose %r" % vb
+        raise ValueError(emsg)
+    plog.setLevel(level)
+    plog.info("log level set to %r", level)
+    return
+
+# End of file

diffpy/pdfmorph/morphs/__init__.py

@@ -26,14 +26,15 @@
 from diffpy.pdfmorph.morphs.morphrgrid import MorphRGrid
 from diffpy.pdfmorph.morphs.morphscale import MorphScale
 from diffpy.pdfmorph.morphs.morphshape import MorphSphere, MorphSpheroid
+from diffpy.pdfmorph.morphs.morphishape import MorphISphere, MorphISpheroid
 from diffpy.pdfmorph.morphs.morphshift import MorphShift
 from diffpy.pdfmorph.morphs.morphsmear import MorphSmear
 from diffpy.pdfmorph.morphs.morphstretch import MorphStretch
 
 # List of morphs
 morphs = [ MorphRGrid, MorphScale, MorphStretch, MorphXtalPDFtoRDF, MorphSmear,
-        MorphXtalRDFtoPDF, MorphSphere, MorphSpheroid, MorphResolutionDamping,
-        MorphShift]
+        MorphXtalRDFtoPDF, MorphSphere, MorphSpheroid, MorphISphere,
+        MorphISpheroid, MorphResolutionDamping, MorphShift]
 
 # obtain version information
 from diffpy.pdfmorph.version import __version__

diffpy/pdfmorph/morphs/morph.py

@@ -204,7 +204,7 @@ def __getattr__(self, name):
         else:
             emsg = 'Object has no attribute %r' % name
             raise AttributeError(emsg)
-        return rv
+        return
 
 
     def __setattr__(self, name, val):

diffpy/pdfmorph/morphs/morphchain.py

@@ -133,7 +133,7 @@ def __getattr__(self, name):
         else:
             emsg = 'Object has no attribute %r' % name
             raise AttributeError(emsg)
-        return rv
+        return
 
 
     def __setattr__(self, name, val):

diffpy/pdfmorph/morphs/morphishape.py

@@ -0,0 +1,79 @@
+##############################################################################
+#
+# diffpy.pdfmorph   by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2010 Trustees of the Columbia University
+#                   in the City of New York.  All rights reserved.
+#
+# File coded by:    Chris Farrow
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+
+"""class MorphISphere -- apply inverse spherical shape function
+class MorphISpheroid -- apply inverse spheroidal shape function 
+"""
+
+# module version
+__id__ = "$Id$"
+
+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
+
+    Configuration variables:
+
+    iradius  --  The radius of the sphere
+
+    '''
+
+    # Define input output types
+    summary = 'Apply inverse spherical characteristic function to objective'
+    xinlabel = LABEL_RA
+    yinlabel = LABEL_GR
+    xoutlabel = LABEL_RA
+    youtlabel = LABEL_GR
+    parnames = ["iradius"]
+
+    def morph(self, xobj, yobj, xref, yref):
+        """Apply a scale factor."""
+        Morph.morph(self, xobj, yobj, xref, yref)
+        f = _sphericalCF(xobj, 2 * self.iradius)
+        self.yobjout /= f
+        self.yobjout[f == 0] = 0
+        return self.xyallout
+
+# End of class MorphISphere
+
+class MorphISpheroid(Morph):
+    '''Apply inverse spherical characteristic function to the objective
+
+    Configuration variables:
+
+    iradius   --  The equatorial radius of the spheroid
+    ipradius  --  The polar radius of the spheroid
+
+    '''
+
+    # Define input output types
+    summary = 'Apply inverse spheroidal characteristic function to objective'
+    xinlabel = LABEL_RA
+    yinlabel = LABEL_GR
+    xoutlabel = LABEL_RA
+    youtlabel = LABEL_GR
+    parnames = ["iradius", "ipradius"]
+
+    def morph(self, xobj, yobj, xref, yref):
+        """Apply a scale factor."""
+        Morph.morph(self, xobj, yobj, xref, yref)
+        f = _spheroidalCF(xobj, self.iradius, self.ipradius)
+        self.yobjout /= f
+        self.yobjout[f == 0] == 0
+        return self.xyallout
+
+# End of class MorphSpheroid

diffpy/pdfmorph/morphs/morphpdftordf.py

@@ -19,10 +19,8 @@
 # module version
 __id__ = "$Id$"
 
-
 from diffpy.pdfmorph.morphs.morph import *
 
-
 class MorphXtalPDFtoRDF(Morph):
     '''Morph crystal PDFs to RDFs.
 

diffpy/pdfmorph/morphs/morphrdftopdf.py

@@ -20,7 +20,6 @@
 __id__ = "$Id$"
 
 
-import numpy
 from diffpy.pdfmorph.morphs.morph import *
 
 

diffpy/pdfmorph/morphs/morphshape.py

@@ -21,7 +21,7 @@ class MorphSpheroid -- apply a spheroidal shape function to the objective
 __id__ = "$Id$"
 
 import numpy
-from numpy import pi, sqrt, log, exp, log2, ceil, sign
+from numpy import sqrt
 from numpy import arctan as atan
 from numpy import arctanh as atanh
 
@@ -78,7 +78,7 @@ def morph(self, xobj, yobj, xref, yref):
         self.yobjout *= f
         return self.xyallout
 
-# End of class MorphScale
+# End of class MorphSpheroid
 
 def _sphericalCF(r, psize):
     """Spherical nanoparticle characteristic function.

diffpy/pdfmorph/pdfmorphapp.py

@@ -82,7 +82,10 @@ def createOptionParser():
     group.add_option('--pradius', type="float", metavar="PRADIUS",
             help="""Apply characteristic function of spheroid with equatorial
 radius RADIUS and polar radius PRADIUS. If only PRADIUS is specified, instead apply characteristic function of sphere with radius PRADIUS.""")
-    
+    group.add_option('--iradius', type="float", metavar="IRADIUS",
+            help="""Apply inverse characteristic function of sphere with radius IRADIUS.  If IPRADIUS is also specified, instead apply inverse characteristic function of spheroid with equatorial radius IRADIUS and polar radius IPRADIUS.""")
+    group.add_option('--ipradius', type="float", metavar="IPRADIUS",
+            help="""Apply inverse characteristic function of spheroid with equatorial radius IRADIUS and polar radius IPRADIUS. If only IPRADIUS is specified, instead apply inverse characteristic function of sphere with radius IPRADIUS.""")
 
     # Plot Options
     group = optparse.OptionGroup(parser, "Plot Options",
@@ -122,9 +125,9 @@ def main():
 
     # Get configuration values
     config = {}
-    config.setdefault("rmin", None)
-    config.setdefault("rmax", None)
-    config.setdefault("rstep", None)
+    config["rmin"] = opts.rmin
+    config["rmax"] = opts.rmax
+    config["rstep"] = None
     if opts.rmin is not None and opts.rmax is not None and \
             opts.rmax <= opts.rmin:
         e = "rmin must be less than rmax"
@@ -168,9 +171,23 @@ def main():
     elif nrad == 2:
         config["radius"] = radii[0]
         refpars.append("radius")
-        config["pradius"] = radii[0]
+        config["pradius"] = radii[1]
         refpars.append("pradius")
         chain.append( morphs.MorphSpheroid() )
+    iradii = [opts.iradius, opts.ipradius]
+    inrad = 2 - iradii.count(None)
+    if inrad == 1:
+        iradii.remove(None)
+        config["iradius"] = iradii[0]
+        chain.append( morphs.MorphISphere() )
+        refpars.append("iradius")
+    elif inrad == 2:
+        config["iradius"] = iradii[0]
+        refpars.append("iradius")
+        config["ipradius"] = iradii[1]
+        refpars.append("ipradius")
+        chain.append( morphs.MorphISpheroid() )
+
     ## Resolution
     if opts.qdamp is not None:
         chain.append( morphs.MorphResolutionDamping() )
@@ -243,7 +260,7 @@ def main():
         maglim = opts.maglim
         mag = opts.mag
         pdfplot.comparePDFs(pairlist, labels, rmin = pmin, rmax = pmax, maglim
-                = maglim, mag = mag)
+                = maglim, mag = mag, rw = rw)
 
     return
 

diffpy/pdfmorph/pdfplot.py

@@ -59,7 +59,7 @@ def plotPDFs(pairlist, labels = [], offset = 'auto', rmin = None, rmax = None):
     return
 
 def comparePDFs(pairlist, labels = [], rmin = None, rmax = None, show = True,
-        maglim = None, mag = 5):
+        maglim = None, mag = 5, rw = None, legend = True):
     """Plot two PDFs on top of each other and difference curve.
 
     pairlist    --  iterable of (r, gr) pairs to plot
@@ -74,6 +74,8 @@ def comparePDFs(pairlist, labels = [], rmin = None, rmax = None, show = True,
     maglim      --  Point after which to magnify the signal by mag. If None
                     (default), no magnification will take place.
     mag         --  Magnification factor (default 5)
+    rw          --  Rw value to display on the plot, if any.
+    legend      --  Display the legend (default True).
 
     The second PDF will be shown as blue circles below and the first as a red
     line.  The difference curve will be in green and offset for clarity.
@@ -101,8 +103,9 @@ def comparePDFs(pairlist, labels = [], rmin = None, rmax = None, show = True,
     diff = grdat - gtemp
 
     # Put rw in the label
-    rw = (sum(diff**2) / sum(grdat**2))**0.5
-    labeldiff = "difference (Rw = %.2f)"%rw if len(labels) < 3 else labels[2]
+    labeldiff = "difference" if len(labels) < 3 else labels[2]
+    if rw is not None:
+        labeldiff += " (Rw = %.3f)"%rw
 
     # Magnify if necessary
     if maglim is not None:
@@ -176,8 +179,9 @@ def comparePDFs(pairlist, labels = [], rmin = None, rmax = None, show = True,
     pylab.xlabel("r $(\AA)$")
     pylab.ylabel("G $(\AA^{-1})$")
     #pylab.legend(loc = 0)
-    pylab.legend(bbox_to_anchor=(0.005, 1.02, 0.99, .10), loc=3,
-            ncol=3, mode="expand", borderaxespad=0)
+    if legend:
+        pylab.legend(bbox_to_anchor=(0.005, 1.02, 0.99, .10), loc=3,
+                ncol=3, mode="expand", borderaxespad=0)
     if show: pylab.show()
 
     return