Should have scrubbed all reference to the mise subpackage, and changed all imports accordingly. In addition:

1) The default logger name has been changed to "diffpy.srmise"
2) The error and logging modules have been renamed.
3) The exception classes have had Sr prepended.
4) The .srmise files should now write and read "SrMiseMetaData" rather than "MiseMetaData" fields.

Author: Ainamacar

diffpy/srmise/__init__.py

@@ -13,7 +13,7 @@
 
 """Tools for peak extraction from PDF."""
 
-__all__ = ["basefunction", "miseerrors", "miselog", "dataclusters",
+__all__ = ["basefunction", "srmiseerrors", "srmiselog", "dataclusters",
            "modelcluster", "modelparts", "pdfdataset", "pdfpeakextraction",
            "peakextraction", "peakstability", "multimodelselection"]
 

diffpy/srmise/applications/extract.py

@@ -70,18 +70,18 @@ def main():
     dg_defaults = {'absolute':None, 'max-fraction':.05, 'ptp-fraction':.05, 'dG-fraction':1.}
 
     parser.add_option("--peakfunction", dest="peakfunction", metavar="PF",
-                      help="Fit peak function PF defined in diffpy.srmise.mise.peaks. "
+                      help="Fit peak function PF defined in diffpy.srmise.peaks. "
                            "e.g. 'GaussianOverR(maxwidth=0.7)'")
     parser.add_option("--me", "-m", dest="modelevaluator", metavar="ME",
-                      help="ModelEvaluator defined in diffpy.srmise.mise.modelevaluators. "
+                      help="ModelEvaluator defined in diffpy.srmise.modelevaluators. "
                            "e.g. 'AICc'")
 
     group = OptionGroup(parser, "Baseline Options",
                         "The PDF baseline is considered fixed until final stages of peak extraction, "
                         "and a good estimate is critical to reliable results.  Automated estimation "
                         "implemented only for linear baseline, and crudely.")
     group.add_option("--baseline", dest="baseline", metavar="BL",
-                      help="Estimate baseline from baseline function BL defined in diffpy.srmise.mise.baselines. "
+                      help="Estimate baseline from baseline function BL defined in diffpy.srmise.baselines. "
                            "e.g. 'Polynomial(degree=1)'.  All parameters are free.")
     group.add_option("--bcrystal", dest="bcrystal", type="string", metavar="rho0[c]",
                       help="Use linear baseline defined by crystal number density rho0.  "
@@ -181,15 +181,15 @@ def main():
     if len(args) != 1:
         parser.error("Exactly one argument required. \n"+usage)
 
-    from diffpy.srmise.mise import miselog
-    miselog.setlevel(options.verbosity)
+    from diffpy.srmise import srmiselog
+    srmiselog.setlevel(options.verbosity)
 
     import numpy as np
-    from diffpy.srmise.mise.pdfpeakextraction import PDFPeakExtraction
-    from diffpy.srmise.mise.miseerrors import MiseDataFormatError, MiseFileError
+    from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction
+    from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, SrMiseFileError
 
     if options.peakfunction is not None:
-        from diffpy.srmise.mise import peaks
+        from diffpy.srmise import peaks
         try:
             options.peakfunction = eval("peaks."+options.peakfunction)
         except Exception, err:
@@ -198,7 +198,7 @@ def main():
             options.peakfunction = None
 
     if options.modelevaluator is not None:
-        from diffpy.srmise.mise import modelevaluators
+        from diffpy.srmise import modelevaluators
         try:
             options.modelevaluator = eval("modelevaluators."+options.modelevaluator)
         except Exception,  err:
@@ -207,7 +207,7 @@ def main():
             options.modelevaluator = None
 
     if options.bcrystal is not None:
-        from diffpy.srmise.mise.baselines import Polynomial
+        from diffpy.srmise.baselines import Polynomial
         bl = Polynomial(degree=1)
         options.baseline = parsepars(bl, [options.bcrystal, '0c'])
         options.baseline.pars[0] = -4*np.pi*options.baseline.pars[0]
@@ -217,28 +217,28 @@ def main():
         blext.read(options.bsrmise)
         options.baseline = blext.extracted.baseline
     elif options.bpoly0 is not None:
-        from diffpy.srmise.mise.baselines import Polynomial
+        from diffpy.srmise.baselines import Polynomial
         bl = Polynomial(degree=0)
         options.baseline = parsepars(bl, [options.bpoly0])
         #options.baseline = bl.actualize([options.bpoly0], "internal")
     elif options.bpoly1 is not None:
-        from diffpy.srmise.mise.baselines import Polynomial
+        from diffpy.srmise.baselines import Polynomial
         bl = Polynomial(degree=1)
         options.baseline = parsepars(bl, options.bpoly1)
     elif options.bpoly2 is not None:
-        from diffpy.srmise.mise.baselines import Polynomial
+        from diffpy.srmise.baselines import Polynomial
         bl = Polynomial(degree=2)
         options.baseline = parsepars(bl, options.bpoly2)
     elif options.bseq is not None:
-        from diffpy.srmise.mise.baselines import FromSequence
+        from diffpy.srmise.baselines import FromSequence
         bl = FromSequence(options.bseq)
         options.baseline = bl.actualize([], "internal")
     elif options.bspherical is not None:
-        from diffpy.srmise.mise.baselines import NanoSpherical
+        from diffpy.srmise.baselines import NanoSpherical
         bl = NanoSpherical()
         options.baseline = parsepars(bl, options.bspherical)
     elif options.baseline is not None:
-        from diffpy.srmise.mise import baselines
+        from diffpy.srmise import baselines
         try:
             options.baseline = eval("baselines."+options.baseline)
         except Exception, err:
@@ -252,7 +252,7 @@ def main():
         ext = PDFPeakExtraction()
         try:
             ext.read(filename)
-        except (MiseDataFormatError, MiseFileError, Exception):
+        except (SrMiseDataFormatError, SrMiseFileError, Exception):
             ext.loadpdf(filename)
 
         pdict = {}
@@ -284,8 +284,8 @@ def main():
             pdict["error_method"] = options.modelevaluator
 
         if options.liveplot:
-            from diffpy.srmise.mise import miselog
-            miselog.liveplotting(True, options.wait)
+            from diffpy.srmise import srmiselog
+            srmiselog.liveplotting(True, options.wait)
 
         ext.setvars(**pdict)
         if options.performextraction:
@@ -295,15 +295,15 @@ def main():
         if options.savefile is not None:
             try:
                 ext.write(options.savefile)
-            except MiseFileError, err:
+            except SrMiseFileError, err:
                 print err
                 print "Could not save result to '%s'." %options.savefile
 
 
         if options.pwafile is not None:
             try:
                 ext.writepwa(options.pwafile)
-            except MiseFileError, err:
+            except SrMiseFileError, err:
                 print err
                 print "Could not save pwa summary to '%s'." %options.pwafile
 

diffpy/srmise/applications/plot.py

@@ -15,8 +15,8 @@
 import sys
 import optparse
 
-from diffpy.srmise.mise import PDFPeakExtraction, PeakStability
-from diffpy.srmise.mise.pdfpeakextraction import resample
+from diffpy.srmise import PDFPeakExtraction, PeakStability
+from diffpy.srmise.pdfpeakextraction import resample
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -460,7 +460,7 @@ def on_draw(event):
 
 def readcompare(filename):
     """Returns a list of distances read from filename, otherwise None."""
-    from diffpy.srmise.mise.miseerrors import MiseDataFormatError, MiseFileError
+    from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, SrMiseFileError
 
     # TODO: Make this safer
     try:
@@ -495,7 +495,7 @@ def main():
     descr = ("A very basic tool for somewhat prettier plotting than provided by "
              "the basic SrMise classes.  Can be used to compare peak positions "
              "with those from a list.\n"
-             "NOTE: At this time the utility only works with peaks extracted using diffpy.srmise.mise.PDFPeakExtraction.")
+             "NOTE: At this time the utility only works with peaks extracted using diffpy.srmise.PDFPeakExtraction.")
 
     parser = optparse.OptionParser(usage=usage, description=descr)
     parser.add_option("--compare", type="string",

diffpy/srmise/basefunction.py

@@ -16,11 +16,11 @@
 import re
 
 import numpy as np
-from diffpy.srmise.mise.miseerrors import *
-from diffpy.srmise.mise.modelparts import ModelParts, ModelPart
+from diffpy.srmise.srmiseerrors import *
+from diffpy.srmise.modelparts import ModelParts, ModelPart
 
 import logging
-logger = logging.getLogger("mise.peakextraction")
+logger = logging.getLogger("diffpy.srmise")
 
 class BaseFunction(object):
     """Base class for mathematical functions which model numeric sequences.
@@ -320,8 +320,8 @@ def pgradient(self, p, format):
         return
 
     def getmodule(self):
-        """Return 'diffpy.srmise.mise.basefunction'"""
-        return "diffpy.srmise.mise.basefunction"
+        """Return 'diffpy.srmise.basefunction'"""
+        return "diffpy.srmise.basefunction"
 
     def writestr(self, baselist):
         """Return string representation of self.
@@ -379,7 +379,7 @@ def factory(functionstr, baselist):
             except Exception, e:
                 logger.exception(e)
                 emsg = ("Invalid parameter: %s=%s" %(k,v))
-                raise MiseDataFormatError(emsg)
+                raise SrMiseDataFormatError(emsg)
 
         function_name = pdict["function"]
         del pdict["function"]
@@ -441,7 +441,7 @@ def safefunction(f, fsafe):
 
 if __name__ == '__main__':
 
-    from diffpy.srmise.mise.peaks import GaussianOverR, TerminationRipples
+    from diffpy.srmise.peaks import GaussianOverR, TerminationRipples
 
     p = GaussianOverR(0.8)
     outstr = p.writestr([])

diffpy/srmise/baselines/arbitrary.py

@@ -12,13 +12,13 @@
 ##############################################################################
 
 import numpy as np
-from diffpy.srmise.mise.baselines.base import BaselineFunction
-from diffpy.srmise.mise.miseerrors import MiseEstimationError
+from diffpy.srmise.baselines.base import BaselineFunction
+from diffpy.srmise.srmiseerrors import SrMiseEstimationError
 
 import matplotlib.pyplot as plt
 
-import logging, diffpy.srmise.mise.miselog
-logger = logging.getLogger("mise.peakextraction")
+import logging, diffpy.srmise.srmiselog
+logger = logging.getLogger("diffpy.srmise")
 
 class Arbitrary (BaselineFunction):
     """Methods for evaluating a baseline from an arbitrary function.
@@ -104,7 +104,7 @@ def estimate_parameters(self, r, y):
 
         Returns Numpy array of parameters in the default internal format.
         Raises NotImplementedError if no estimation routine is defined, and
-        MiseEstimationError if parameters cannot be estimated for any other."""
+        SrMiseEstimationError if parameters cannot be estimated for any other."""
         if self.estimatef is None:
             emsg = "No estimation routine provided to Arbitrary."
             raise NotImplementedError(emsg)
@@ -115,7 +115,7 @@ def estimate_parameters(self, r, y):
         except Exception, e:
             emsg = "Error within estimation routine provided to Arbitrary:\n"+\
                    str(e)
-            raise MiseEstimationError(emsg)
+            raise SrMiseEstimationError(emsg)
 
     def _jacobianraw(self, pars, r, free):
         """Return the Jacobian of a polynomial.

diffpy/srmise/baselines/base.py

@@ -12,12 +12,12 @@
 ##############################################################################
 
 import numpy as np
-from diffpy.srmise.mise.miseerrors import *
-from diffpy.srmise.mise.basefunction import BaseFunction
-from diffpy.srmise.mise.modelparts import ModelPart
+from diffpy.srmise.srmiseerrors import *
+from diffpy.srmise.basefunction import BaseFunction
+from diffpy.srmise.modelparts import ModelPart
 
-import logging, diffpy.srmise.mise.miselog
-logger = logging.getLogger("mise.peakextraction")
+import logging, diffpy.srmise.srmiselog
+logger = logging.getLogger("diffpy.srmise")
 
 class BaselineFunction(BaseFunction):
     """Base class for functions which represent some data's baseline term.
@@ -131,10 +131,10 @@ def factory(baselinestr, ownerlist):
                     pdict[l[0]] = eval(l[1])
                 except Exception:
                     emsg = ("Invalid parameter: %s" %d)
-                    raise MiseDataFormatError(emsg)
+                    raise SrMiseDataFormatError(emsg)
             else:
                 emsg = ("Invalid parameter: %s" %d)
-                raise MiseDataFormatError(emsg)
+                raise SrMiseDataFormatError(emsg)
 
         # Correctly initialize the base function, if one exists.
         idx = pdict["owner"]
@@ -152,9 +152,9 @@ def factory(baselinestr, ownerlist):
 
     from numpy.random import randn
     import matplotlib.pyplot as plt
-    from diffpy.srmise.mise.modelevaluators import AICc
-    from diffpy.srmise.mise.modelcluster import ModelCluster
-    from diffpy.srmise.mise.peaks import GaussianOverR
+    from diffpy.srmise.modelevaluators import AICc
+    from diffpy.srmise.modelcluster import ModelCluster
+    from diffpy.srmise.peaks import GaussianOverR
 
     res = .01
     r = np.arange(2,4,res)

diffpy/srmise/baselines/fromsequence.py

@@ -13,12 +13,12 @@
 
 import numpy as np
 import scipy.interpolate as spi
-from diffpy.srmise.mise.baselines.base import BaselineFunction
+from diffpy.srmise.baselines.base import BaselineFunction
 
 import matplotlib.pyplot as plt
 
-import logging, diffpy.srmise.mise.miselog
-logger = logging.getLogger("mise.peakextraction")
+import logging, diffpy.srmise.srmiselog
+logger = logging.getLogger("diffpy.srmise")
 
 class FromSequence (BaselineFunction):
     """Methods for evaluation of a baseline from discrete data via interpolation.
@@ -165,7 +165,7 @@ def xyrepr(self, var):
 
     def readxy(self, filename):
         """ """
-        from diffpy.srmise.mise.miseerrors import MiseDataFormatError, MiseFileError
+        from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, SrMiseFileError
 
         # TODO: Make this safer
         try:
@@ -187,7 +187,7 @@ def readxy(self, filename):
                 x.append(float(v[0]))
                 y.append(float(v[1]))
         except (ValueError, IndexError), err:
-            raise MiseDataFormatError(str(err))
+            raise SrMiseDataFormatError(str(err))
 
         return (np.array(x), np.array(y))
 

diffpy/srmise/baselines/nanospherical.py

@@ -12,12 +12,12 @@
 ##############################################################################
 
 import numpy as np
-from diffpy.srmise.mise.baselines.base import BaselineFunction
-from diffpy.srmise.mise.miseerrors import MiseEstimationError
+from diffpy.srmise.baselines.base import BaselineFunction
+from diffpy.srmise.srmiseerrors import SrMiseEstimationError
 import matplotlib.pyplot as plt
 
-import logging, diffpy.srmise.mise.miselog
-logger = logging.getLogger("mise.peakextraction")
+import logging, diffpy.srmise.srmiselog
+logger = logging.getLogger("diffpy.srmise")
 
 class NanoSpherical (BaselineFunction):
     """Methods for evaluation of baseline of spherical nanoparticle of uniform density.
@@ -61,7 +61,7 @@ def __init__(self, Cache=None):
 #
 #        Returns Numpy array of parameters in the default internal format.
 #        Raises NotImplementedError if estimation is not implemented for this
-#        degree, or MiseEstimationError if parameters cannot be estimated for
+#        degree, or SrMiseEstimationError if parameters cannot be estimated for
 #        any other reason.
 #        """
 #        if len(r) != len(y):

diffpy/srmise/baselines/polynomial.py

@@ -12,12 +12,12 @@
 ##############################################################################
 
 import numpy as np
-from diffpy.srmise.mise.baselines.base import BaselineFunction
-from diffpy.srmise.mise.miseerrors import MiseEstimationError
+from diffpy.srmise.baselines.base import BaselineFunction
+from diffpy.srmise.srmiseerrors import SrMiseEstimationError
 import matplotlib.pyplot as plt
 
-import logging, diffpy.srmise.mise.miselog
-logger = logging.getLogger("mise.peakextraction")
+import logging, diffpy.srmise.srmiselog
+logger = logging.getLogger("diffpy.srmise")
 
 class Polynomial (BaselineFunction):
     """Methods for evaluation and parameter estimation of a polynomial baseline."""
@@ -65,7 +65,7 @@ def estimate_parameters(self, r, y):
 
         Returns Numpy array of parameters in the default internal format.
         Raises NotImplementedError if estimation is not implemented for this
-        degree, or MiseEstimationError if parameters cannot be estimated for
+        degree, or SrMiseEstimationError if parameters cannot be estimated for
         any other reason."""
         if self.degree > 1:
             emsg = "Polynomial implements estimation for baselines of degree <= 1 only."
@@ -97,7 +97,7 @@ def estimate_parameters(self, r, y):
             except Exception, e:
                 emsg = "Error during estimation -- "+str(e)
                 raise
-                raise MiseEstimationError(emsg)
+                raise SrMiseEstimationError(emsg)
 
     def _jacobianraw(self, pars, r, free):
         """Return the Jacobian of a polynomial.