diff --git a/MANIFEST.in b/MANIFEST.in index 9440747..68fc353 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -9,4 +9,3 @@ include doc/examples/README recursive-include doc/manual/source *.rst *.txt include doc/manual/source/conf.py include doc/manual/Makefile - diff --git a/devutils/prep.py b/devutils/prep.py index 527dbb3..c63ce0f 100644 --- a/devutils/prep.py +++ b/devutils/prep.py @@ -1,8 +1,10 @@ #!/usr/bin/env python # Run examples and other scripts that should be updated before release. -import io, os, sys +import io +import os import re +import sys __basedir__ = os.getcwdu() @@ -25,15 +27,15 @@ def test(self, call, *args, **kwds): except Exception, e: self.messages.append("%s: error, details below.\n%s" %(testname, e)) finally: - os.chdir(__basedir__) - + os.chdir(__basedir__) + def report(self): print '==== Results of Tests ====' print '\n'.join(self.messages) - + def scrubeol(directory, filerestr): """Use unix-style endlines for files in directory matched by regex string. - + Parameters ---------- directory - A directory to scrub @@ -42,22 +44,22 @@ def scrubeol(directory, filerestr): os.chdir(directory) files = [re.match(filerestr, f) for f in os.listdir(".")] files = [f.group(0) for f in files if f] - + for f in files: original = open(f) text = unicode(original.read()) original.close() - + updated = io.open(f, 'w', newline='\n') updated.write(text) updated.close() - + print "Updated %s to unix-style endlines." %f def rm(directory, filerestr): """Delete files in directory matched by regex string. - + Parameters ---------- directory - A directory to scrub @@ -66,12 +68,12 @@ def rm(directory, filerestr): os.chdir(directory) files = [re.match(filerestr, f) for f in os.listdir(".")] files = [f.group(0) for f in files if f] - + for f in files: os.remove(f) - + print "Deleted %s." %f - + if __name__ == "__main__": @@ -79,7 +81,7 @@ def rm(directory, filerestr): # Temporarily add examples to path lib_path = os.path.abspath(os.path.join('..','doc','examples')) sys.path.append(lib_path) - + # Delete existing files that don't necessarily have a fixed name. rm("../doc/examples/output", r"known_dG.*\.pwa") rm("../doc/examples/output", r"unknown_dG.*\.pwa") @@ -88,7 +90,7 @@ def rm(directory, filerestr): examples = Test() test_names = ["extract_single_peak", "parameter_summary", - "fit_initial", + "fit_initial", "query_results", "multimodel_known_dG1", "multimodel_known_dG2", @@ -103,11 +105,11 @@ def rm(directory, filerestr): examples.test(test.run, plot=False) examples.report() - + ### Convert output of example files to Unix-style endlines for sdist. if os.linesep != '\n': print "==== Scrubbing Endlines ====" # All *.srmise and *.pwa files in examples directory. scrubeol("../doc/examples/output", r".*(\.srmise|\.pwa)") - + diff --git a/diffpy/__init__.py b/diffpy/__init__.py index f075d1b..7170a04 100644 --- a/diffpy/__init__.py +++ b/diffpy/__init__.py @@ -20,7 +20,7 @@ """ -__import__('pkg_resources').declare_namespace(__name__) +__import__("pkg_resources").declare_namespace(__name__) # End of file diff --git a/diffpy/srmise/__init__.py b/diffpy/srmise/__init__.py index f69dfb5..532c767 100644 --- a/diffpy/srmise/__init__.py +++ b/diffpy/srmise/__init__.py @@ -13,18 +13,28 @@ """Tools for peak extraction from PDF.""" -__all__ = ["basefunction", "srmiseerrors", "srmiselog", "dataclusters", - "modelcluster", "modelparts", "pdfdataset", "pdfpeakextraction", - "peakextraction", "peakstability", "multimodelselection"] - -from diffpy.srmise.version import __version__ +__all__ = [ + "basefunction", + "srmiseerrors", + "srmiselog", + "dataclusters", + "modelcluster", + "modelparts", + "pdfdataset", + "pdfpeakextraction", + "peakextraction", + "peakstability", + "multimodelselection", +] from basefunction import BaseFunction from dataclusters import DataClusters from modelcluster import ModelCluster, ModelCovariance from modelparts import ModelPart, ModelParts +from multimodelselection import MultimodelSelection from pdfdataset import PDFDataSet from pdfpeakextraction import PDFPeakExtraction from peakextraction import PeakExtraction from peakstability import PeakStability -from multimodelselection import MultimodelSelection + +from diffpy.srmise.version import __version__ diff --git a/diffpy/srmise/applications/extract.py b/diffpy/srmise/applications/extract.py index 5fbe927..5bbc646 100755 --- a/diffpy/srmise/applications/extract.py +++ b/diffpy/srmise/applications/extract.py @@ -11,9 +11,11 @@ # ############################################################################## -from optparse import OptionParser, OptionGroup -import numpy as np +from optparse import OptionGroup, OptionParser + import matplotlib.pyplot as plt +import numpy as np + def main(): """Default SrMise entry-point.""" @@ -78,7 +80,7 @@ def main(): version=version, formatter=IndentedHelpFormatterWithNL()) - parser.set_defaults(plot=False, liveplot=False, wait=False, + parser.set_defaults(plot=False, liveplot=False, wait=False, performextraction=True, verbosity="warning") dg_defaults = {'absolute':None, 'data':None, 'max-fraction':.05, 'ptp-fraction':.05, 'dG-fraction':1.} @@ -203,7 +205,7 @@ def main(): "'absolute'=%s\n" "'max-fraction'=%s\n" "'ptp-fraction'=%s\n" - "'dG-fraction'=%s" %(dg_defaults['absolute'], + "'dG-fraction'=%s" %(dg_defaults['absolute'], dg_defaults['max-fraction'], dg_defaults['ptp-fraction'], dg_defaults['dG-fraction'])) @@ -269,8 +271,7 @@ def main(): srmiselog.setlevel(options.verbosity) from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction - from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, \ - SrMiseFileError + from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, SrMiseFileError if options.peakfunction is not None: from diffpy.srmise import peaks @@ -364,7 +365,7 @@ def main(): elif options.dg_mode == "ptp-fraction": pdict["effective_dy"] = options.dg*ext.y.ptp()*np.ones(len(ext.y)) elif options.dg_mode == "dG-fraction": - pdict["effective_dy"] = options.dg*ext.dy + pdict["effective_dy"] = options.dg*ext.dy if options.rng is not None: pdict["rng"] = list(options.rng) if options.qmax is not None: @@ -403,7 +404,7 @@ def main(): print err print "Could not save pwa summary to '%s'." %options.pwafile - + print ext if cov is not None: print cov @@ -442,8 +443,9 @@ def parsepars(mp, parseq): # Borrowed, with minor changes, from # http://groups.google.com/group/comp.lang.python/browse_frm/thread/6df6e6b541a15bc2/09f28e26af0699b1 -from optparse import IndentedHelpFormatter import textwrap +from optparse import IndentedHelpFormatter + class IndentedHelpFormatterWithNL(IndentedHelpFormatter): def _format_text(self, text): diff --git a/diffpy/srmise/applications/plot.py b/diffpy/srmise/applications/plot.py index b4894e5..b696aa8 100755 --- a/diffpy/srmise/applications/plot.py +++ b/diffpy/srmise/applications/plot.py @@ -12,18 +12,17 @@ ############################################################################## """plot extracted peaks and comparison to ideal distances (if given)""" -import sys import optparse - -from diffpy.srmise import PDFPeakExtraction, PeakStability -from diffpy.srmise.pdfpeakextraction import resample +import sys import matplotlib.pyplot as plt +import mpl_toolkits.axisartist as AA import numpy as np - from mpl_toolkits.axes_grid1 import make_axes_locatable from mpl_toolkits.axes_grid1.inset_locator import inset_axes -import mpl_toolkits.axisartist as AA + +from diffpy.srmise import PDFPeakExtraction, PeakStability +from diffpy.srmise.pdfpeakextraction import resample # For a given figure, returns a label of interest labeldict = {} diff --git a/diffpy/srmise/basefunction.py b/diffpy/srmise/basefunction.py index b0fc10d..18a55e4 100644 --- a/diffpy/srmise/basefunction.py +++ b/diffpy/srmise/basefunction.py @@ -12,14 +12,15 @@ ############################################################################## """Defines BaseFunction, the base class for mathematical functions in srmise.""" -import sys +import logging import re +import sys import numpy as np + +from diffpy.srmise.modelparts import ModelPart, ModelParts from diffpy.srmise.srmiseerrors import * -from diffpy.srmise.modelparts import ModelParts, ModelPart -import logging logger = logging.getLogger("diffpy.srmise") class BaseFunction(object): diff --git a/diffpy/srmise/baselines/__init__.py b/diffpy/srmise/baselines/__init__.py index e4ddead..fc8ad98 100644 --- a/diffpy/srmise/baselines/__init__.py +++ b/diffpy/srmise/baselines/__init__.py @@ -13,8 +13,8 @@ __all__ = ["base", "arbitrary", "fromsequence", "nanospherical", "polynomial"] -from base import Baseline from arbitrary import Arbitrary +from base import Baseline from fromsequence import FromSequence from nanospherical import NanoSpherical from polynomial import Polynomial diff --git a/diffpy/srmise/baselines/arbitrary.py b/diffpy/srmise/baselines/arbitrary.py index d24d6ee..2588740 100644 --- a/diffpy/srmise/baselines/arbitrary.py +++ b/diffpy/srmise/baselines/arbitrary.py @@ -11,13 +11,15 @@ # ############################################################################## +import logging + +import matplotlib.pyplot as plt import numpy as np + +import diffpy.srmise.srmiselog from diffpy.srmise.baselines.base import BaselineFunction from diffpy.srmise.srmiseerrors import SrMiseEstimationError -import matplotlib.pyplot as plt - -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class Arbitrary (BaselineFunction): diff --git a/diffpy/srmise/baselines/base.py b/diffpy/srmise/baselines/base.py index 8d9a902..d84160a 100644 --- a/diffpy/srmise/baselines/base.py +++ b/diffpy/srmise/baselines/base.py @@ -11,14 +11,18 @@ # ############################################################################## +import logging + import numpy as np -from diffpy.srmise.srmiseerrors import * + +import diffpy.srmise.srmiselog from diffpy.srmise.basefunction import BaseFunction from diffpy.srmise.modelparts import ModelPart +from diffpy.srmise.srmiseerrors import * -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") + class BaselineFunction(BaseFunction): """Base class for functions which represent some data's baseline term. @@ -55,7 +59,15 @@ class BaselineFunction(BaseFunction): transform_parameters() """ - def __init__(self, parameterdict, parformats, default_formats, metadict, base=None, Cache=None): + def __init__( + self, + parameterdict, + parformats, + default_formats, + metadict, + base=None, + Cache=None, + ): """Set parameterdict defined by subclass parameterdict: A dictionary mapping string keys to their index in a @@ -71,22 +83,31 @@ def __init__(self, parameterdict, parformats, default_formats, metadict, base=No additional functionality. Cache: A class (not instance) which implements caching of BaseFunction evaluations.""" - BaseFunction.__init__(self, parameterdict, parformats, default_formats, metadict, base, Cache) - + BaseFunction.__init__( + self, parameterdict, parformats, default_formats, metadict, base, Cache + ) #### "Virtual" class methods #### - #### Methods required by BaseFunction #### - def actualize(self, pars, in_format="default_input", free=None, removable=False, static_owner=False): + def actualize( + self, + pars, + in_format="default_input", + free=None, + removable=False, + static_owner=False, + ): converted = self.transform_parameters(pars, in_format, out_format="internal") return Baseline(self, converted, free, removable, static_owner) def getmodule(self): return __name__ -#end of class BaselineFunction + +# end of class BaselineFunction + class Baseline(ModelPart): """Represents a baseline associated with a BaselineFunction subclass.""" @@ -129,10 +150,10 @@ def factory(baselinestr, ownerlist): try: pdict[l[0]] = eval(l[1]) except Exception: - emsg = ("Invalid parameter: %s" %d) + emsg = "Invalid parameter: %s" % d raise SrMiseDataFormatError(emsg) else: - emsg = ("Invalid parameter: %s" %d) + emsg = "Invalid parameter: %s" % d raise SrMiseDataFormatError(emsg) # Correctly initialize the base function, if one exists. @@ -144,23 +165,25 @@ def factory(baselinestr, ownerlist): return Baseline(**pdict) + # End of class Baseline # simple test code -if __name__ == '__main__': +if __name__ == "__main__": - from numpy.random import randn import matplotlib.pyplot as plt - from diffpy.srmise.modelevaluators import AICc + from numpy.random import randn + from diffpy.srmise.modelcluster import ModelCluster + from diffpy.srmise.modelevaluators import AICc from diffpy.srmise.peaks import GaussianOverR - res = .01 - r = np.arange(2,4,res) - err = np.ones(len(r)) #default unknown errors - pf = GaussianOverR(.7) + res = 0.01 + r = np.arange(2, 4, res) + err = np.ones(len(r)) # default unknown errors + pf = GaussianOverR(0.7) evaluator = AICc() - pars = [[3, .2, 10], [3.5, .2, 10]] + pars = [[3, 0.2, 10], [3.5, 0.2, 10]] ideal_peaks = Peaks([pf.createpeak(p, "pwa") for p in pars]) - y = ideal_peaks.value(r) + .1*randn(len(r)) + y = ideal_peaks.value(r) + 0.1 * randn(len(r)) diff --git a/diffpy/srmise/baselines/fromsequence.py b/diffpy/srmise/baselines/fromsequence.py index 2eb5a5f..c06e2de 100644 --- a/diffpy/srmise/baselines/fromsequence.py +++ b/diffpy/srmise/baselines/fromsequence.py @@ -11,13 +11,15 @@ # ############################################################################## +import logging + +import matplotlib.pyplot as plt import numpy as np import scipy.interpolate as spi -from diffpy.srmise.baselines.base import BaselineFunction -import matplotlib.pyplot as plt +import diffpy.srmise.srmiselog +from diffpy.srmise.baselines.base import BaselineFunction -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class FromSequence (BaselineFunction): diff --git a/diffpy/srmise/baselines/nanospherical.py b/diffpy/srmise/baselines/nanospherical.py index 2d9e876..04c1d43 100644 --- a/diffpy/srmise/baselines/nanospherical.py +++ b/diffpy/srmise/baselines/nanospherical.py @@ -11,12 +11,15 @@ # ############################################################################## +import logging + +import matplotlib.pyplot as plt import numpy as np + +import diffpy.srmise.srmiselog from diffpy.srmise.baselines.base import BaselineFunction from diffpy.srmise.srmiseerrors import SrMiseEstimationError -import matplotlib.pyplot as plt -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class NanoSpherical (BaselineFunction): diff --git a/diffpy/srmise/baselines/polynomial.py b/diffpy/srmise/baselines/polynomial.py index a31e3db..4d95c4f 100644 --- a/diffpy/srmise/baselines/polynomial.py +++ b/diffpy/srmise/baselines/polynomial.py @@ -11,12 +11,15 @@ # ############################################################################## +import logging + +import matplotlib.pyplot as plt import numpy as np + +import diffpy.srmise.srmiselog from diffpy.srmise.baselines.base import BaselineFunction from diffpy.srmise.srmiseerrors import SrMiseEstimationError -import matplotlib.pyplot as plt -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class Polynomial (BaselineFunction): diff --git a/diffpy/srmise/dataclusters.py b/diffpy/srmise/dataclusters.py index 98b9522..077c1a8 100644 --- a/diffpy/srmise/dataclusters.py +++ b/diffpy/srmise/dataclusters.py @@ -12,10 +12,13 @@ ############################################################################## """Defines class to partition sequences representing the x and y axis into peak-like clusters.""" -import numpy as np +import logging + import matplotlib.pyplot as plt +import numpy as np + +import diffpy.srmise.srmiselog -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class DataClusters: diff --git a/diffpy/srmise/modelcluster.py b/diffpy/srmise/modelcluster.py index 04a7261..10c0677 100644 --- a/diffpy/srmise/modelcluster.py +++ b/diffpy/srmise/modelcluster.py @@ -18,23 +18,30 @@ ModelCovariance: Helper class for model covariance. """ -import numpy as np -import scipy as sp -from scipy.optimize import leastsq -from diffpy.srmise.peaks import Peak, Peaks -from diffpy.srmise.modelparts import ModelParts -from diffpy.srmise.srmiseerrors import SrMiseEstimationError, SrMiseFitError, SrMiseDataFormatError, SrMiseUndefinedCovarianceError -from diffpy.srmise.baselines import Baseline +import logging import re import sys import matplotlib.pyplot as plt +import numpy as np +import scipy as sp +from scipy.optimize import leastsq + +from diffpy.srmise.baselines import Baseline +from diffpy.srmise.modelparts import ModelParts +from diffpy.srmise.peaks import Peak, Peaks +from diffpy.srmise.srmiseerrors import ( + SrMiseDataFormatError, + SrMiseEstimationError, + SrMiseFitError, + SrMiseUndefinedCovarianceError, +) -import logging logger = logging.getLogger("diffpy.srmise") from diffpy.srmise import srmiselog + class ModelCovariance(object): """Helper class preserves uncertainty info (full covariance matrix) for a fit model. @@ -58,7 +65,7 @@ def __init__(self, *args, **kwds): # Map (i,j)->n of jth parameter of ith ModelPart to nth parameter in cov. self.pmap = {} - + # Map n->(i,j), inverse of pmap. self.ipmap = {} @@ -211,21 +218,21 @@ def transform(self, in_format, out_format, **kwds): def getcorrelation(self, i, j): """Return the correlation between variables i and j, Corr_ij=Cov_ij/(sigma_i sigma_j) - + The variables may be specified as integers, or as a two-component tuple of integers (l, m) which indicate the mth parameter in peak l. - + The standard deviation of fixed parameters is 0, in which case the correlation is undefined, but return 0 for simplicity. """ if self.cov is None: emsg = "Cannot get correlation on undefined covariance matrix." raise SrMiseUndefinedCovarianceError(emsg) - + # Map peak/parameter tuples to the proper index i1 = self.pmap[i] if i in self.pmap else i j1 = self.pmap[j] if j in self.pmap else j - + if self.cov[i1,i1] == 0. or self.cov[j1,j1] == 0.: return 0. # Avoiding undefined quantities is sensible in this context. else: @@ -251,18 +258,18 @@ def getuncertainty(self, i): def getcovariance(self, i, j): """Return the covariance between variables i and j. - + The variables may be specified as integers, or as a two-component tuple of integers (l, m) which indicate the mth parameter of modelpart l. """ if self.cov is None: emsg = "Cannot get correlation on undefined covariance matrix." raise SrMiseUndefinedCovarianceError(emsg) - + # Map peak/parameter tuples to the proper index i1 = self.pmap[i] if i in self.pmap else i j1 = self.pmap[j] if j in self.pmap else j - + return self.cov[i1,j1] def get(self, i): @@ -308,7 +315,7 @@ def __str__(self): def prettypar(self, i): """Return string 'value (uncertainty)' for parameter i. - + The variable may be specified as an integer, or as a two-component tuple of integers (l, m) which indicate the mth parameter of modelpart l. """ @@ -814,7 +821,7 @@ def replacepeaks(self, newpeaks, delslice=slice(0,0)): self.model[delslice] = newpeaks self.model.sort(key="position") return - + def deletepeak(self, idx): """Delete the peak at the given index.""" self.replacepeaks([], slice(idx,idx+1)) diff --git a/diffpy/srmise/modelevaluators/aic.py b/diffpy/srmise/modelevaluators/aic.py index b845197..915cace 100644 --- a/diffpy/srmise/modelevaluators/aic.py +++ b/diffpy/srmise/modelevaluators/aic.py @@ -11,11 +11,14 @@ # ############################################################################## +import logging + import numpy as np + +import diffpy.srmise.srmiselog from diffpy.srmise.modelevaluators.base import ModelEvaluator from diffpy.srmise.srmiseerrors import SrMiseModelEvaluatorError -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class AIC (ModelEvaluator): diff --git a/diffpy/srmise/modelevaluators/aicc.py b/diffpy/srmise/modelevaluators/aicc.py index 6420441..57f0713 100644 --- a/diffpy/srmise/modelevaluators/aicc.py +++ b/diffpy/srmise/modelevaluators/aicc.py @@ -11,11 +11,14 @@ # ############################################################################## +import logging + import numpy as np + +import diffpy.srmise.srmiselog from diffpy.srmise.modelevaluators.base import ModelEvaluator from diffpy.srmise.srmiseerrors import SrMiseModelEvaluatorError -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class AICc (ModelEvaluator): diff --git a/diffpy/srmise/modelevaluators/base.py b/diffpy/srmise/modelevaluators/base.py index b6bdd24..eb28272 100644 --- a/diffpy/srmise/modelevaluators/base.py +++ b/diffpy/srmise/modelevaluators/base.py @@ -39,20 +39,24 @@ # ######################################################################## +import logging + import numpy as np + +import diffpy.srmise.srmiselog from diffpy.srmise.srmiseerrors import SrMiseModelEvaluatorError -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") + class ModelEvaluator: """Class for evaluating the quality of a fit. Comparison between different - models of the same type is defined so that better models are 'greater than' - worse models.""" + models of the same type is defined so that better models are 'greater than' + worse models.""" def __init__(self, method, higher_is_better): """method = name of method (string) - higher_is_better = boolean + higher_is_better = boolean """ self.method = method self.higher_is_better = higher_is_better @@ -61,10 +65,12 @@ def __init__(self, method, higher_is_better): return def __lt__(self, other): - """ """ + """ """ - assert self.method == other.method #Comparison between same types required - assert self.stat != None and other.stat != None #The statistic must already be calculated + assert self.method == other.method # Comparison between same types required + assert ( + self.stat != None and other.stat != None + ) # The statistic must already be calculated if self.higher_is_better: return self.stat < other.stat @@ -72,10 +78,12 @@ def __lt__(self, other): return other.stat < self.stat def __le__(self, other): - """ """ + """ """ - assert self.method == other.method #Comparison between same types required - assert self.stat != None and other.stat != None #The statistic must already be calculated + assert self.method == other.method # Comparison between same types required + assert ( + self.stat != None and other.stat != None + ) # The statistic must already be calculated if self.higher_is_better: return self.stat <= other.stat @@ -83,26 +91,32 @@ def __le__(self, other): return other.stat <= self.stat def __eq__(self, other): - """ """ + """ """ - assert self.method == other.method #Comparison between same types required - assert self.stat != None and other.stat != None #The statistic must already be calculated + assert self.method == other.method # Comparison between same types required + assert ( + self.stat != None and other.stat != None + ) # The statistic must already be calculated return self.stat == other.stat def __ne__(self, other): - """ """ + """ """ - assert self.method == other.method #Comparison between same types required - assert self.stat != None and other.stat != None #The statistic must already be calculated + assert self.method == other.method # Comparison between same types required + assert ( + self.stat != None and other.stat != None + ) # The statistic must already be calculated return self.stat != other.stat def __gt__(self, other): - """ """ + """ """ - assert self.method == other.method #Comparison between same types required - assert self.stat != None and other.stat != None #The statistic must already be calculated + assert self.method == other.method # Comparison between same types required + assert ( + self.stat != None and other.stat != None + ) # The statistic must already be calculated if self.higher_is_better: return self.stat > other.stat @@ -110,21 +124,23 @@ def __gt__(self, other): return other.stat > self.stat def __ge__(self, other): - """ """ + """ """ - assert self.method == other.method #Comparison between same types required - assert self.stat != None and other.stat != None #The statistic must already be calculated + assert self.method == other.method # Comparison between same types required + assert ( + self.stat != None and other.stat != None + ) # The statistic must already be calculated if self.higher_is_better: return self.stat >= other.stat else: return other.stat >= self.stat - def chi_squared(self, expected, observed, error): """Calculates chi-squared statistic.""" - self.chisq = np.sum((expected-observed)**2/error**2) + self.chisq = np.sum((expected - observed) ** 2 / error**2) return self.chisq + # end of class ModelEvaluator diff --git a/diffpy/srmise/modelparts.py b/diffpy/srmise/modelparts.py index 9c1a04c..1cb6412 100644 --- a/diffpy/srmise/modelparts.py +++ b/diffpy/srmise/modelparts.py @@ -18,12 +18,14 @@ ModelParts: Collection (list) of ModelPart instances. """ +import logging + import numpy as np from scipy.optimize import leastsq -from diffpy.srmise.srmiseerrors import * + from diffpy.srmise import srmiselog +from diffpy.srmise.srmiseerrors import * -import logging logger = logging.getLogger("diffpy.srmise") import matplotlib.pyplot as plt @@ -31,6 +33,7 @@ # Output of scipy.optimize.leastsq for a single parameter changed in scipy 0.8.0 # Before it returned a scalar, later it returned an array of length 1. import pkg_resources as pr + __spv__ = pr.get_distribution('scipy').version __oldleastsqbehavior__ = (pr.parse_version(__spv__) < pr.parse_version('0.8.0')) diff --git a/diffpy/srmise/multimodelselection.py b/diffpy/srmise/multimodelselection.py index e38f668..35d9e08 100644 --- a/diffpy/srmise/multimodelselection.py +++ b/diffpy/srmise/multimodelselection.py @@ -11,14 +11,16 @@ # ############################################################################## -import numpy as np +import logging + import matplotlib.pyplot as plt +import numpy as np from matplotlib import transforms + +import diffpy.srmise.srmiselog +from diffpy.srmise import ModelCluster, PeakStability from diffpy.srmise.modelevaluators.base import ModelEvaluator -from diffpy.srmise import ModelCluster -from diffpy.srmise import PeakStability -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") def eatkwds(*args, **kwds): @@ -482,9 +484,9 @@ def plot3dclassprobs(self, **kwds): "cbaxis" - The colorbar axis, if it exists. "cb" - The colorbar, if it exists.""" - from mpl_toolkits.mplot3d import Axes3D + from matplotlib import cm, colorbar, colors from matplotlib.collections import PolyCollection - from matplotlib import cm, colors, colorbar + from mpl_toolkits.mplot3d import Axes3D fig = kwds.pop("figure", plt.gcf()) ax = fig.add_subplot(kwds.pop("subplot",111), projection='3d') diff --git a/diffpy/srmise/pdfdataset.py b/diffpy/srmise/pdfdataset.py index f79f004..2bdd9bf 100644 --- a/diffpy/srmise/pdfdataset.py +++ b/diffpy/srmise/pdfdataset.py @@ -10,7 +10,7 @@ # See LICENSE.txt for license information. # # This file uses source code from the PDFgui files pdfdataset.py and -# pdfcomponent.py, (c) 2006 trustees of the Michigan State University. See +# pdfcomponent.py, (c) 2006 trustees of the Michigan State University. See # LICENSE_PDFgui.txt for the full PDFgui license. # ############################################################################## @@ -20,28 +20,27 @@ """ +import copy import os.path import re -import copy import time from getpass import getuser -from diffpy.srmise.srmiseerrors import \ - SrMisePDFKeyError, SrMiseFileError +from diffpy.srmise.srmiseerrors import SrMiseFileError, SrMisePDFKeyError class PDFComponent(object): - """Common base class.""" + """Common base class.""" def __init__(self, name): """initialize - + name -- object name """ self.name = name - + def close ( self, force = False ): """close myself - + force -- if forcibly (no wait) """ pass @@ -185,14 +184,14 @@ def readStr(self, datastring): start_data = 0 header = datastring[:start_data] databody = datastring[start_data:].strip() - + # find where the metadata starts metadata = '' res = re.search(r'^#+\ +metadata\b\n', header, re.M) if res: metadata = header[res.end():] - header = header[:res.start()] - + header = header[:res.start()] + # parse header # stype if re.search('(x-?ray|PDFgetX)', header, re.I): @@ -234,7 +233,7 @@ def readStr(self, datastring): res = re.search(regexp, header) if res: self.metadata['doping'] = float(res.groups()[0]) - + # parsing gerneral metadata if metadata: regexp = r"\b(\w+)\ *=\ *(%(f)s)\b" % rx diff --git a/diffpy/srmise/pdfpeakextraction.py b/diffpy/srmise/pdfpeakextraction.py index 04b0757..8f9ecd6 100644 --- a/diffpy/srmise/pdfpeakextraction.py +++ b/diffpy/srmise/pdfpeakextraction.py @@ -11,24 +11,25 @@ # ############################################################################## -import numpy as np +import logging import os.path import re -from diffpy.srmise.peakextraction import PeakExtraction +import matplotlib.pyplot as plt +import numpy as np + from diffpy.srmise.modelcluster import ModelCluster, ModelCovariance -from diffpy.srmise.srmiseerrors import * -#from diffpy.pdfgui.control.pdfdataset import PDFDataSet +# from diffpy.pdfgui.control.pdfdataset import PDFDataSet from diffpy.srmise.pdfdataset import PDFDataSet +from diffpy.srmise.peakextraction import PeakExtraction +from diffpy.srmise.srmiseerrors import * -import matplotlib.pyplot as plt - -import logging logger = logging.getLogger("diffpy.srmise") from diffpy.srmise import srmiselog + class PDFPeakExtraction(PeakExtraction): """Class for peak extraction of peaks from the PDF. @@ -63,9 +64,8 @@ class PDFPeakExtraction(PeakExtraction): """ def __init__(self): - """Initialize. - """ - newvars = ['qmax', 'supersample', 'nyquist', 'scale'] + """Initialize.""" + newvars = ["qmax", "supersample", "nyquist", "scale"] PeakExtraction.__init__(self, newvars) return @@ -141,7 +141,7 @@ def setvars(self, quiet=False, **kwds): emsg = "Qmax could not be automatically determined." raise SrMiseQmaxError(emsg) if "supersample" in kwds: - if kwds["supersample"] < 1.: + if kwds["supersample"] < 1.0: emsg = "Supersample must be a value greater than 1." raise ValueError(emsg) PeakExtraction.setvars(self, quiet, **kwds) @@ -157,8 +157,9 @@ def defaultvars(self, *args): elif self.qmax_fromdata is not None: self.qmax = self.qmax_fromdata else: - self.qmax = 0. - if "qmax" in args: nargs.remove("qmax") + self.qmax = 0.0 + if "qmax" in args: + nargs.remove("qmax") # nyquist if self.nyquist is None or "nyquist" in args: @@ -166,7 +167,8 @@ def defaultvars(self, *args): self.nyquist = True else: self.nyquist = False - if "nyquist" in args: nargs.remove("nyquist") + if "nyquist" in args: + nargs.remove("nyquist") # scale if self.scale is None or "scale" in args: @@ -174,23 +176,28 @@ def defaultvars(self, *args): self.scale = False else: self.scale = False - if "scale" in args: nargs.remove("scale") + if "scale" in args: + nargs.remove("scale") # supersample if self.supersample is None or "supersample" in args: - self.supersample = 4. - if "supersample" in args: nargs.remove("supersample") + self.supersample = 4.0 + if "supersample" in args: + nargs.remove("supersample") # Override defaults from PeakExtraction if self.cres is None or "cres" in args: if self.qmax > 0: - self.cres = np.pi/self.qmax - if "cres" in args: nargs.remove("cres") + self.cres = np.pi / self.qmax + if "cres" in args: + nargs.remove("cres") if self.pf is None or "pf" in args: from diffpy.srmise.peaks import GaussianOverR - self.pf = [GaussianOverR(.7)] - if "pf" in args: nargs.remove("pf") + + self.pf = [GaussianOverR(0.7)] + if "pf" in args: + nargs.remove("pf") # Enable "dg" as alias for "effective_dy" if "dg" in args and "effective_dy" not in args: @@ -199,7 +206,6 @@ def defaultvars(self, *args): # Set other defaults PeakExtraction.defaultvars(self, *nargs) - def resampledata(self, dr, **kwds): """Return (x, y, error in x, effective error in y) resampled by interval dr. @@ -217,17 +223,20 @@ def resampledata(self, dr, **kwds): Keywords eps: [10^-6] Suppress information lost warning when dr-dr_nyquist < eps""" - self.defaultvars() # Find correct range if necessary. + self.defaultvars() # Find correct range if necessary. eps = kwds.get("eps", 10**-6) if self.qmax == 0: logger.warning("Resampling when qmax=0. Information may be lost!") else: - dr_nyquist = np.pi/self.qmax + dr_nyquist = np.pi / self.qmax # Not a robust epsilon test, but all physical Nyquist rates in same oom. if dr - dr_nyquist > eps: - logger.warning("Resampling at %s, below Nyquist rate of %s. Information will be lost!" %(dr, dr_nyquist)) + logger.warning( + "Resampling at %s, below Nyquist rate of %s. Information will be lost!" + % (dr, dr_nyquist) + ) r = np.arange(max(self.x[0], self.rng[0]), min(self.x[-1], self.rng[1]), dr) y = resample(self.x, self.y, r) @@ -238,7 +247,7 @@ def resampledata(self, dr, **kwds): r_error = None else: r_error = np.interp(r, self.x, self.dx) - y_error = self.errorscale(dr)*np.interp(r, self.x, self.effective_dy) + y_error = self.errorscale(dr) * np.interp(r, self.x, self.effective_dy) return (r, y, r_error, y_error) @@ -251,10 +260,10 @@ def errorscale(self, dr): Parameters dr: The sampling interval""" if self.qmax > 0 and self.nyquist and self.scale: - dr_nyquist = np.pi/self.qmax - return np.max([np.sqrt(dr_nyquist/dr), 1.]) + dr_nyquist = np.pi / self.qmax + return np.max([np.sqrt(dr_nyquist / dr), 1.0]) else: - return 1. + return 1.0 def extract(self, **kwds): """Extract peaks from the PDF. Returns ModelCovariance instance summarizing results.""" @@ -276,22 +285,24 @@ def extract(self, **kwds): self.defaultvars() # Determine grid spacing - dr_raw = (self.x[-1]-self.x[0])/(len(self.x)-1) + dr_raw = (self.x[-1] - self.x[0]) / (len(self.x) - 1) logger.info("Extract using qmax=%s", self.qmax) if self.qmax > 0: - dr_nyquist = np.pi/self.qmax + dr_nyquist = np.pi / self.qmax if dr_raw > dr_nyquist: # Technically I should yell for dr_raw >= dr_nyquist, since information # loss may occur at equality. - logger.warn("The input PDF appears to be missing information: The " - "sampling interval of the input PDF (%s) is larger than " - "the Nyquist interval (%s) defined by qmax=%s. This information " - "is irretrievable." %(dr_raw, dr_nyquist, self.qmax)) + logger.warn( + "The input PDF appears to be missing information: The " + "sampling interval of the input PDF (%s) is larger than " + "the Nyquist interval (%s) defined by qmax=%s. This information " + "is irretrievable." % (dr_raw, dr_nyquist, self.qmax) + ) else: # Do I actually need this? - dr_nyquist = dr_raw # not actually Nyquist sampling, natch + dr_nyquist = dr_raw # not actually Nyquist sampling, natch # Define grids rngslice = self.getrangeslice() @@ -300,27 +311,34 @@ def extract(self, **kwds): y1 = self.y[rngslice] y_error1 = self.effective_dy[rngslice] else: - if dr_nyquist/dr_raw < self.supersample: + if dr_nyquist / dr_raw < self.supersample: # supersample PDF for initial extraction - dr = dr_nyquist/self.supersample + dr = dr_nyquist / self.supersample (r1, y1, r_error1, y_error1) = self.resampledata(dr) else: # provided PDF already sufficiently oversampled r1 = self.x[rngslice] y1 = self.y[rngslice] - y_error1 = self.errorscale(dr_raw)*self.effective_dy[rngslice] + y_error1 = self.errorscale(dr_raw) * self.effective_dy[rngslice] # Set up initial extraction pe = PeakExtraction() pe.setdata(r1, y1, None, None) - msg = ["Performing initial peak extraction", - "----------------------------------"] + msg = [ + "Performing initial peak extraction", + "----------------------------------", + ] logger.info("\n".join(msg)) - pe.setvars(cres=self.cres, pf=self.pf, effective_dy = y_error1, - baseline=self.baseline, error_method=self.error_method, - initial_peaks=self.initial_peaks) + pe.setvars( + cres=self.cres, + pf=self.pf, + effective_dy=y_error1, + baseline=self.baseline, + error_method=self.error_method, + initial_peaks=self.initial_peaks, + ) # Initial extraction pe.extract_single() @@ -330,19 +348,20 @@ def extract(self, **kwds): # Prune model with termination ripples if self.qmax > 0: - msg = ["Model after initial extraction.", - "%s", - "\n", - "-----------------------------", - "Adding termination ripples."] + msg = [ + "Model after initial extraction.", + "%s", + "\n", + "-----------------------------", + "Adding termination ripples.", + ] - logger.info("\n".join(msg), - ext) + logger.info("\n".join(msg), ext) from diffpy.srmise.peaks import TerminationRipples owners = list(set([p.owner() for p in ext.model])) - tfuncs={} + tfuncs = {} for o in owners: tfuncs[o] = TerminationRipples(o, self.qmax) for p in ext.model: @@ -373,35 +392,57 @@ def extract(self, **kwds): # indicates that effective_dy is too small. while True: totalfreepars = ext.npars(count_fixed=False) - if totalfreepars >= (r1[-1]-r1[0])/dr_nyquist: - dr_resample = .9999*(r1[-1]-r1[0])/totalfreepars + if totalfreepars >= (r1[-1] - r1[0]) / dr_nyquist: + dr_resample = 0.9999 * (r1[-1] - r1[0]) / totalfreepars else: dr_resample = dr_nyquist - logger.info("Data resampled at dr=%s. (Nyquist rate=%s)", dr_resample, dr_nyquist) + logger.info( + "Data resampled at dr=%s. (Nyquist rate=%s)", + dr_resample, + dr_nyquist, + ) (r2, y2, r_error2, y_error2) = self.resampledata(dr_resample) - ext = ModelCluster(ext.model, bl, r2, y2, y_error2, None, self.error_method, self.pf) - ext.fit() # Clean up parameters after resampling. + ext = ModelCluster( + ext.model, + bl, + r2, + y2, + y_error2, + None, + self.error_method, + self.pf, + ) + ext.fit() # Clean up parameters after resampling. ext.prune() if dr_resample == dr_nyquist: logger.info("Nyquist sampling complete.") break - elif ext.npars(count_fixed=False)==totalfreepars: - msg = ["Warning: Nyquist sampling could not be completed, too many free parameters.", - "The data have been oversampled by the least possible amount, but their ", - "uncertainties are correlated and the model is probably overfit.", - "Data sampled at dr=%s", - "Nyquist rate=%s", - "Degree of oversampling: %s"] - logger.warning("\n".join(msg), dr_resample, dr_nyquist, dr_nyquist/dr_resample) + elif ext.npars(count_fixed=False) == totalfreepars: + msg = [ + "Warning: Nyquist sampling could not be completed, too many free parameters.", + "The data have been oversampled by the least possible amount, but their ", + "uncertainties are correlated and the model is probably overfit.", + "Data sampled at dr=%s", + "Nyquist rate=%s", + "Degree of oversampling: %s", + ] + logger.warning( + "\n".join(msg), + dr_resample, + dr_nyquist, + dr_nyquist / dr_resample, + ) break else: - ext = ModelCluster(ext.model, bl, r1, y1, y_error1, None, self.error_method, self.pf) + ext = ModelCluster( + ext.model, bl, r1, y1, y_error1, None, self.error_method, self.pf + ) ext.prune() logger.info("Model after resampling and termination ripples:\n%s", ext) @@ -414,9 +455,11 @@ def extract(self, **kwds): logger.info("Model after fitting with baseline:") try: logger.info(str(cov)) - #logger.info("Correlations > .8:\n%s", "\n".join(str(c) for c in cov.correlationwarning(.8))) + # logger.info("Correlations > .8:\n%s", "\n".join(str(c) for c in cov.correlationwarning(.8))) except SrMiseUndefinedCovarianceError as e: - logger.warn("Covariance not defined for final model. Fit may not have converged.") + logger.warn( + "Covariance not defined for final model. Fit may not have converged." + ) logger.info(str(ext)) # Update calculated instance variables @@ -427,7 +470,6 @@ def extract(self, **kwds): return cov - def fit(self, **kwds): """Fit peaks in the PDF. Returns ModelCovariance instance summarizing results.""" @@ -437,22 +479,24 @@ def fit(self, **kwds): self.defaultvars() # Determine grid spacing - dr_raw = (self.x[-1]-self.x[0])/(len(self.x)-1) + dr_raw = (self.x[-1] - self.x[0]) / (len(self.x) - 1) logger.info("Fit using qmax=%s", self.qmax) if self.qmax > 0: - dr_nyquist = np.pi/self.qmax + dr_nyquist = np.pi / self.qmax if dr_raw > dr_nyquist: # Technically I should yell for dr_raw >= dr_nyquist, since information # loss may occur at equality. - logger.warn("The input PDF appears to be missing information: The " - "sampling interval of the input PDF (%s) is larger than " - "the Nyquist interval (%s) defined by qmax=%s. This information " - "is irretrievable." %(dr_raw, dr_nyquist, self.qmax)) + logger.warn( + "The input PDF appears to be missing information: The " + "sampling interval of the input PDF (%s) is larger than " + "the Nyquist interval (%s) defined by qmax=%s. This information " + "is irretrievable." % (dr_raw, dr_nyquist, self.qmax) + ) else: # Do I actually need this? - dr_nyquist = dr_raw # not actually Nyquist sampling, natch + dr_nyquist = dr_raw # not actually Nyquist sampling, natch # Define grids rngslice = self.getrangeslice() @@ -463,18 +507,21 @@ def fit(self, **kwds): else: (r1, y1, r_error1, y_error1) = self.resampledata(dr_nyquist) - # Set up for fit_single pe = PeakExtraction() pe.setdata(r1, y1, None, None) - msg = ["Performing peak fitting", - "-----------------------"] + msg = ["Performing peak fitting", "-----------------------"] logger.info("\n".join(msg)) - pe.setvars(cres=self.cres, pf=self.pf, effective_dy = y_error1, - baseline=self.baseline, error_method=self.error_method, - initial_peaks=self.initial_peaks) + pe.setvars( + cres=self.cres, + pf=self.pf, + effective_dy=y_error1, + baseline=self.baseline, + error_method=self.error_method, + initial_peaks=self.initial_peaks, + ) # Perform fit cov = pe.fit_single() @@ -485,7 +532,9 @@ def fit(self, **kwds): try: logger.info(str(cov)) except SrMiseUndefinedCovarianceError as e: - logger.warn("Covariance not defined for final model. Fit may not have converged.") + logger.warn( + "Covariance not defined for final model. Fit may not have converged." + ) # Update calculated instance variables self.extraction_type = "fit" @@ -493,26 +542,25 @@ def fit(self, **kwds): return cov - def writemetadata(self): """Return string representation of peak extraction from PDF.""" lines = [] - lines.append('filename=%s' %repr(self.filename)) - lines.append('nyquist=%s' %repr(self.nyquist)) - lines.append('qmax=%s' %repr(self.qmax)) - lines.append('qmax_reportedbypdf=%s' %repr(self.qmax_reportedbypdf)) - lines.append('qmax_fromdata=%s' %repr(self.qmax_fromdata)) - lines.append('scale=%s' %repr(self.scale)) - lines.append('supersample=%s' %repr(self.supersample)) - - datastring = "\n".join(lines)+"\n" + lines.append("filename=%s" % repr(self.filename)) + lines.append("nyquist=%s" % repr(self.nyquist)) + lines.append("qmax=%s" % repr(self.qmax)) + lines.append("qmax_reportedbypdf=%s" % repr(self.qmax_reportedbypdf)) + lines.append("qmax_fromdata=%s" % repr(self.qmax_fromdata)) + lines.append("scale=%s" % repr(self.scale)) + lines.append("supersample=%s" % repr(self.supersample)) + + datastring = "\n".join(lines) + "\n" return datastring def readmetadata(self, metastr): """Read metadata from string.""" # filename - res = re.search(r'^filename=(.*)$', metastr, re.M) + res = re.search(r"^filename=(.*)$", metastr, re.M) if res: self.filename = eval(res.groups()[0].strip()) else: @@ -520,7 +568,7 @@ def readmetadata(self, metastr): raise SrMiseDataFormatError(emsg) # nyquist - res = re.search(r'^nyquist=(.*)$', metastr, re.M) + res = re.search(r"^nyquist=(.*)$", metastr, re.M) if res: self.nyquist = eval(res.groups()[0].strip()) else: @@ -528,7 +576,7 @@ def readmetadata(self, metastr): raise SrMiseDataFormatError(emsg) # qmax - res = re.search(r'^qmax=(.*)$', metastr, re.M) + res = re.search(r"^qmax=(.*)$", metastr, re.M) if res: self.qmax = eval(res.groups()[0].strip()) else: @@ -536,7 +584,7 @@ def readmetadata(self, metastr): raise SrMiseDataFormatError(emsg) # qmax_reportedbypdf - res = re.search(r'^qmax_reportedbypdf=(.*)$', metastr, re.M) + res = re.search(r"^qmax_reportedbypdf=(.*)$", metastr, re.M) if res: self.qmax_reportedbypdf = eval(res.groups()[0].strip()) else: @@ -544,7 +592,7 @@ def readmetadata(self, metastr): raise SrMiseDataFormatError(emsg) # qmax_fromdata - res = re.search(r'^qmax_fromdata=(.*)$', metastr, re.M) + res = re.search(r"^qmax_fromdata=(.*)$", metastr, re.M) if res: self.qmax_fromdata = eval(res.groups()[0].strip()) else: @@ -552,7 +600,7 @@ def readmetadata(self, metastr): raise SrMiseDataFormatError(emsg) # scale - res = re.search(r'^scale=(.*)$', metastr, re.M) + res = re.search(r"^scale=(.*)$", metastr, re.M) if res: self.scale = eval(res.groups()[0].strip()) else: @@ -560,7 +608,7 @@ def readmetadata(self, metastr): raise SrMiseDataFormatError(emsg) # supersample - res = re.search(r'^supersample=(.*)$', metastr, re.M) + res = re.search(r"^supersample=(.*)$", metastr, re.M) if res: self.supersample = eval(res.groups()[0].strip()) else: @@ -573,7 +621,7 @@ def writepwa(self, filename, comments="n/a"): Parameters filename: the name of the file to write""" bytes = self.writepwastr(comments) - f = open(filename, 'w') + f = open(filename, "w") f.write(bytes) f.close() return @@ -594,76 +642,88 @@ def writepwastr(self, comments): import time from getpass import getuser - from diffpy.srmise.basefunction import BaseFunction + from diffpy.srmise import __version__ + from diffpy.srmise.basefunction import BaseFunction lines = [] # Header - lines.extend([ - 'Summary written: ' + time.ctime(), - 'produced by ' + getuser(), - 'diffpy.srmise version %s' %__version__, - '##### User comments']) + lines.extend( + [ + "Summary written: " + time.ctime(), + "produced by " + getuser(), + "diffpy.srmise version %s" % __version__, + "##### User comments", + ] + ) tcomments = [] for c in comments.splitlines(): - tcomments.append('# '+c) + tcomments.append("# " + c) lines.extend(tcomments) - lines.extend([ - '##### PDF Peak Extraction Summary', - '# The information below is not sufficient to replicate extraction.']) + lines.extend( + [ + "##### PDF Peak Extraction Summary", + "# The information below is not sufficient to replicate extraction.", + ] + ) # PDF peak extraction metadata - lines.append('## PDF metadata') - lines.append('filename=%s' %self.filename) - lines.append('nyquist=%s' %repr(self.nyquist)) - lines.append('qmax=%s' %repr(self.qmax)) - lines.append('qmax_reportedbypdf=%s' %repr(self.qmax_reportedbypdf)) - lines.append('qmax_fromdata=%s' %repr(self.qmax_fromdata)) - lines.append('scale=%s' %repr(self.scale)) - lines.append('supersample=%s' %repr(self.supersample)) - lines.append('') - - lines.append('## Peak extraction metadata') + lines.append("## PDF metadata") + lines.append("filename=%s" % self.filename) + lines.append("nyquist=%s" % repr(self.nyquist)) + lines.append("qmax=%s" % repr(self.qmax)) + lines.append("qmax_reportedbypdf=%s" % repr(self.qmax_reportedbypdf)) + lines.append("qmax_fromdata=%s" % repr(self.qmax_fromdata)) + lines.append("scale=%s" % repr(self.scale)) + lines.append("supersample=%s" % repr(self.supersample)) + lines.append("") + + lines.append("## Peak extraction metadata") # Extraction range - lines.append("Range=%s" %repr(self.rng)) + lines.append("Range=%s" % repr(self.rng)) # Clustering resolution - lines.append('cres=%g' %self.cres) + lines.append("cres=%g" % self.cres) # Average effective dy - lines.append("effective_dy=%s (mean)" %np.mean(self.effective_dy)) + lines.append("effective_dy=%s (mean)" % np.mean(self.effective_dy)) # Passing the entire thing is something we're avoiding in the summary. - lines.append('') + lines.append("") # Initial peaks # I'm not sure what I want for this, but probably nothing. - #lines.append('## Initial Peaks') - #lines.append('') + # lines.append('## Initial Peaks') + # lines.append('') - lines.append('## Model Quality') + lines.append("## Model Quality") # Quality of fit - lines.append("# Quality reported by ModelEvaluator: %s" %self.extracted.quality().stat) - lines.append("# Free parameters in extracted peaks: %s" %self.extracted.model.npars(count_fixed=False)) + lines.append( + "# Quality reported by ModelEvaluator: %s" % self.extracted.quality().stat + ) + lines.append( + "# Free parameters in extracted peaks: %s" + % self.extracted.model.npars(count_fixed=False) + ) if self.baseline is not None: fblpars = self.baseline.npars(count_fixed=False) else: fblpars = 0 - lines.append("# Free parameters in baseline: %s" %fblpars) - lines.append("# Length of data in final fit: %s" %len(self.extracted.r_data)) + lines.append("# Free parameters in baseline: %s" % fblpars) + lines.append("# Length of data in final fit: %s" % len(self.extracted.r_data)) # Model evaluator if self.error_method is None: - lines.append('ModelEvaluator=None') + lines.append("ModelEvaluator=None") else: - lines.append('ModelEvaluator=%s' %self.error_method.__name__) + lines.append("ModelEvaluator=%s" % self.error_method.__name__) - lines.append('') + lines.append("") # Generate list of PeakFunctions and BaselineFunctions # so I can refer to them by index. @@ -676,7 +736,7 @@ def writepwastr(self, comments): if self.baseline is not None: if isinstance(self.baseline, BaseFunction): allbf.append(self.baseline) - else: # should be a ModelPart + else: # should be a ModelPart allbf.append(self.baseline.owner()) if self.extracted is not None: allpf.extend(self.extracted.peak_funcs) @@ -689,57 +749,57 @@ def writepwastr(self, comments): safebf = BaseFunction.safefunctionlist(allbf) # Baseline Functions - lines.append('## Baseline Functions') - lines.append('# Index Type') + lines.append("## Baseline Functions") + lines.append("# Index Type") for i, bf in enumerate(safebf): if bf.base is not None: base = "(base=%s)" % safebf.index(bf.base) else: base = "" - lines.append('%s %s %s' %(i, bf.getmodule(), base)) + lines.append("%s %s %s" % (i, bf.getmodule(), base)) - lines.append('') + lines.append("") # Baseline - lines.append('## Baseline') - lines.append('# Parameters of baseline, followed by comment which') - lines.append('# gives the index of corresponding Baseline Function.') + lines.append("## Baseline") + lines.append("# Parameters of baseline, followed by comment which") + lines.append("# gives the index of corresponding Baseline Function.") if self.extracted.baseline is None: - lines.append('None') + lines.append("None") else: # Generate parameter labels from the baseline function's parameterdict blf = self.extracted.baseline.owner() if blf.npars > 0: parlbl = blf.parameterdict.keys() paridx = np.array(blf.parameterdict.values()).argsort() - lines.append('# '+' '.join([str(parlbl[i]) for i in paridx])) - blpars = ' '.join([str(p) for p in self.extracted.baseline.pars]) + lines.append("# " + " ".join([str(parlbl[i]) for i in paridx])) + blpars = " ".join([str(p) for p in self.extracted.baseline.pars]) else: - blpars = '(no parameters)' + blpars = "(no parameters)" blidx = safebf.index(blf) - lines.append("%s # %s" %(blpars, blidx)) + lines.append("%s # %s" % (blpars, blidx)) - lines.append('') + lines.append("") # Peak Functions - lines.append('## Peak Functions') - lines.append('# Index Type') + lines.append("## Peak Functions") + lines.append("# Index Type") for i, pf in enumerate(safepf): if pf.base is not None: base = "(base=%s)" % safepf.index(pf.base) else: base = "" - lines.append('%s %s %s' %(i, pf.getmodule(), base)) + lines.append("%s %s %s" % (i, pf.getmodule(), base)) - lines.append('') + lines.append("") # PWA - lines.append('## Extracted Peaks') - lines.append('# Parameters are given in the natural units of the data,') - lines.append('# where width is measured as full-width at half maximum.') - lines.append('# Each line is followd by a comment which gives the index') - lines.append('# of the corresponding Peak Function.') - lines.append('#L position fwhm area') + lines.append("## Extracted Peaks") + lines.append("# Parameters are given in the natural units of the data,") + lines.append("# where width is measured as full-width at half maximum.") + lines.append("# Each line is followd by a comment which gives the index") + lines.append("# of the corresponding Peak Function.") + lines.append("#L position fwhm area") for p in self.extracted.model: pf = p.owner() pwa = pf.transform_parameters(p, in_format="internal", out_format="pwa") @@ -747,12 +807,14 @@ def writepwastr(self, comments): widx = pf.parameterdict["width"] aidx = pf.parameterdict["area"] pfidx = safepf.index(pf) - lines.append("%s %s %s # %s" %(pwa[pidx], pwa[widx], pwa[aidx], pfidx)) + lines.append("%s %s %s # %s" % (pwa[pidx], pwa[widx], pwa[aidx], pfidx)) - datastring = "\n".join(lines)+"\n" + datastring = "\n".join(lines) + "\n" return datastring -#end PDFPeakExtraction class + +# end PDFPeakExtraction class + def resample(orig_r, orig_y, new_r): """Resample sequence with Whittaker-Shannon interpolation formula. @@ -765,21 +827,28 @@ def resample(orig_r, orig_y, new_r): Returns sequence of same type as new_r with the resampled values. """ n = len(orig_r) - dr = (orig_r[-1]-orig_r[0])/(n-1) + dr = (orig_r[-1] - orig_r[0]) / (n - 1) if new_r[0] < orig_r[0]: - logger.warning("Resampling outside original grid: %s (requested) < %s (original)" %(new_r[0], orig_r[0])) + logger.warning( + "Resampling outside original grid: %s (requested) < %s (original)" + % (new_r[0], orig_r[0]) + ) if new_r[-1] > orig_r[-1]: - logger.warning("Resampling outside original grid: %s (requested) > %s (original)" %(new_r[-1], orig_r[-1])) + logger.warning( + "Resampling outside original grid: %s (requested) > %s (original)" + % (new_r[-1], orig_r[-1]) + ) - new_y = new_r * 0. - shift = orig_r[0]/dr + new_y = new_r * 0.0 + shift = orig_r[0] / dr for i, y in enumerate(orig_y): - new_y += y*np.sinc(new_r/dr-(i+shift)) + new_y += y * np.sinc(new_r / dr - (i + shift)) return new_y + def find_qmax(r, y, showgraphs=False): """Determine approximate qmax from PDF. @@ -789,17 +858,17 @@ def find_qmax(r, y, showgraphs=False): if len(r) != len(y): emsg = "Argument arrays must have the same length." raise ValueError(emsg) - - dr = (r[-1]-r[0])/(len(r)-1) - + + dr = (r[-1] - r[0]) / (len(r) - 1) + # Nyquist-sampled PDFs already have the minimum number of data points, so # they must be resampled so sudden changes in reciprocal space amplitudes # can be observed. - new_r = np.linspace(r[0], r[-1], 2*len(r)) + new_r = np.linspace(r[0], r[-1], 2 * len(r)) new_y = resample(r, y, new_r) - new_dr = (new_r[-1]-r[0])/(len(new_r)-1) + new_dr = (new_r[-1] - r[0]) / (len(new_r) - 1) - yfft = np.imag(np.fft.fft(new_y))[:len(new_y)/2] + yfft = np.imag(np.fft.fft(new_y))[: len(new_y) / 2] d_ratio = stdratio(yfft) @@ -818,29 +887,29 @@ def find_qmax(r, y, showgraphs=False): # it appears more than once, while argmax returns the first.) m_idx = len(dder) - np.argmax(dder[::-1]) + 1 - dq = 2*np.pi/((len(new_y)-1)*new_dr) + dq = 2 * np.pi / ((len(new_y) - 1) * new_dr) qmax = dq * m_idx - + # Calculate dq again for original grid - dq = 2*np.pi/((len(y)-1)*dr) + dq = 2 * np.pi / ((len(y) - 1) * dr) if showgraphs: import matplotlib.pyplot as plt v1 = np.max([m_idx - int(np.sqrt(m_idx)), 2]) - v2 = np.min([m_idx + int(np.sqrt(len(yfft)-1-m_idx)), len(d_ratio)]) + v2 = np.min([m_idx + int(np.sqrt(len(yfft) - 1 - m_idx)), len(d_ratio)]) plt.ion() # DFT of the PDF plt.figure() - plt.subplot(211) # near obtained qmax - plt.plot(dq*np.arange(v1,v2), yfft[v1:v2]) - plt.axvline(x=qmax, color='r') - plt.suptitle("qmax: %s (dq=%s)" % (qmax,dq)) - plt.subplot(212) # over whole range - plt.plot(dq*np.arange(len(yfft)), yfft) - plt.axvline(x=qmax, color='r') + plt.subplot(211) # near obtained qmax + plt.plot(dq * np.arange(v1, v2), yfft[v1:v2]) + plt.axvline(x=qmax, color="r") + plt.suptitle("qmax: %s (dq=%s)" % (qmax, dq)) + plt.subplot(212) # over whole range + plt.plot(dq * np.arange(len(yfft)), yfft) + plt.axvline(x=qmax, color="r") plt.show() plt.ioff() @@ -848,6 +917,7 @@ def find_qmax(r, y, showgraphs=False): return (qmax, dq) + def stdratio(data): """Calculate ratio of standard deviation for runs of equal length in data. @@ -860,26 +930,26 @@ def stdratio(data): Returns an array of length floor(len(data)/2)-1. The ith element is equivalent to std(data[:i+2])/std(data[i+2:2i+4]).""" - limit = int(np.floor(len(data)/2)) + limit = int(np.floor(len(data) / 2)) std_left = np.zeros(limit) std_right = np.zeros(limit) n = 0 - mean = 0. - m2 = 0. + mean = 0.0 + m2 = 0.0 # Update std_left. This is the usual online algorithm. for i in range(limit): n = n + 1 delta = data[i] - mean - mean = mean + delta/n - m2 = m2 + delta*(data[i]-mean) + mean = mean + delta / n + m2 = m2 + delta * (data[i] - mean) std_left[i] = m2 n = 2 - mean = (data[2]+data[3])/2 - m2 = (data[2]-mean)**2 + (data[3]-mean)**2 - std_right[0] = 0. + mean = (data[2] + data[3]) / 2 + m2 = (data[2] - mean) ** 2 + (data[3] - mean) ** 2 + std_right[0] = 0.0 std_right[1] = m2 # Update std_right. Remove one from left side, add two on right. @@ -887,22 +957,23 @@ def stdratio(data): # Remove one from left n = n - 1 delta = data[i] - mean - mean = mean - delta/n - m2 = m2 - delta*(data[i] - mean) + mean = mean - delta / n + m2 = m2 - delta * (data[i] - mean) # Add two to right n = n + 2 - mean_add = (data[2*i] + data[2*i+1])/2 - m2_add = (data[2*i]-mean_add)**2 + (data[2*i+1]-mean_add)**2 + mean_add = (data[2 * i] + data[2 * i + 1]) / 2 + m2_add = (data[2 * i] - mean_add) ** 2 + (data[2 * i + 1] - mean_add) ** 2 delta = mean_add - mean - mean = mean + (2*delta)/n - m2 = m2 + m2_add + (delta**2)*(2*n-4)/n + mean = mean + (2 * delta) / n + m2 = m2 + m2_add + (delta**2) * (2 * n - 4) / n std_right[i] = m2 - return np.sqrt(std_left[1:]/std_right[1:]) + return np.sqrt(std_left[1:] / std_right[1:]) # Redirect to main extraction script -if __name__ == '__main__': +if __name__ == "__main__": from diffpy.srmise.applications import extract + extract.main() diff --git a/diffpy/srmise/peakextraction.py b/diffpy/srmise/peakextraction.py index 555b4ae..73da8a2 100644 --- a/diffpy/srmise/peakextraction.py +++ b/diffpy/srmise/peakextraction.py @@ -11,25 +11,26 @@ # ############################################################################## -import numpy as np +import logging import os.path import re import sys +import matplotlib.pyplot as plt +import numpy as np + +from diffpy.srmise.baselines import Baseline from diffpy.srmise.dataclusters import DataClusters from diffpy.srmise.modelcluster import ModelCluster, ModelCovariance from diffpy.srmise.modelparts import ModelPart, ModelParts -from diffpy.srmise.srmiseerrors import * from diffpy.srmise.peaks import Peak, Peaks -from diffpy.srmise.baselines import Baseline - -import matplotlib.pyplot as plt +from diffpy.srmise.srmiseerrors import * -import logging logger = logging.getLogger("diffpy.srmise") from diffpy.srmise import srmiselog + class PeakExtraction(object): """Class for peak extraction. @@ -173,6 +174,7 @@ def defaultvars(self, *args): if self.pf is None or "pf" in args: from diffpy.srmise.peaks import GaussianOverR + # TODO: Make a more useful default. self.pf = [GaussianOverR(self.x[-1]-self.x[0])] @@ -491,8 +493,9 @@ def writestr(self): """Return string representation of PeakExtraction object.""" import time from getpass import getuser - from diffpy.srmise.basefunction import BaseFunction + from diffpy.srmise import __version__ + from diffpy.srmise.basefunction import BaseFunction lines = [] @@ -1185,9 +1188,9 @@ def fit_single(self): from numpy.random import randn + from diffpy.srmise import srmiselog from diffpy.srmise.modelevaluators import AICc from diffpy.srmise.peaks import GaussianOverR - from diffpy.srmise import srmiselog srmiselog.setlevel("info") srmiselog.liveplotting(False) diff --git a/diffpy/srmise/peaks/base.py b/diffpy/srmise/peaks/base.py index 450e0b8..d8e3469 100644 --- a/diffpy/srmise/peaks/base.py +++ b/diffpy/srmise/peaks/base.py @@ -11,12 +11,15 @@ # ############################################################################## +import logging + import numpy as np -from diffpy.srmise.srmiseerrors import * + +import diffpy.srmise.srmiselog from diffpy.srmise.basefunction import BaseFunction -from diffpy.srmise.modelparts import ModelParts, ModelPart +from diffpy.srmise.modelparts import ModelPart, ModelParts +from diffpy.srmise.srmiseerrors import * -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class PeakFunction(BaseFunction): @@ -273,10 +276,11 @@ def factory(peakstr, ownerlist): # simple test code if __name__ == '__main__': - from numpy.random import randn import matplotlib.pyplot as plt - from diffpy.srmise.modelevaluators import AICc + from numpy.random import randn + from diffpy.srmise.modelcluster import ModelCluster + from diffpy.srmise.modelevaluators import AICc from diffpy.srmise.peaks import GaussianOverR res = .01 diff --git a/diffpy/srmise/peaks/gaussian.py b/diffpy/srmise/peaks/gaussian.py index d75e80a..3eae227 100644 --- a/diffpy/srmise/peaks/gaussian.py +++ b/diffpy/srmise/peaks/gaussian.py @@ -11,12 +11,15 @@ # ############################################################################## +import logging + +import matplotlib.pyplot as plt import numpy as np + +import diffpy.srmise.srmiselog from diffpy.srmise.peaks.base import PeakFunction from diffpy.srmise.srmiseerrors import SrMiseEstimationError, SrMiseScalingError, SrMiseTransformationError -import matplotlib.pyplot as plt -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class Gaussian (PeakFunction): @@ -314,10 +317,11 @@ def max(self, pars): # simple test code if __name__ == '__main__': - from numpy.random import randn import matplotlib.pyplot as plt - from diffpy.srmise.modelevaluators import AICc + from numpy.random import randn + from diffpy.srmise.modelcluster import ModelCluster + from diffpy.srmise.modelevaluators import AICc from diffpy.srmise.peaks import Peaks res = .01 diff --git a/diffpy/srmise/peaks/gaussianoverr.py b/diffpy/srmise/peaks/gaussianoverr.py index 3818640..f699d9f 100644 --- a/diffpy/srmise/peaks/gaussianoverr.py +++ b/diffpy/srmise/peaks/gaussianoverr.py @@ -11,12 +11,15 @@ # ############################################################################## +import logging + +import matplotlib.pyplot as plt import numpy as np + +import diffpy.srmise.srmiselog from diffpy.srmise.peaks.base import PeakFunction from diffpy.srmise.srmiseerrors import SrMiseEstimationError, SrMiseScalingError, SrMiseTransformationError -import matplotlib.pyplot as plt -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class GaussianOverR (PeakFunction): @@ -381,10 +384,11 @@ def max(self, pars): # simple test code if __name__ == '__main__': - from numpy.random import randn import matplotlib.pyplot as plt - from diffpy.srmise.modelevaluators import AICc + from numpy.random import randn + from diffpy.srmise.modelcluster import ModelCluster + from diffpy.srmise.modelevaluators import AICc from diffpy.srmise.peaks import Peaks res = .01 diff --git a/diffpy/srmise/peaks/terminationripples.py b/diffpy/srmise/peaks/terminationripples.py index e103fb3..cdce773 100644 --- a/diffpy/srmise/peaks/terminationripples.py +++ b/diffpy/srmise/peaks/terminationripples.py @@ -11,11 +11,14 @@ # ############################################################################## +import logging + import numpy as np import scipy.fftpack as fp + +import diffpy.srmise.srmiselog from diffpy.srmise.peaks.base import PeakFunction -import logging, diffpy.srmise.srmiselog logger = logging.getLogger("diffpy.srmise") class TerminationRipples (PeakFunction): @@ -267,13 +270,14 @@ def extend_grid(self, r, dr): # simple test code if __name__ == '__main__': - from numpy.random import randn import matplotlib.pyplot as plt - from diffpy.srmise.modelevaluator import AICc + from numpy.random import randn + from diffpy.srmise.modelcluster import ModelCluster + from diffpy.srmise.modelevaluator import AICc from diffpy.srmise.peakfunctions.gaussianoverr import GaussianOverR - from diffpy.srmise.peakfunctions.terminationripples import TerminationRipples from diffpy.srmise.peakfunctions.peaks import Peaks + from diffpy.srmise.peakfunctions.terminationripples import TerminationRipples res = .01 r = np.arange(2,4,res) diff --git a/diffpy/srmise/peakstability.py b/diffpy/srmise/peakstability.py index 527885c..3897a2d 100644 --- a/diffpy/srmise/peakstability.py +++ b/diffpy/srmise/peakstability.py @@ -11,11 +11,11 @@ # ############################################################################## -import numpy as np import matplotlib.pyplot as plt +import numpy as np + +from diffpy.srmise import ModelCluster, PDFPeakExtraction -from diffpy.srmise import PDFPeakExtraction -from diffpy.srmise import ModelCluster # This is a total hack-job right now, and isn't suitable for # general use. Limitations include: diff --git a/diffpy/srmise/srmiseerrors.py b/diffpy/srmise/srmiseerrors.py index b6cb1d2..f7ef037 100644 --- a/diffpy/srmise/srmiseerrors.py +++ b/diffpy/srmise/srmiseerrors.py @@ -27,9 +27,11 @@ SrMiseStaticOwnerError: Error when changing ModelPart instance owner. """ + ### Superclass class for diffpy.srmise.mise class SrMiseError(Exception): """Superclass of all diffpy.srmise exceptions.""" + def __init__(self, info): """initialize @@ -43,8 +45,10 @@ def __str__(self): ### SrMiseError subclasses ### + class SrMiseDataFormatError(SrMiseError): """diffpy.srmise exception class. Error in formatted data.""" + def __init__(self, info): """initialize @@ -54,15 +58,17 @@ def __init__(self, info): class SrMiseEstimationError(SrMiseError): """diffpy.srmise.modelevaluator exception class. Parameter estimation error.""" + def __init__(self, info): - """initialize + """initialize - info -- description string""" - SrMiseError.__init__(self, info) + info -- description string""" + SrMiseError.__init__(self, info) class SrMiseFileError(SrMiseError): """diffpy.srmise exception class. Error while reading/writing files.""" + def __init__(self, info): """initialize @@ -72,6 +78,7 @@ def __init__(self, info): class SrMiseFitError(SrMiseError): """diffpy.srmise exception class. Error occurred during fitting.""" + def __init__(self, info): """initialize @@ -81,6 +88,7 @@ def __init__(self, info): class SrMiseLogError(SrMiseError): """diffpy.srmise exception class. Error while handling logging capabilities.""" + def __init__(self, info): """initialize @@ -90,56 +98,67 @@ def __init__(self, info): class SrMiseModelEvaluatorError(SrMiseError): """diffpy.srmise.modelevaluator exception class. Error when comparing models.""" + def __init__(self, info): - """initialize + """initialize - info -- description string""" - SrMiseError.__init__(self, info) + info -- description string""" + SrMiseError.__init__(self, info) class SrMiseQmaxError(SrMiseError): """diffpy.srmise.modelevaluator exception class. Error when setting qmax.""" + def __init__(self, info): - """initialize + """initialize + + info -- description string""" + SrMiseError.__init__(self, info) - info -- description string""" - SrMiseError.__init__(self, info) class SrMiseScalingError(SrMiseError): """diffpy.srmise.peaks exception class. Error when scaling a peak function.""" + def __init__(self, info): - """initialize + """initialize - info -- description string""" - SrMiseError.__init__(self, info) + info -- description string""" + SrMiseError.__init__(self, info) class SrMiseStaticOwnerError(SrMiseError): """diffpy.srmise exception class. Attempt to change owner of static model part.""" + def __init__(self, info): """initialize info -- description string""" SrMiseError.__init__(self, info) + class SrMiseTransformationError(SrMiseError): """diffpy.srmise exception class. Error transforming model/covariance parameters.""" + def __init__(self, info): """initialize info -- description string""" SrMiseError.__init__(self, info) + class SrMiseUndefinedCovarianceError(SrMiseError): """diffpy.srmise exception class. Attempted to perform on undefined covariance.""" + def __init__(self, info): """initialize info -- description string""" SrMiseError.__init__(self, info) - + + class SrMisePDFKeyError(SrMiseError): """diffpy.srmise exception class. Requested PDF key can't be found.""" + def __init__(self, info): """initialize diff --git a/diffpy/srmise/srmiselog.py b/diffpy/srmise/srmiselog.py index 4325aef..3ea2c50 100644 --- a/diffpy/srmise/srmiselog.py +++ b/diffpy/srmise/srmiselog.py @@ -37,9 +37,12 @@ gettracer: Get a TracePeaks instance for tracing peak extraction. """ -import sys, os.path, re import logging -from diffpy.srmise.srmiseerrors import SrMiseLogError, SrMiseDataFormatError, SrMiseFileError +import os.path +import re +import sys + +from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, SrMiseFileError, SrMiseLogError ### Default settings ### defaultformat = "%(message)s" diff --git a/diffpy/srmise/version.py b/diffpy/srmise/version.py index 913cd10..d0c6e1d 100644 --- a/diffpy/srmise/version.py +++ b/diffpy/srmise/version.py @@ -14,16 +14,16 @@ """Definition of __version__, __date__, __gitsha__. """ -from pkg_resources import resource_stream from ConfigParser import SafeConfigParser +from pkg_resources import resource_stream # obtain version information from the version.cfg file cp = SafeConfigParser() -cp.readfp(resource_stream(__name__, 'version.cfg')) +cp.readfp(resource_stream(__name__, "version.cfg")) -__version__ = cp.get('DEFAULT', 'version') -__date__ = cp.get('DEFAULT', 'date') -__gitsha__ = cp.get('DEFAULT', 'commit') +__version__ = cp.get("DEFAULT", "version") +__date__ = cp.get("DEFAULT", "date") +__gitsha__ = cp.get("DEFAULT", "commit") del cp diff --git a/doc/examples/README b/doc/examples/README index eeb10fd..08003b5 100644 --- a/doc/examples/README +++ b/doc/examples/README @@ -1,7 +1,7 @@ Purpose ======= -This tutorial is an introduction to the SrMise library and command-line tool, +This tutorial is an introduction to the SrMise library and command-line tool, intended to expose new users and developers to the major use cases and options anticipated for SrMise. @@ -70,11 +70,11 @@ Getting Started The examples are contained in the *doc/examples/* directory of the SrMise `source distribution `_, -available as both a |zip| and |tar.gz| archive. Download one of these files +available as both a |zip| and |tar.gz| archive. Download one of these files (Windows users will generally favor the .zip, while Linux/Mac users the .tar.gz) -to a directory of your choosing. +to a directory of your choosing. -Uncompress the archive. If the downloaded file is *archivename.zip* or +Uncompress the archive. If the downloaded file is *archivename.zip* or *archivename.tar.gz* this will create a new directory *archivename* in its current directory. On Windows this can be accomplished by right-clicking and choosing "Extract all". On Linux/Mac OS X run, from the containing @@ -144,7 +144,7 @@ First, plot the data without performing peak extraction. The first argument must be either a PDF (as here) or a .srmise file (described later) saved by SrMise. :: - srmise data/Ag_nyquist_qmax30.gr --no-extract --plot + srmise data/Ag_nyquist_qmax30.gr --no-extract --plot This should result in an image very similar to the one below. The top shows the experimental data in blue. The bottom shows the difference curve, which is @@ -196,7 +196,7 @@ the Gaussian divided by radius which is the actual function being fit to the PDF. SrMise has two basic formats for saving data. The first are .srmise files, -which record all information about the parameters and results of peak +which record all information about the parameters and results of peak extraction. These files may be loaded by ``srmise`` and in Python scripts. The second are .pwa files, which are intended as a human readable summary, but do not contain enough information to reproduce peak extraction results. These @@ -437,7 +437,7 @@ nyquist | Whether to evaluate results on Nyquist-sampled grid with dr = |pi/Qmax| . | *Accepts* - True or False | *Default* - True when |Qmax|>0, otherwise False. - + When nyquist is False, the PDF's original sampling rate is used. By the Nyquist-Shannon sampling theorem, all PDFs sampled faster than the Nyquist rate contain all the information which the experiment can provide. Points @@ -631,7 +631,7 @@ basic methods for querying SrMise objects about their parameters and values within scripts. First, visually check that the baseline obtained in the earlier silver example -(set using the ``--bsrmise filename.srmise`` option) is reasonable over a +(set using the ``--bsrmise filename.srmise`` option) is reasonable over a larger range. :: srmise data/Ag_nyquist_qmax30.gr --no-extract --plot --range 2 10 @@ -664,13 +664,13 @@ area. Thus, the area of the nearest-neighbor peak is denoted by the tuple the baseline. The methods of greatest interest are as follows. :: # Get (value, uncertainty) tuple for this parameter - cov.get((i,j)) + cov.get((i,j)) # Get just the value of the parameter cov.getvalue((i,j)) # Get just the uncertainty of the parameter - cov.getuncertainty((i,j)) + cov.getuncertainty((i,j)) # Get the covariance between two parameters cov.getcovariance((i1,j1), (i2,j2)) @@ -708,7 +708,7 @@ usual methods are :: # The baseline evaluated on r ppe.extracted.baseline.value(r) - + .. ~Example 5~ .. @@ -847,7 +847,7 @@ propagated uncertainties was obtained using `FIT2D`_. All other data reduction was performed using `PDFgetX2`_. This PDF is unnormalized, so the scale of the y-axis is arbitrary. The nanoparticle baseline used for testing this PDF with SrMise is a fit to the observed interparticle contribution using an empirical -model of thin spherical shells of constant density in an FCC lattice. +model of thin spherical shells of constant density in an FCC lattice. This PDF has unreliable uncertainties. Since the 1D pattern reports no uncertainty, PDFgetX2 treats the uncertainty as equal to the square-root of the diff --git a/doc/examples/data/Ag_nyquist_qmax30.gr b/doc/examples/data/Ag_nyquist_qmax30.gr index 802c2e6..abdd2df 100644 --- a/doc/examples/data/Ag_nyquist_qmax30.gr +++ b/doc/examples/data/Ag_nyquist_qmax30.gr @@ -26,7 +26,7 @@ sambkgfile=bkgd_1-14_srXp_qspace.chi num_sambkgs=1 confile= num_cons=1 conbkgfile= num_conbkgs=1 det# used xcol detcol deterrcol xmin xmax add_det mul_det add_bkg mul_bkg add_con mul_con add_conbkg mul_conbkg - 0 1 0 1 2 0.700000 36.0000 0.000000 6.00000 0.000000 1.50000 0.000000 1.00000 0.000000 1.00000 + 0 1 0 1 2 0.700000 36.0000 0.000000 6.00000 0.000000 1.50000 0.000000 1.00000 0.000000 1.00000 ##### Experiment_Setup title=PDF analysis @@ -128,341 +128,341 @@ gropttype=OptFq miscdatatype=AtomASF ##### start data #F Ag_1-6_srXp_qspace.gr #D Sat Feb 21 19:07:17 2015 -#C +#C #S 1 G(r) -#D +#D #L r(A) G(r) d_r d_Gr - 1.047198e-001 -8.482171e-001 -5.263789e-002 2.765272e-001 - 2.094395e-001 -4.389751e-001 -1.052758e-001 3.758883e-001 - 3.141593e-001 -7.245989e-002 -1.579137e-001 3.993384e-001 - 4.188790e-001 7.010412e-002 -2.105516e-001 4.062425e-001 - 5.235988e-001 2.410039e-001 -2.631895e-001 4.092704e-001 - 6.283185e-001 -1.081419e+000 -3.158273e-001 4.108721e-001 - 7.330383e-001 -7.305268e-001 -3.684652e-001 4.118211e-001 - 8.377581e-001 -7.892482e-001 -4.211031e-001 4.124392e-001 - 9.424778e-001 -4.799765e-001 -4.737410e-001 4.128434e-001 - 1.047198e+000 -5.515252e-001 -5.263789e-001 4.131494e-001 - 1.151917e+000 -5.276302e-001 -5.790168e-001 4.133937e-001 - 1.256637e+000 -4.785339e-001 -6.316547e-001 4.135703e-001 - 1.361357e+000 -7.453648e-001 -6.842926e-001 4.136500e-001 - 1.466077e+000 -8.511180e-001 -7.369305e-001 4.140212e-001 - 1.570796e+000 -8.502626e-001 -7.895684e-001 4.138731e-001 - 1.675516e+000 -8.591459e-001 -8.422062e-001 4.139608e-001 - 1.780236e+000 -9.441510e-001 -8.948441e-001 4.140158e-001 - 1.884956e+000 -9.574570e-001 -9.474820e-001 4.140681e-001 - 1.989675e+000 -9.424363e-001 -1.000120e+000 4.140688e-001 - 2.094395e+000 -1.062015e+000 -1.052758e+000 4.141887e-001 - 2.199115e+000 -9.869438e-001 -1.105396e+000 4.141705e-001 - 2.303835e+000 -1.155167e+000 -1.158034e+000 4.142069e-001 - 2.408554e+000 -9.980358e-001 -1.210671e+000 4.142000e-001 - 2.513274e+000 -1.075531e+000 -1.263309e+000 4.142505e-001 - 2.617994e+000 -6.605810e-001 -1.315947e+000 4.142869e-001 - 2.722714e+000 2.096964e+000 -1.368585e+000 4.142760e-001 - 2.827433e+000 8.654147e+000 -1.421223e+000 4.142350e-001 - 2.932153e+000 9.775080e+000 -1.473861e+000 4.143683e-001 - 3.036873e+000 3.943275e+000 -1.526499e+000 4.143157e-001 - 3.141593e+000 -2.514541e-001 -1.579137e+000 4.142939e-001 - 3.246312e+000 -1.592664e+000 -1.631775e+000 4.143335e-001 - 3.351032e+000 -1.876345e+000 -1.684412e+000 4.143717e-001 - 3.455752e+000 -2.079538e+000 -1.737050e+000 4.143361e-001 - 3.560472e+000 -2.093879e+000 -1.789688e+000 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9.421571e-001 -1.684412e+001 4.144725e-001 + 3.361504e+001 6.686023e-001 -1.689676e+001 4.144718e-001 + 3.371976e+001 4.162514e-001 -1.694940e+001 4.144688e-001 + 3.382448e+001 2.132572e-001 -1.700204e+001 4.144638e-001 + 3.392920e+001 1.289128e-001 -1.705468e+001 4.144631e-001 + 3.403392e+001 1.010848e-001 -1.710731e+001 4.144619e-001 + 3.413864e+001 1.262606e-001 -1.715995e+001 4.144626e-001 + 3.424336e+001 -8.824295e-002 -1.721259e+001 4.144662e-001 + 3.434808e+001 -5.052811e-001 -1.726523e+001 4.144635e-001 + 3.445280e+001 -8.654572e-001 -1.731787e+001 4.144605e-001 + 3.455752e+001 -9.314267e-001 -1.737050e+001 4.144651e-001 + 3.466224e+001 -6.776269e-001 -1.742314e+001 4.144694e-001 + 3.476696e+001 -2.196178e-001 -1.747578e+001 4.144720e-001 + 3.487168e+001 2.622648e-001 -1.752842e+001 4.144754e-001 + 3.497640e+001 4.972950e-001 -1.758106e+001 4.144737e-001 diff --git a/doc/examples/data/C60_fine_qmax21.gr b/doc/examples/data/C60_fine_qmax21.gr index a8f408f..396e210 100644 --- a/doc/examples/data/C60_fine_qmax21.gr +++ b/doc/examples/data/C60_fine_qmax21.gr @@ -26,7 +26,7 @@ sambkgfile=emptyKapton1mm_300k_90keV_483-487sum.chi num_sambkgs=1 confile= num_cons=1 conbkgfile= num_conbkgs=1 det# used xcol detcol deterrcol xmin xmax add_det mul_det add_bkg mul_bkg add_con mul_con add_conbkg mul_conbkg - 0 1 0 1 3 0.782256 40.0000 0.000000 1.00000 0.000000 1.00000 0.000000 1.00000 0.000000 1.00000 + 0 1 0 1 3 0.782256 40.0000 0.000000 1.00000 0.000000 1.00000 0.000000 1.00000 0.000000 1.00000 ##### Experiment_Setup title=PDF analysis @@ -128,2006 +128,2006 @@ gropttype=OptFq miscdatatype=AtomASF ##### start data #F C60pos01_300k_90keV_410-452sum.gr #D Fri Mar 20 01:26:57 2009 -#C +#C #S 1 G(r) -#D +#D #L r G(r) d_r d_Gr - 1.000000e-002 1.894260e+004 -7.539822e-004 8.536912e+000 - 2.000000e-002 3.772272e+004 -1.507964e-003 1.675464e+001 - 3.000000e-002 5.617755e+004 -2.261947e-003 2.434705e+001 - 4.000000e-002 7.414385e+004 -3.015929e-003 3.103361e+001 - 5.000000e-002 9.145791e+004 -3.769911e-003 3.657098e+001 - 6.000000e-002 1.079561e+005 -4.523893e-003 4.076327e+001 - 7.000000e-002 1.234755e+005 -5.277876e-003 4.347065e+001 - 8.000000e-002 1.378555e+005 -6.031858e-003 4.461615e+001 - 9.000000e-002 1.509396e+005 -6.785840e-003 4.419097e+001 - 1.000000e-001 1.625776e+005 -7.539822e-003 4.225878e+001 - 1.100000e-001 1.726287e+005 -8.293804e-003 3.896113e+001 - 1.200000e-001 1.809643e+005 -9.047787e-003 3.452824e+001 - 1.300000e-001 1.874722e+005 -9.801769e-003 2.930697e+001 - 1.400000e-001 1.920600e+005 -1.055575e-002 2.383587e+001 - 1.500000e-001 1.946585e+005 -1.130973e-002 1.902762e+001 - 1.600000e-001 1.952258e+005 -1.206372e-002 1.638514e+001 - 1.700000e-001 1.937504e+005 -1.281770e-002 1.723828e+001 - 1.800000e-001 1.902538e+005 -1.357168e-002 2.094617e+001 - 1.900000e-001 1.847926e+005 -1.432566e-002 2.582197e+001 - 2.000000e-001 1.774602e+005 -1.507964e-002 3.069799e+001 - 2.100000e-001 1.683863e+005 -1.583363e-002 3.493789e+001 - 2.200000e-001 1.577369e+005 -1.658761e-002 3.818417e+001 - 2.300000e-001 1.457120e+005 -1.734159e-002 4.023614e+001 - 2.400000e-001 1.325429e+005 -1.809557e-002 4.100325e+001 - 2.500000e-001 1.184878e+005 -1.884956e-002 4.048837e+001 - 2.600000e-001 1.038270e+005 -1.960354e-002 3.878377e+001 - 2.700000e-001 8.885653e+004 -2.035752e-002 3.607536e+001 - 2.800000e-001 7.388159e+004 -2.111150e-002 3.265653e+001 - 2.900000e-001 5.920896e+004 -2.186548e-002 2.895580e+001 - 3.000000e-001 4.513929e+004 -2.261947e-002 2.557279e+001 - 3.100000e-001 3.195916e+004 -2.337345e-002 2.326275e+001 - 3.200000e-001 1.993340e+004 -2.412743e-002 2.270262e+001 - 3.300000e-001 9.297645e+003 -2.488141e-002 2.402850e+001 - 3.400000e-001 2.517043e+002 -2.563540e-002 2.670812e+001 - 3.500000e-001 -7.046274e+003 -2.638938e-002 2.996591e+001 - 3.600000e-001 -1.248447e+004 -2.714336e-002 3.314959e+001 - 3.700000e-001 -1.600078e+004 -2.789734e-002 3.580905e+001 - 3.800000e-001 -1.758475e+004 -2.865132e-002 3.766190e+001 - 3.900000e-001 -1.727796e+004 -2.940531e-002 3.855493e+001 - 4.000000e-001 -1.517287e+004 -3.015929e-002 3.844112e+001 - 4.100000e-001 -1.141006e+004 -3.091327e-002 3.736925e+001 - 4.200000e-001 -6.173989e+003 -3.166725e-002 3.548194e+001 - 4.300000e-001 3.126408e+002 -3.242124e-002 3.302011e+001 - 4.400000e-001 7.795703e+003 -3.317522e-002 3.033101e+001 - 4.500000e-001 1.599747e+004 -3.392920e-002 2.786765e+001 - 4.600000e-001 2.462518e+004 -3.468318e-002 2.614265e+001 - 4.700000e-001 3.338004e+004 -3.543716e-002 2.558220e+001 - 4.800000e-001 4.196639e+004 -3.619115e-002 2.631236e+001 - 4.900000e-001 5.010074e+004 -3.694513e-002 2.807912e+001 - 5.000000e-001 5.752033e+004 -3.769911e-002 3.040568e+001 - 5.100000e-001 6.399094e+004 -3.845309e-002 3.280443e+001 - 5.200000e-001 6.931374e+004 -3.920708e-002 3.488602e+001 - 5.300000e-001 7.333084e+004 -3.996106e-002 3.638107e+001 - 5.400000e-001 7.592949e+004 -4.071504e-002 3.713103e+001 - 5.500000e-001 7.704472e+004 -4.146902e-002 3.707615e+001 - 5.600000e-001 7.666028e+004 -4.222300e-002 3.624777e+001 - 5.700000e-001 7.480809e+004 -4.297699e-002 3.476520e+001 - 5.800000e-001 7.156590e+004 -4.373097e-002 3.283546e+001 - 5.900000e-001 6.705361e+004 -4.448495e-002 3.075143e+001 - 6.000000e-001 6.142812e+004 -4.523893e-002 2.887649e+001 - 6.100000e-001 5.487708e+004 -4.599292e-002 2.759254e+001 - 6.200000e-001 4.761168e+004 -4.674690e-002 2.719280e+001 - 6.300000e-001 3.985885e+004 -4.750088e-002 2.775707e+001 - 6.400000e-001 3.185305e+004 -4.825486e-002 2.911213e+001 - 6.500000e-001 2.382798e+004 -4.900884e-002 3.092008e+001 - 6.600000e-001 1.600861e+004 -4.976283e-002 3.280949e+001 - 6.700000e-001 8.603690e+003 -5.051681e-002 3.446217e+001 - 6.800000e-001 1.798989e+003 -5.127079e-002 3.564602e+001 - 6.900000e-001 -4.248345e+003 -5.202477e-002 3.621989e+001 - 7.000000e-001 -9.414296e+003 -5.277876e-002 3.612981e+001 - 7.100000e-001 -1.361113e+004 -5.353274e-002 3.540484e+001 - 7.200000e-001 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b/doc/examples/data/TiO2_fine_qmax26.gr @@ -26,7 +26,7 @@ sambkgfile=kapton_bgrd_300k_2-3_srXp_qspace.chi num_sambkgs=1 confile= num_cons=1 conbkgfile= num_conbkgs=1 det# used xcol detcol deterrcol xmin xmax add_det mul_det add_bkg mul_bkg add_con mul_con add_conbkg mul_conbkg - 0 1 0 1 2 0.500000 27.0000 0.000000 0.526067 0.000000 0.0776796 0.000000 1.00000 0.000000 1.00000 + 0 1 0 1 2 0.500000 27.0000 0.000000 0.526067 0.000000 0.0776796 0.000000 1.00000 0.000000 1.00000 ##### Experiment_Setup title=PDF analysis @@ -129,2006 +129,2006 @@ gropttype=OptFq miscdatatype=AtomASF ##### start data #F tio2r_300k_1-6_srXp_qspace.gr #D Tue May 19 20:13:15 2015 -#C +#C #S 1 G(r) -#D +#D #L r(A) G(r) d_r d_Gr - 3.000000e-002 -1.708577e-001 -2.261947e-003 7.534023e-001 - 6.000000e-002 -3.474954e-001 -4.523893e-003 1.146748e+000 - 9.000000e-002 -5.413945e-001 -6.785840e-003 1.013071e+000 - 1.200000e-001 -7.685137e-001 -9.047787e-003 5.227350e-001 - 1.500000e-001 -1.039247e+000 -1.130973e-002 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4.620160e-001 -2.693978e+000 8.386327e-001 - 3.576000e+001 4.074220e-001 -2.696240e+000 8.363030e-001 - 3.579000e+001 3.453082e-001 -2.698502e+000 8.382169e-001 - 3.582000e+001 2.872411e-001 -2.700764e+000 8.405705e-001 - 3.585000e+001 2.395061e-001 -2.703026e+000 8.387104e-001 - 3.588000e+001 2.012521e-001 -2.705288e+000 8.363243e-001 - 3.591000e+001 1.662759e-001 -2.707550e+000 8.381423e-001 - 3.594000e+001 1.274868e-001 -2.709812e+000 8.405487e-001 - 3.597000e+001 8.168516e-002 -2.712074e+000 8.387816e-001 - 3.600000e+001 3.211113e-002 -2.714336e+000 8.363444e-001 - 3.603000e+001 -1.261951e-002 -2.716598e+000 8.380719e-001 - 3.606000e+001 -4.267789e-002 -2.718860e+000 8.405308e-001 - 3.609000e+001 -5.212728e-002 -2.721122e+000 8.388539e-001 - 3.612000e+001 -4.228810e-002 -2.723384e+000 8.363634e-001 - 3.615000e+001 -2.154998e-002 -2.725646e+000 8.379982e-001 - 3.618000e+001 -1.635972e-003 -2.727908e+000 8.405086e-001 - 3.621000e+001 7.850377e-003 -2.730170e+000 8.389258e-001 - 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8.366012e-001 + 5.994000e+001 -4.215427e-003 -4.519369e+000 8.389632e-001 + 5.997000e+001 1.303937e-002 -4.521631e+000 8.402923e-001 diff --git a/doc/examples/extract_single_peak.py b/doc/examples/extract_single_peak.py index 917f793..99edd4c 100644 --- a/doc/examples/extract_single_peak.py +++ b/doc/examples/extract_single_peak.py @@ -28,15 +28,16 @@ import matplotlib.pyplot as plt from diffpy.srmise import PDFPeakExtraction -from diffpy.srmise.baselines import Polynomial from diffpy.srmise.applications.plot import makeplot +from diffpy.srmise.baselines import Polynomial + def run(plot=True): - + ## Initialize peak extraction # Create peak extraction object ppe = PDFPeakExtraction() - + # Load the PDF from a file ppe.loadpdf("data/Ag_nyquist_qmax30.gr") @@ -53,16 +54,16 @@ def run(plot=True): # linear for a crystal. If a linear baseline is specified without # numerical parameters diffpy.srmise attempts to estimate them from the # data, and this is usually sufficient when peaks do not overlap much. - kwds = {} + kwds = {} kwds["rng"] = [2.0, 3.5] kwds["baseline"] = Polynomial(degree=1) - + # Apply peak extraction parameters. ppe.setvars(**kwds) ## Perform peak extraction ppe.extract() - + ## Save output # The write() method saves a file which preserves all aspects of peak # extraction and its results, by convention using the .srmise extension, @@ -85,5 +86,6 @@ def run(plot=True): makeplot(ppe) plt.show() -if __name__ == '__main__': + +if __name__ == "__main__": run() diff --git a/doc/examples/fit_initial.py b/doc/examples/fit_initial.py index 263027c..33bf4e6 100644 --- a/doc/examples/fit_initial.py +++ b/doc/examples/fit_initial.py @@ -19,13 +19,14 @@ ripples, or otherwise do anything beyond chi-square fitting using the specified grid.""" -import numpy as np import matplotlib.pyplot as plt +import numpy as np from diffpy.srmise import PDFPeakExtraction -from diffpy.srmise.baselines import FromSequence -from diffpy.srmise.peaks import TerminationRipples, Peaks from diffpy.srmise.applications.plot import makeplot +from diffpy.srmise.baselines import FromSequence +from diffpy.srmise.peaks import Peaks, TerminationRipples + def run(plot=True): @@ -58,11 +59,11 @@ def run(plot=True): # "cres" - Estimation of peak parameters given an approximate position uses # clustering for peak finding. No other effect on peak fitting. # "supersample" - No effect. - kwds={} - kwds["rng"] = [1., 7.25] + kwds = {} + kwds["rng"] = [1.0, 7.25] kwds["baseline"] = bl kwds["cres"] = 0.05 - kwds["dg"] = 5000 # ad hoc, but gives each point equal weight in fit. + kwds["dg"] = 5000 # ad hoc, but gives each point equal weight in fit. ppe.setvars(**kwds) ## Set up termination ripples @@ -82,9 +83,8 @@ def run(plot=True): # Specify some peaks explicitly. These may be constructed from any peak # function, or combination of peak functions. - explicit_guess = [[6.7, .3, 100000], [7.0, .15, 50000]] - explicit_peaks = Peaks([pf.actualize(eg, in_format="pwa") \ - for eg in explicit_guess]) + explicit_guess = [[6.7, 0.3, 100000], [7.0, 0.15, 50000]] + explicit_peaks = Peaks([pf.actualize(eg, in_format="pwa") for eg in explicit_guess]) ppe.add_peaks(explicit_peaks) # Plot initial peaks @@ -104,5 +104,6 @@ def run(plot=True): makeplot(ppe) plt.show() -if __name__ == '__main__': + +if __name__ == "__main__": run() diff --git a/doc/examples/multimodel_known_dG1.py b/doc/examples/multimodel_known_dG1.py index 07eab2c..aa50c41 100644 --- a/doc/examples/multimodel_known_dG1.py +++ b/doc/examples/multimodel_known_dG1.py @@ -36,9 +36,10 @@ import numpy as np -from diffpy.srmise import PDFPeakExtraction, MultimodelSelection -from diffpy.srmise.applications.plot import makeplot import diffpy.srmise.srmiselog as sml +from diffpy.srmise import MultimodelSelection, PDFPeakExtraction +from diffpy.srmise.applications.plot import makeplot + def run(plot=True): @@ -57,8 +58,8 @@ def run(plot=True): ## Set up extraction parameters # All parameters loaded from .srmise file. # Setting new values will override the previous values. - kwds={} - kwds["rng"] = [10.9, 15] # Region of PDF with some overlap. + kwds = {} + kwds["rng"] = [10.9, 15] # Region of PDF with some overlap. ppe.setvars(**kwds) ## Create multimodel selection object. @@ -71,7 +72,7 @@ def run(plot=True): # For the purpose of illustration use 15 evenly-spaced values of dg where # 50% < dg < 120% of mean experimental dG in extraction range. dg_mean = np.mean(ppe.dy[ppe.getrangeslice()]) - dgs = np.linspace(.5*dg_mean, 1.2*dg_mean, 15) + dgs = np.linspace(0.5 * dg_mean, 1.2 * dg_mean, 15) ## Perform peak extraction for each of the assumed uncertainties. ms.run(dgs) @@ -81,9 +82,10 @@ def run(plot=True): # known_dG_aics.dat saves the value of the AIC of each model when evaluated # on a Nyquist-sampled grid using each of the dg values used to generate # the models in the first place. - dr = np.pi/ppe.qmax + dr = np.pi / ppe.qmax ms.save("output/known_dG_models.dat") ms.makeaics(dgs, dr, filename="output/known_dG_aics.dat") -if __name__ == '__main__': + +if __name__ == "__main__": run() diff --git a/doc/examples/multimodel_known_dG2.py b/doc/examples/multimodel_known_dG2.py index 9ef0490..d061981 100644 --- a/doc/examples/multimodel_known_dG2.py +++ b/doc/examples/multimodel_known_dG2.py @@ -31,12 +31,12 @@ [2] Burnham and Anderson. (2002). Model Selection and Multimodel Inference. New York, NY: Springer. doi:10.1007/b97636 """ -import numpy as np import matplotlib.pyplot as plt +import numpy as np +import diffpy.srmise.srmiselog as sml from diffpy.srmise import MultimodelSelection from diffpy.srmise.applications.plot import makeplot -import diffpy.srmise.srmiselog as sml # distances from ideal Ag (refined to PDF) dcif = np.array([11.2394, 11.608, 11.9652, 12.3121, 12.6495, 12.9781, 13.2986, @@ -72,7 +72,7 @@ def run(plot=True): # to redundant poor models (since they contribute very little to the Akaike # probabilities in any case), but redundant good models can significantly # alter how models are ranked. See Granlund (2015) for details. - tolerance = 0.2 + tolerance = 0.2 ms.classify(r, tolerance) ## Summarize various facts about the analysis. diff --git a/doc/examples/multimodel_unknown_dG1.py b/doc/examples/multimodel_unknown_dG1.py index 1a3ca30..3016fb3 100644 --- a/doc/examples/multimodel_unknown_dG1.py +++ b/doc/examples/multimodel_unknown_dG1.py @@ -35,9 +35,10 @@ import numpy as np -from diffpy.srmise import PDFPeakExtraction, MultimodelSelection -from diffpy.srmise.baselines import FromSequence import diffpy.srmise.srmiselog as sml +from diffpy.srmise import MultimodelSelection, PDFPeakExtraction +from diffpy.srmise.baselines import FromSequence + def run(plot=True): @@ -58,8 +59,8 @@ def run(plot=True): # calculated by approximating the C60 sample as a face-centered cubic # lattice of hollow spheres. blfunc = FromSequence("data/C60baseline.dat") - kwds={} - kwds["rng"] = [1., 7.25] + kwds = {} + kwds["rng"] = [1.0, 7.25] kwds["baseline"] = blfunc.actualize([]) kwds["cres"] = 0.05 ppe.setvars(**kwds) @@ -74,7 +75,7 @@ def run(plot=True): # For the purpose of illustration use 20 evenly-spaced values of dg where # 1% < dg < 10% of max gr value between r=1 and 7.25. grmax = np.max(ppe.y[ppe.getrangeslice()]) - dgs = np.linspace(.01*grmax, .10*grmax, 20) + dgs = np.linspace(0.01 * grmax, 0.10 * grmax, 20) ## Perform peak extraction for each of the assumed uncertainties. ms.run(dgs) @@ -84,9 +85,10 @@ def run(plot=True): # C60_aics.dat saves the value of the AIC of each model when evaluated # on a Nyquist-sampled grid using each of the dg values used to generate # the models in the first place. - dr = np.pi/ppe.qmax + dr = np.pi / ppe.qmax ms.save("output/unknown_dG_models.dat") ms.makeaics(dgs, dr, filename="output/unknown_dG_aics.dat") -if __name__ == '__main__': + +if __name__ == "__main__": run() diff --git a/doc/examples/multimodel_unknown_dG2.py b/doc/examples/multimodel_unknown_dG2.py index 37a249a..1bc9f60 100644 --- a/doc/examples/multimodel_unknown_dG2.py +++ b/doc/examples/multimodel_unknown_dG2.py @@ -38,14 +38,14 @@ [2] Burnham and Anderson. (2002). Model Selection and Multimodel Inference. New York, NY: Springer. doi:10.1007/b97636 """ -import numpy as np import matplotlib.pyplot as plt +import numpy as np +import diffpy.srmise.srmiselog as sml from diffpy.srmise import MultimodelSelection from diffpy.srmise.applications.plot import makeplot -import diffpy.srmise.srmiselog as sml -# distances from ideal (unrefined) C60 +# distances from ideal (unrefined) C60 dcif = np.array([1.44, 2.329968944, 2.494153163, 2.88, 3.595985339, 3.704477734, 4.132591264, 4.520339129, 4.659937888, 4.877358006, 5.209968944, 5.405310018, 5.522583786, @@ -82,7 +82,7 @@ def run(plot=True): # to redundant poor models (since they contribute very little to the Akaike # probabilities in any case), but redundant good models can significantly # alter how models are ranked. See Granlund (2015) for details. - tolerance = 0.2 + tolerance = 0.2 ms.classify(r, tolerance) ## Summarize various facts about the analysis. diff --git a/doc/examples/output/extract_single_peak.pwa b/doc/examples/output/extract_single_peak.pwa index 68455a2..6d32360 100644 --- a/doc/examples/output/extract_single_peak.pwa +++ b/doc/examples/output/extract_single_peak.pwa @@ -28,7 +28,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.polynomial +0 diffpy.srmise.baselines.polynomial ## Baseline # Parameters of baseline, followed by comment which @@ -38,7 +38,7 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr 1 diffpy.srmise.peaks.terminationripples (base=0) ## Extracted Peaks diff --git a/doc/examples/output/extract_single_peak.srmise b/doc/examples/output/extract_single_peak.srmise index 920f69d..0a57729 100644 --- a/doc/examples/output/extract_single_peak.srmise +++ b/doc/examples/output/extract_single_peak.srmise @@ -420,4 +420,3 @@ static_owner=False 3.25664 -1.63658 0.414337 3.36136 -1.90301 0.414368 3.46608 -2.08411 0.414339 - diff --git a/doc/examples/output/fit_initial.pwa b/doc/examples/output/fit_initial.pwa index a781033..157518f 100644 --- a/doc/examples/output/fit_initial.pwa +++ b/doc/examples/output/fit_initial.pwa @@ -28,7 +28,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.fromsequence +0 diffpy.srmise.baselines.fromsequence ## Baseline # Parameters of baseline, followed by comment which @@ -37,7 +37,7 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr 1 diffpy.srmise.peaks.terminationripples (base=0) ## Extracted Peaks diff --git a/doc/examples/output/fit_initial.srmise b/doc/examples/output/fit_initial.srmise index 0ec5d93..9deeec6 100644 --- a/doc/examples/output/fit_initial.srmise +++ b/doc/examples/output/fit_initial.srmise @@ -2289,4 +2289,3 @@ static_owner=False 6.8997 3686.4 5000 7.0472 6321.19 5000 7.19469 -14234.2 5000 - diff --git a/doc/examples/output/known_dG_aics.dat b/doc/examples/output/known_dG_aics.dat index bec6f7c..5ed556e 100644 --- a/doc/examples/output/known_dG_aics.dat +++ b/doc/examples/output/known_dG_aics.dat @@ -987,4 +987,4 @@ ag2 (g4 S'\x1dWX\x9c1SM@' tRp259 -as. \ No newline at end of file +as. diff --git a/doc/examples/output/known_dG_m0.pwa b/doc/examples/output/known_dG_m0.pwa index 14f77fb..c2a78b7 100644 --- a/doc/examples/output/known_dG_m0.pwa +++ b/doc/examples/output/known_dG_m0.pwa @@ -34,7 +34,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.polynomial +0 diffpy.srmise.baselines.polynomial ## Baseline # Parameters of baseline, followed by comment which @@ -44,8 +44,8 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr -1 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr +1 diffpy.srmise.peaks.gaussianoverr 2 diffpy.srmise.peaks.terminationripples (base=1) ## Extracted Peaks diff --git a/doc/examples/output/known_dG_m1.pwa b/doc/examples/output/known_dG_m1.pwa index c8d03d3..d8a8d72 100644 --- a/doc/examples/output/known_dG_m1.pwa +++ b/doc/examples/output/known_dG_m1.pwa @@ -34,7 +34,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.polynomial +0 diffpy.srmise.baselines.polynomial ## Baseline # Parameters of baseline, followed by comment which @@ -44,8 +44,8 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr -1 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr +1 diffpy.srmise.peaks.gaussianoverr 2 diffpy.srmise.peaks.terminationripples (base=1) ## Extracted Peaks diff --git a/doc/examples/output/known_dG_m12.pwa b/doc/examples/output/known_dG_m12.pwa index 635f48f..9ed48bf 100644 --- a/doc/examples/output/known_dG_m12.pwa +++ b/doc/examples/output/known_dG_m12.pwa @@ -34,7 +34,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.polynomial +0 diffpy.srmise.baselines.polynomial ## Baseline # Parameters of baseline, followed by comment which @@ -44,8 +44,8 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr -1 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr +1 diffpy.srmise.peaks.gaussianoverr 2 diffpy.srmise.peaks.terminationripples (base=1) ## Extracted Peaks diff --git a/doc/examples/output/known_dG_m8.pwa b/doc/examples/output/known_dG_m8.pwa index 43a9e7e..b1da608 100644 --- a/doc/examples/output/known_dG_m8.pwa +++ b/doc/examples/output/known_dG_m8.pwa @@ -34,7 +34,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.polynomial +0 diffpy.srmise.baselines.polynomial ## Baseline # Parameters of baseline, followed by comment which @@ -44,8 +44,8 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr -1 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr +1 diffpy.srmise.peaks.gaussianoverr 2 diffpy.srmise.peaks.terminationripples (base=1) ## Extracted Peaks diff --git a/doc/examples/output/known_dG_models.dat b/doc/examples/output/known_dG_models.dat index dd45ac7..5fe1270 100644 --- a/doc/examples/output/known_dG_models.dat +++ b/doc/examples/output/known_dG_models.dat @@ -5279,4 +5279,4 @@ S'\x00\xec{\xf3\xe9\xce\xba?' tRp753 aaaS"History written: Wed Jul 1 09:54:31 2015\nproduced by luke\ndiffpy.srmise version 0.5.2\n##### PDF Peak Extraction\n## BaselineFunctions\n# BaselineFunction 0\nfunction='Polynomial'\nmodule='diffpy.srmise.baselines.polynomial'\nbase=None\ndegree=1\n\n## PeakFunctions\n# PeakFunction 0\nfunction='GaussianOverR'\nmodule='diffpy.srmise.peaks.gaussianoverr'\nbase=None\nmaxwidth=0.7\n\n# PeakFunction 1\nfunction='TerminationRipples'\nmodule='diffpy.srmise.peaks.terminationripples'\nbase=0\nsupersample=5.0\nqmax=30.0\nextension=4.0\n\n# BaselineObject\nowner=0\npars=[-0.51041840174180308, 0.0084074335508157114]\nfree=[True, True]\nremovable=False\nstatic_owner=False\n\n## InitialPeaks\n# SrMiseMetadata\npf=[0]\ncres=0.10472\nModelEvaluator=AIC\nRange=[10.9, 15]\n# Metadata\nfilename='/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/Ag_nyquist_qmax30.gr'\nnyquist=True\nqmax=30.0\nqmax_reportedbypdf=30.0\nqmax_fromdata=29.729728241905356\nscale=False\nsupersample=4.0\n\n##### start data\n#L x y dx dy edy\n0.10472 -0.848217 0 0.276527 0.497353\n0.20944 -0.438975 0 0.375888 0.497353\n0.314159 -0.0724599 0 0.399338 0.497353\n0.418879 0.0701041 0 0.406243 0.497353\n0.523599 0.241004 0 0.40927 0.497353\n0.628319 -1.08142 0 0.410872 0.497353\n0.733038 -0.730527 0 0.411821 0.497353\n0.837758 -0.789248 0 0.412439 0.497353\n0.942478 -0.479976 0 0.412843 0.497353\n1.0472 -0.551525 0 0.413149 0.497353\n1.15192 -0.52763 0 0.413394 0.497353\n1.25664 -0.478534 0 0.41357 0.497353\n1.36136 -0.745365 0 0.41365 0.497353\n1.46608 -0.851118 0 0.414021 0.497353\n1.5708 -0.850263 0 0.413873 0.497353\n1.67552 -0.859146 0 0.413961 0.497353\n1.78024 -0.944151 0 0.414016 0.497353\n1.88496 -0.957457 0 0.414068 0.497353\n1.98968 -0.942436 0 0.414069 0.497353\n2.0944 -1.06201 0 0.414189 0.497353\n2.19911 -0.986944 0 0.41417 0.497353\n2.30383 -1.15517 0 0.414207 0.497353\n2.40855 -0.998036 0 0.4142 0.497353\n2.51327 -1.07553 0 0.414251 0.497353\n2.61799 -0.660581 0 0.414287 0.497353\n2.72271 2.09696 0 0.414276 0.497353\n2.82743 8.65415 0 0.414235 0.497353\n2.93215 9.77508 0 0.414368 0.497353\n3.03687 3.94327 0 0.414316 0.497353\n3.14159 -0.251454 0 0.414294 0.497353\n3.24631 -1.59266 0 0.414334 0.497353\n3.35103 -1.87634 0 0.414372 0.497353\n3.45575 -2.07954 0 0.414336 0.497353\n3.56047 -2.09388 0 0.414361 0.497353\n3.66519 -2.13669 0 0.414378 0.497353\n3.76991 -1.95955 0 0.414216 0.497353\n3.87463 -1.37209 0 0.414521 0.497353\n3.97935 -0.0329757 0 0.41436 0.497353\n4.08407 1.10031 0 0.414367 0.497353\n4.18879 0.469554 0 0.414408 0.497353\n4.29351 -1.15114 0 0.414303 0.497353\n4.39823 -2.15357 0 0.414507 0.497353\n4.50295 -2.41179 0 0.414366 0.497353\n4.60767 -2.41213 0 0.414445 0.497353\n4.71239 -1.88485 0 0.414396 0.497353\n4.81711 0.46476 0 0.414419 0.497353\n4.92183 5.56323 0 0.41442 0.497353\n5.02655 8.65254 0 0.414425 0.497353\n5.13127 5.24024 0 0.41438 0.497353\n5.23599 0.0409454 0 0.414433 0.497353\n5.34071 -2.48627 0 0.41447 0.497353\n5.44543 -3.02423 0 0.414428 0.497353\n5.55015 -2.60297 0 0.414347 0.497353\n5.65487 -0.84228 0 0.414496 0.497353\n5.75959 1.18901 0 0.414408 0.497353\n5.86431 0.894119 0 0.41444 0.497353\n5.96903 -1.28837 0 0.414399 0.497353\n6.07375 -2.72173 0 0.414454 0.497353\n6.17847 -2.7103 0 0.414469 0.497353\n6.28318 -0.941738 0 0.414354 0.497353\n6.3879 2.42598 0 0.414536 0.497353\n6.49263 4.33279 0 0.414436 0.497353\n6.59734 2.21093 0 0.41439 0.497353\n6.70207 -1.306 0 0.414491 0.497353\n6.80678 -3.03265 0 0.414432 0.497353\n6.9115 -2.90582 0 0.414391 0.497353\n7.01622 -1.87167 0 0.41448 0.497353\n7.12094 -1.23044 0 0.414423 0.497353\n7.22566 -1.92941 0 0.414359 0.497353\n7.33038 -2.5179 0 0.414509 0.497353\n7.4351 -0.969886 0 0.41442 0.497353\n7.53982 3.96972 0 0.414436 0.497353\n7.64454 8.8855 0 0.41445 0.497353\n7.74926 7.4236 0 0.414469 0.497353\n7.85398 1.53836 0 0.414469 0.497353\n7.9587 -2.44643 0 0.414443 0.497353\n8.06342 -3.26112 0 0.414411 0.497353\n8.16814 -2.94882 0 0.414522 0.497353\n8.27286 -2.90904 0 0.41438 0.497353\n8.37758 -3.05689 0 0.414496 0.497353\n8.4823 -1.78758 0 0.414444 0.497353\n8.58702 1.38353 0 0.414446 0.497353\n8.69174 3.94127 0 0.41445 0.497353\n8.79646 2.45676 0 0.414399 0.497353\n8.90118 -0.591625 0 0.414515 0.497353\n9.0059 -1.30696 0 0.414422 0.497353\n9.11062 0.12014 0 0.414465 0.497353\n9.21534 0.431331 0 0.414439 0.497353\n9.32006 -1.16176 0 0.414455 0.497353\n9.42478 -1.8613 0 0.41443 0.497353\n9.5295 -0.544258 0 0.414482 0.497353\n9.63422 0.450605 0 0.414444 0.497353\n9.73894 -0.669103 0 0.414465 0.497353\n9.84366 -1.7389 0 0.414464 0.497353\n9.94838 -0.816268 0 0.414442 0.497353\n10.0531 0.290376 0 0.414455 0.497353\n10.1578 0.0115737 0 0.414453 0.497353\n10.2625 1.15071 0 0.414487 0.497353\n10.3673 5.36598 0 0.414456 0.497353\n10.472 7.70779 0 0.414461 0.497353\n10.5767 4.12092 0 0.414484 0.497353\n10.6814 -1.35374 0 0.414425 0.497353\n10.7861 -4.23359 0 0.414497 0.497353\n10.8909 -4.71367 0 0.414424 0.497353\n10.9956 -3.61547 0 0.414463 0.497353\n11.1003 -0.719766 0 0.414456 0.497353\n11.205 2.04711 0 0.414463 0.497353\n11.3097 1.71502 0 0.414441 0.497353\n11.4145 -0.861729 0 0.414477 0.497353\n11.5192 -2.49413 0 0.414453 0.497353\n11.6239 -2.74042 0 0.414485 0.497353\n11.7286 -2.25884 0 0.414466 0.497353\n11.8333 -0.265838 0 0.414432 0.497353\n11.9381 1.90138 0 0.414504 0.497353\n12.0428 1.58808 0 0.414449 0.497353\n12.1475 0.0070566 0 0.414473 0.497353\n12.2522 -0.295937 0 0.414475 0.497353\n12.3569 0.0151809 0 0.414424 0.497353\n12.4617 0.90539 0 0.414498 0.497353\n12.5664 3.2162 0 0.414433 0.497353\n12.6711 4.236 0 0.414449 0.497353\n12.7758 1.95719 0 0.414468 0.497353\n12.8805 -0.763835 0 0.414439 0.497353\n12.9853 -1.66267 0 0.414462 0.497353\n13.09 -1.55113 0 0.414458 0.497353\n13.1947 -0.362846 0 0.414474 0.497353\n13.2994 0.530654 0 0.414469 0.497353\n13.4041 -0.240443 0 0.414474 0.497353\n13.5089 -1.58126 0 0.414444 0.497353\n13.6136 -1.90816 0 0.414468 0.497353\n13.7183 -1.58124 0 0.41445 0.497353\n13.823 -0.47036 0 0.414455 0.497353\n13.9277 0.0528224 0 0.414455 0.497353\n14.0325 -1.06936 0 0.414474 0.497353\n14.1372 -2.69992 0 0.41446 0.497353\n14.2419 -2.63203 0 0.41443 0.497353\n14.3466 -0.307332 0 0.414487 0.497353\n14.4513 2.93352 0 0.414453 0.497353\n14.5561 3.69013 0 0.414472 0.497353\n14.6608 1.35399 0 0.414434 0.497353\n14.7655 -0.4856 0 0.414482 0.497353\n14.8702 -0.000276016 0 0.414449 0.497353\n14.9749 2.48563 0 0.414464 0.497353\n15.0797 4.27674 0 0.414459 0.497353\n15.1844 3.33366 0 0.41448 0.497353\n15.2891 1.21759 0 0.414457 0.497353\n15.3938 -0.37143 0 0.414471 0.497353\n15.4985 -1.80234 0 0.414452 0.497353\n15.6032 -2.85825 0 0.414473 0.497353\n15.708 -3.70676 0 0.414457 0.497353\n15.8127 -4.2802 0 0.414474 0.497353\n15.9174 -3.47037 0 0.414451 0.497353\n16.0221 -0.522252 0 0.414455 0.497353\n16.1268 2.43719 0 0.414459 0.497353\n16.2316 2.03817 0 0.414473 0.497353\n16.3363 -0.703543 0 0.414468 0.497353\n16.441 -1.77019 0 0.41448 0.497353\n16.5457 0.231127 0 0.414477 0.497353\n16.6504 2.64325 0 0.414463 0.497353\n16.7552 2.8064 0 0.414479 0.497353\n16.8599 1.24821 0 0.414472 0.497353\n16.9646 0.147782 0 0.414471 0.497353\n17.0693 -0.285568 0 0.414463 0.497353\n17.174 -0.467344 0 0.414472 0.497353\n17.2788 -0.778432 0 0.414461 0.497353\n17.3835 -0.588839 0 0.414454 0.497353\n17.4882 0.996117 0 0.414463 0.497353\n17.5929 3.103 0 0.414464 0.497353\n17.6976 3.11809 0 0.414474 0.497353\n17.8024 0.614726 0 0.414465 0.497353\n17.9071 -1.62203 0 0.414465 0.497353\n18.0118 -2.07547 0 0.41448 0.497353\n18.1165 -1.83835 0 0.414466 0.497353\n18.2212 -2.03303 0 0.414484 0.497353\n18.326 -2.36859 0 0.414472 0.497353\n18.4307 -2.10356 0 0.414457 0.497353\n18.5354 -1.36772 0 0.414466 0.497353\n18.6401 -0.713728 0 0.414465 0.497353\n18.7448 -0.0613967 0 0.414472 0.497353\n18.8496 1.14241 0 0.41448 0.497353\n18.9543 2.73659 0 0.414472 0.497353\n19.059 2.89613 0 0.414476 0.497353\n19.1637 1.20826 0 0.414465 0.497353\n19.2684 0.137683 0 0.414472 0.497353\n19.3732 1.07538 0 0.414477 0.497353\n19.4779 1.56895 0 0.414466 0.497353\n19.5826 -0.10718 0 0.414469 0.497353\n19.6873 -1.77146 0 0.414461 0.497353\n19.792 -1.19471 0 0.414458 0.497353\n19.8968 0.0394425 0 0.414477 0.497353\n20.0015 -0.209379 0 0.414475 0.497353\n20.1062 -0.746729 0 0.414462 0.497353\n20.2109 0.0585856 0 0.41447 0.497353\n20.3156 0.860572 0 0.414472 0.497353\n20.4203 0.243239 0 0.414467 0.497353\n20.5251 -1.16833 0 0.41447 0.497353\n20.6298 -1.58629 0 0.414473 0.497353\n20.7345 -1.08777 0 0.414483 0.497353\n20.8392 -0.300338 0 0.414478 0.497353\n20.944 0.29465 0 0.414476 0.497353\n21.0487 0.425193 0 0.414469 0.497353\n21.1534 -0.00136946 0 0.414465 0.497353\n21.2581 -0.393033 0 0.414473 0.497353\n21.3628 0.387682 0 0.414463 0.497353\n21.4675 1.6689 0 0.414463 0.497353\n21.5723 1.4581 0 0.414459 0.497353\n21.677 -0.361992 0 0.414462 0.497353\n21.7817 -1.00177 0 0.414469 0.497353\n21.8864 0.0128308 0 0.414467 0.497353\n21.9912 0.809515 0 0.414477 0.497353\n22.0959 0.672339 0 0.414477 0.497353\n22.2006 0.272683 0 0.414474 0.497353\n22.3053 -0.111194 0 0.41448 0.497353\n22.41 -0.327024 0 0.414476 0.497353\n22.5147 0.0407522 0 0.414467 0.497353\n22.6195 0.533048 0 0.414474 0.497353\n22.7242 0.0614679 0 0.414475 0.497353\n22.8289 -0.830564 0 0.414475 0.497353\n22.9336 -0.355731 0 0.414475 0.497353\n23.0384 0.411435 0 0.414477 0.497353\n23.1431 -0.198643 0 0.414481 0.497353\n23.2478 -1.53097 0 0.414475 0.497353\n23.3525 -1.8586 0 0.41448 0.497353\n23.4572 -1.25444 0 0.41448 0.497353\n23.5619 0.0161056 0 0.414478 0.497353\n23.6667 1.66708 0 0.414479 0.497353\n23.7714 2.42556 0 0.414481 0.497353\n23.8761 1.63544 0 0.41448 0.497353\n23.9808 0.480166 0 0.414483 0.497353\n24.0855 0.0681919 0 0.414479 0.497353\n24.1903 -0.367436 0 0.414473 0.497353\n24.295 -0.985321 0 0.414472 0.497353\n24.3997 -1.42046 0 0.414469 0.497353\n24.5044 -1.35023 0 0.414474 0.497353\n24.6091 -0.437157 0 0.414467 0.497353\n24.7139 1.26422 0 0.414462 0.497353\n24.8186 1.92459 0 0.414465 0.497353\n24.9233 1.10257 0 0.414468 0.497353\n25.028 0.232537 0 0.414472 0.497353\n25.1327 0.313857 0 0.414476 0.497353\n25.2375 0.347515 0 0.41448 0.497353\n25.3422 0.0119498 0 0.414475 0.497353\n25.4469 -0.627585 0 0.414474 0.497353\n25.5516 -1.41904 0 0.414471 0.497353\n25.6563 -1.73891 0 0.414463 0.497353\n25.7611 -1.39368 0 0.414465 0.497353\n25.8658 -0.98749 0 0.414462 0.497353\n25.9705 -0.709065 0 0.414461 0.497353\n26.0752 0.00727748 0 0.414463 0.497353\n26.1799 0.820796 0 0.414465 0.497353\n26.2847 1.28029 0 0.414468 0.497353\n26.3894 1.20257 0 0.414464 0.497353\n26.4941 0.847178 0 0.41447 0.497353\n26.5988 0.532713 0 0.414472 0.497353\n26.7035 0.449797 0 0.414474 0.497353\n26.8083 0.311282 0 0.414476 0.497353\n26.913 -0.0359985 0 0.414474 0.497353\n27.0177 -0.0274541 0 0.414472 0.497353\n27.1224 -0.168312 0 0.414475 0.497353\n27.2271 -0.539714 0 0.414476 0.497353\n27.3319 -0.629106 0 0.414471 0.497353\n27.4366 -0.218378 0 0.414468 0.497353\n27.5413 0.255966 0 0.414467 0.497353\n27.646 0.536293 0 0.414469 0.497353\n27.7507 0.399817 0 0.414473 0.497353\n27.8555 0.11408 0 0.414476 0.497353\n27.9602 -0.17124 0 0.414475 0.497353\n28.0649 -0.82576 0 0.414473 0.497353\n28.1696 -1.63377 0 0.414469 0.497353\n28.2743 -1.91638 0 0.41447 0.497353\n28.379 -1.1421 0 0.414474 0.497353\n28.4838 0.377505 0 0.414475 0.497353\n28.5885 1.61749 0 0.414476 0.497353\n28.6932 1.60999 0 0.414476 0.497353\n28.7979 0.924994 0 0.414476 0.497353\n28.9027 0.539661 0 0.414475 0.497353\n29.0074 0.273788 0 0.414475 0.497353\n29.1121 -0.140046 0 0.41447 0.497353\n29.2168 -0.202034 0 0.414471 0.497353\n29.3215 0.433365 0 0.414469 0.497353\n29.4262 1.13571 0 0.414469 0.497353\n29.531 0.836727 0 0.414468 0.497353\n29.6357 -0.101336 0 0.414469 0.497353\n29.7404 -0.669691 0 0.41447 0.497353\n29.8451 -0.721992 0 0.414471 0.497353\n29.9499 -0.766688 0 0.414472 0.497353\n30.0546 -0.547158 0 0.414473 0.497353\n30.1593 -0.308248 0 0.414473 0.497353\n30.264 -0.255524 0 0.414473 0.497353\n30.3687 -0.551494 0 0.414474 0.497353\n30.4734 -0.636365 0 0.414471 0.497353\n30.5782 -0.34684 0 0.41447 0.497353\n30.6829 -0.16534 0 0.414469 0.497353\n30.7876 -0.175003 0 0.414473 0.497353\n30.8923 0.0582915 0 0.414478 0.497353\n30.9971 0.617427 0 0.414476 0.497353\n31.1018 1.14323 0 0.414472 0.497353\n31.2065 1.20366 0 0.414469 0.497353\n31.3112 1.01078 0 0.414467 0.497353\n31.4159 0.829863 0 0.414469 0.497353\n31.5206 0.342908 0 0.414471 0.497353\n31.6254 -0.438775 0 0.414473 0.497353\n31.7301 -0.98495 0 0.414474 0.497353\n31.8348 -0.949941 0 0.414473 0.497353\n31.9395 -0.536897 0 0.414469 0.497353\n32.0442 -0.098742 0 0.414469 0.497353\n32.149 0.198955 0 0.414469 0.497353\n32.2537 0.26835 0 0.414467 0.497353\n32.3584 0.158842 0 0.414467 0.497353\n32.4631 -0.217961 0 0.414468 0.497353\n32.5678 -0.359842 0 0.414469 0.497353\n32.6726 -0.400725 0 0.414469 0.497353\n32.7773 -0.388053 0 0.414472 0.497353\n32.882 -0.53186 0 0.414471 0.497353\n32.9867 -0.452224 0 0.414473 0.497353\n33.0914 -0.258411 0 0.414473 0.497353\n33.1962 -0.0783268 0 0.414472 0.497353\n33.3009 0.34702 0 0.414477 0.497353\n33.4056 0.813758 0 0.414477 0.497353\n33.5103 0.942157 0 0.414473 0.497353\n33.615 0.668602 0 0.414472 0.497353\n33.7198 0.416251 0 0.414469 0.497353\n33.8245 0.213257 0 0.414464 0.497353\n33.9292 0.128913 0 0.414463 0.497353\n34.0339 0.101085 0 0.414462 0.497353\n34.1386 0.126261 0 0.414463 0.497353\n34.2434 -0.088243 0 0.414466 0.497353\n34.3481 -0.505281 0 0.414463 0.497353\n34.4528 -0.865457 0 0.414461 0.497353\n34.5575 -0.931427 0 0.414465 0.497353\n34.6622 -0.677627 0 0.414469 0.497353\n34.767 -0.219618 0 0.414472 0.497353\n34.8717 0.262265 0 0.414475 0.497353\n34.9764 0.497295 0 0.414474 0.497353\n##### Results\nextraction_type='extract'\n### ModelCluster\npeak_funcs=[0]\nModelEvaluator=AIC\nslice=slice(None, 40, None)\n# BaselineObject\nowner=0\npars=[-0.49612799331518148, 0.009243028322946871]\nfree=[True, True]\nremovable=False\nstatic_owner=False\n\n## ModelPeaks\n# ModelPeak\nowner=1\npars=[11.257345641524847, -0.44326181455202407, 34.616301647118242]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[12.008712299446687, 0.31580138324858892, 54.419674496243019]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[12.65116694083374, -0.17004315124028255, 60.463492845884261]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[13.304659414498092, 0.070450559400331986, 49.892861341339824]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[13.919411195913245, -0.073794900748365463, 47.673856467841304]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[14.51438047487288, -0.43472084163912061, 59.87876735144706]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[15.239631252178969, 1.0190814364846466, 160.4906386912761]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n### start data\n#L r y dy\n10.9 -4.68486 0.497353\n11.0047 -3.42823 0.497353\n11.1094 -0.423569 0.497353\n11.2142 2.16651 0.497353\n11.3189 1.53018 0.497353\n11.4236 -1.07332 0.497353\n11.5283 -2.55496 0.497353\n11.633 -2.73133 0.497353\n11.7378 -2.15436 0.497353\n11.8425 -0.03493 0.497353\n11.9472 1.98801 0.497353\n12.0519 1.45359 0.497353\n12.1566 -0.0851001 0.497353\n12.2614 -0.26845 0.497353\n12.3661 0.0438283 0.497353\n12.4708 1.06552 0.497353\n12.5755 3.41162 0.497353\n12.6802 4.16027 0.497353\n12.785 1.67277 0.497353\n12.8897 -0.907877 0.497353\n12.9944 -1.68923 0.497353\n13.0991 -1.48603 0.497353\n13.2038 -0.242317 0.497353\n13.3086 0.533857 0.497353\n13.4133 -0.369666 0.497353\n13.518 -1.6523 0.497353\n13.6227 -1.90302 0.497353\n13.7274 -1.51247 0.497353\n13.8322 -0.37046 0.497353\n13.9369 0.0173898 0.497353\n14.0416 -1.22208 0.497353\n14.1463 -2.78774 0.497353\n14.251 -2.51037 0.497353\n14.3558 -0.0255009 0.497353\n14.4605 3.15137 0.497353\n14.5652 3.56679 0.497353\n14.6699 1.12682 0.497353\n14.7746 -0.544585 0.497353\n14.8794 0.160077 0.497353\n14.9841 2.71941 0.497353\n\n" p754 -a. \ No newline at end of file +a. diff --git a/doc/examples/output/parameter_summary.pwa b/doc/examples/output/parameter_summary.pwa index 685913f..c100315 100644 --- a/doc/examples/output/parameter_summary.pwa +++ b/doc/examples/output/parameter_summary.pwa @@ -28,7 +28,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.polynomial +0 diffpy.srmise.baselines.polynomial ## Baseline # Parameters of baseline, followed by comment which @@ -38,7 +38,7 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr 1 diffpy.srmise.peaks.terminationripples (base=0) ## Extracted Peaks diff --git a/doc/examples/output/parameter_summary.srmise b/doc/examples/output/parameter_summary.srmise index 3f82037..cb9c966 100644 --- a/doc/examples/output/parameter_summary.srmise +++ b/doc/examples/output/parameter_summary.srmise @@ -2288,4 +2288,3 @@ static_owner=False 9.71647 -1.26973 0.35 9.8373 0.154565 0.35 9.95813 0.982725 0.35 - diff --git a/doc/examples/output/query_results.pwa b/doc/examples/output/query_results.pwa index 3e70b92..202d7b2 100644 --- a/doc/examples/output/query_results.pwa +++ b/doc/examples/output/query_results.pwa @@ -28,7 +28,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.polynomial +0 diffpy.srmise.baselines.polynomial ## Baseline # Parameters of baseline, followed by comment which @@ -38,7 +38,7 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr 1 diffpy.srmise.peaks.terminationripples (base=0) ## Extracted Peaks diff --git a/doc/examples/output/query_results.srmise b/doc/examples/output/query_results.srmise index fe1934a..b4e22c7 100644 --- a/doc/examples/output/query_results.srmise +++ b/doc/examples/output/query_results.srmise @@ -559,4 +559,3 @@ static_owner=False 9.74926 -0.828972 0.414465 9.85398 -1.7376 0.414462 9.9587 -0.661785 0.414443 - diff --git a/doc/examples/output/unknown_dG_aics.dat b/doc/examples/output/unknown_dG_aics.dat index 82a81f2..680a1fd 100644 --- a/doc/examples/output/unknown_dG_aics.dat +++ b/doc/examples/output/unknown_dG_aics.dat @@ -1712,4 +1712,4 @@ ag2 (g4 S'\x8d\x9c\xa5\xb0\x08y[@' tRp444 -as. \ No newline at end of file +as. diff --git a/doc/examples/output/unknown_dG_m11.pwa b/doc/examples/output/unknown_dG_m11.pwa index 699fc10..1f7939d 100644 --- a/doc/examples/output/unknown_dG_m11.pwa +++ b/doc/examples/output/unknown_dG_m11.pwa @@ -34,7 +34,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.fromsequence +0 diffpy.srmise.baselines.fromsequence ## Baseline # Parameters of baseline, followed by comment which @@ -43,8 +43,8 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr -1 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr +1 diffpy.srmise.peaks.gaussianoverr 2 diffpy.srmise.peaks.terminationripples (base=1) ## Extracted Peaks diff --git a/doc/examples/output/unknown_dG_m17.pwa b/doc/examples/output/unknown_dG_m17.pwa index 779ae52..c937269 100644 --- a/doc/examples/output/unknown_dG_m17.pwa +++ b/doc/examples/output/unknown_dG_m17.pwa @@ -34,7 +34,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.fromsequence +0 diffpy.srmise.baselines.fromsequence ## Baseline # Parameters of baseline, followed by comment which @@ -43,8 +43,8 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr -1 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr +1 diffpy.srmise.peaks.gaussianoverr 2 diffpy.srmise.peaks.terminationripples (base=1) ## Extracted Peaks diff --git a/doc/examples/output/unknown_dG_m18.pwa b/doc/examples/output/unknown_dG_m18.pwa index 56b84d6..743bdca 100644 --- a/doc/examples/output/unknown_dG_m18.pwa +++ b/doc/examples/output/unknown_dG_m18.pwa @@ -34,7 +34,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.fromsequence +0 diffpy.srmise.baselines.fromsequence ## Baseline # Parameters of baseline, followed by comment which @@ -43,8 +43,8 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr -1 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr +1 diffpy.srmise.peaks.gaussianoverr 2 diffpy.srmise.peaks.terminationripples (base=1) ## Extracted Peaks diff --git a/doc/examples/output/unknown_dG_m5.pwa b/doc/examples/output/unknown_dG_m5.pwa index b0a914b..4fafa82 100644 --- a/doc/examples/output/unknown_dG_m5.pwa +++ b/doc/examples/output/unknown_dG_m5.pwa @@ -34,7 +34,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.fromsequence +0 diffpy.srmise.baselines.fromsequence ## Baseline # Parameters of baseline, followed by comment which @@ -43,8 +43,8 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr -1 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr +1 diffpy.srmise.peaks.gaussianoverr 2 diffpy.srmise.peaks.terminationripples (base=1) ## Extracted Peaks diff --git a/doc/examples/output/unknown_dG_m7.pwa b/doc/examples/output/unknown_dG_m7.pwa index b52e78b..a4ec085 100644 --- a/doc/examples/output/unknown_dG_m7.pwa +++ b/doc/examples/output/unknown_dG_m7.pwa @@ -34,7 +34,7 @@ ModelEvaluator=AIC ## Baseline Functions # Index Type -0 diffpy.srmise.baselines.fromsequence +0 diffpy.srmise.baselines.fromsequence ## Baseline # Parameters of baseline, followed by comment which @@ -43,8 +43,8 @@ ModelEvaluator=AIC ## Peak Functions # Index Type -0 diffpy.srmise.peaks.gaussianoverr -1 diffpy.srmise.peaks.gaussianoverr +0 diffpy.srmise.peaks.gaussianoverr +1 diffpy.srmise.peaks.gaussianoverr 2 diffpy.srmise.peaks.terminationripples (base=1) ## Extracted Peaks diff --git a/doc/examples/output/unknown_dG_models.dat b/doc/examples/output/unknown_dG_models.dat index a4faa1b..e4cb6d4 100644 --- a/doc/examples/output/unknown_dG_models.dat +++ b/doc/examples/output/unknown_dG_models.dat @@ -9911,4 +9911,4 @@ S"`\xa6'\xc5\t\xe1\xc2?" tRp1339 aaaS"History written: Wed Jul 1 10:01:37 2015\nproduced by luke\ndiffpy.srmise version 0.5.2\n##### PDF Peak Extraction\n## BaselineFunctions\n# BaselineFunction 0\nfunction='FromSequence'\nmodule='diffpy.srmise.baselines.fromsequence'\nbase=None\ny=[-1475.0325650706627, -2950.0651301413254, -4425.0976952119881, -5900.1302602826509, -7375.1628253533127, -8850.1953904239745, -10325.227955494638, -11800.260520565302, -13275.293085635964, -14750.325650706625, -16225.358215777289, -17700.390780847953, -19175.423345918618, -20650.455910989276, -22125.488476059942, -23600.521041130603, -25075.553606201265, -26550.586171271931, -28025.459933459599, -29490.66450359999, -30922.864389112267, -32298.695523408274, -33596.022711102938, -34793.92402828217, -35872.675222770908, -36813.734114401064, -37599.724995279517, -38214.42303005611, -38643.368779986711, -38890.463187607907, -38978.523165803032, -38930.29758324947, -38767.462434741778, -38510.636440923663, -38179.39664801996, -37792.294027568765, -37366.869076153373, -36919.66741513431, -36465.762314723048, -36011.685031151355, -35557.60774757967, -35103.530464007978, -34649.453180436292, -34195.375896864593, -33741.298613292922, -33287.221329721207, -32833.144046149522, -32379.066762577819, -31924.989479006141, -31470.912195434459, -31016.83491186277, -30562.757628291063, -30108.680344719356, -29654.603061147711, -29200.525777575986, -28746.448494004322, -28292.371210432615, -27838.293926860926, -27384.216643289248, -26930.139359411234, -26474.542488478357, -26010.083575850655, -25528.358372275903, -25021.398910324362, -24481.667989050857, -23902.053658656267, -23275.863705149979, -22596.820135010832, -21859.053659849822, -21057.103538030915, -20189.157506289514, -19262.2608478449, -18284.582204221027, -17263.909088500266, -16207.653400662406, -15122.856942922259, -14016.196935068139, -12893.991529799485, -11762.205328065833, -10626.439769837914, -9490.3191584519027, -8354.1985470658783, -7218.0779356797575, -6081.9573242938068, -4945.8367129076605, -3809.7161015215393, -2673.5954901353934, -1537.4748787493209, -401.35426736339457, 734.76028191512512, 1862.3074495985777, 2947.158200990089, 3960.1884858314311, 4888.6048315275966, 5719.7202101002222, 6439.2477046714184, 7031.3497219455321, 7478.6872046947792, 7762.4688442382803, 7862.653161699448]\nx=[0.10000000000000001, 0.20000000000000001, 0.30000000000000004, 0.40000000000000002, 0.5, 0.59999999999999998, 0.70000000000000007, 0.80000000000000004, 0.90000000000000002, 1.0, 1.1000000000000001, 1.2000000000000002, 1.3000000000000003, 1.4000000000000001, 1.5000000000000002, 1.6000000000000001, 1.7000000000000002, 1.8000000000000003, 1.9000000000000001, 2.0, 2.1000000000000001, 2.2000000000000002, 2.3000000000000003, 2.4000000000000004, 2.5000000000000004, 2.6000000000000001, 2.7000000000000002, 2.8000000000000003, 2.9000000000000004, 3.0000000000000004, 3.1000000000000001, 3.2000000000000002, 3.3000000000000003, 3.4000000000000004, 3.5000000000000004, 3.6000000000000001, 3.7000000000000002, 3.8000000000000003, 3.9000000000000004, 4.0, 4.0999999999999996, 4.2000000000000002, 4.2999999999999998, 4.3999999999999995, 4.5, 4.5999999999999996, 4.7000000000000002, 4.7999999999999998, 4.9000000000000004, 5.0, 5.0999999999999996, 5.2000000000000002, 5.2999999999999998, 5.4000000000000004, 5.5, 5.5999999999999996, 5.7000000000000002, 5.7999999999999998, 5.9000000000000004, 6.0, 6.0999999999999996, 6.2000000000000002, 6.2999999999999998, 6.4000000000000004, 6.5, 6.5999999999999996, 6.7000000000000002, 6.7999999999999998, 6.9000000000000004, 7.0, 7.0999999999999996, 7.2000000000000002, 7.2999999999999998, 7.4000000000000004, 7.5, 7.5999999999999996, 7.7000000000000002, 7.7999999999999998, 7.9000000000000004, 8.0, 8.0999999999999996, 8.1999999999999993, 8.3000000000000007, 8.4000000000000004, 8.5, 8.5999999999999996, 8.6999999999999993, 8.8000000000000007, 8.9000000000000004, 9.0, 9.0999999999999996, 9.1999999999999993, 9.3000000000000007, 9.4000000000000004, 9.5, 9.5999999999999996, 9.7000000000000011, 9.8000000000000007, 9.9000000000000004, 10.0]\n\n## PeakFunctions\n# PeakFunction 0\nfunction='GaussianOverR'\nmodule='diffpy.srmise.peaks.gaussianoverr'\nbase=None\nmaxwidth=0.7\n\n# PeakFunction 1\nfunction='TerminationRipples'\nmodule='diffpy.srmise.peaks.terminationripples'\nbase=0\nsupersample=5.0\nqmax=21.299999\nextension=4.0\n\n# BaselineObject\nowner=0\npars=[]\nfree=[]\nremovable=False\nstatic_owner=False\n\n## InitialPeaks\n# SrMiseMetadata\npf=[0]\ncres=0.05\nModelEvaluator=AIC\nRange=[1.0, 7.25]\n# Metadata\nfilename='/home/luke/Workspaces/MSU_Research/diffpy.srmise/doc/examples/data/C60_fine_qmax21.gr'\nnyquist=True\nqmax=21.299999\nqmax_reportedbypdf=21.299999\nqmax_fromdata=20.755266780473114\nscale=False\nsupersample=4.0\n\n##### start data\n#L x y dx dy edy\n0.01 18942.6 0 8.53691 11653.4\n0.02 37722.7 0 16.7546 11653.4\n0.03 56177.6 0 24.347 11653.4\n0.04 74143.9 0 31.0336 11653.4\n0.05 91457.9 0 36.571 11653.4\n0.06 107956 0 40.7633 11653.4\n0.07 123476 0 43.4706 11653.4\n0.08 137856 0 44.6161 11653.4\n0.09 150940 0 44.191 11653.4\n0.1 162578 0 42.2588 11653.4\n0.11 172629 0 38.9611 11653.4\n0.12 180964 0 34.5282 11653.4\n0.13 187472 0 29.307 11653.4\n0.14 192060 0 23.8359 11653.4\n0.15 194658 0 19.0276 11653.4\n0.16 195226 0 16.3851 11653.4\n0.17 193750 0 17.2383 11653.4\n0.18 190254 0 20.9462 11653.4\n0.19 184793 0 25.822 11653.4\n0.2 177460 0 30.698 11653.4\n0.21 168386 0 34.9379 11653.4\n0.22 157737 0 38.1842 11653.4\n0.23 145712 0 40.2361 11653.4\n0.24 132543 0 41.0033 11653.4\n0.25 118488 0 40.4884 11653.4\n0.26 103827 0 38.7838 11653.4\n0.27 88856.5 0 36.0754 11653.4\n0.28 73881.6 0 32.6565 11653.4\n0.29 59209 0 28.9558 11653.4\n0.3 45139.3 0 25.5728 11653.4\n0.31 31959.2 0 23.2628 11653.4\n0.32 19933.4 0 22.7026 11653.4\n0.33 9297.65 0 24.0285 11653.4\n0.34 251.704 0 26.7081 11653.4\n0.35 -7046.27 0 29.9659 11653.4\n0.36 -12484.5 0 33.1496 11653.4\n0.37 -16000.8 0 35.809 11653.4\n0.38 -17584.8 0 37.6619 11653.4\n0.39 -17278 0 38.5549 11653.4\n0.4 -15172.9 0 38.4411 11653.4\n0.41 -11410.1 0 37.3693 11653.4\n0.42 -6173.99 0 35.4819 11653.4\n0.43 312.641 0 33.0201 11653.4\n0.44 7795.7 0 30.331 11653.4\n0.45 15997.5 0 27.8677 11653.4\n0.46 24625.2 0 26.1426 11653.4\n0.47 33380 0 25.5822 11653.4\n0.48 41966.4 0 26.3124 11653.4\n0.49 50100.7 0 28.0791 11653.4\n0.5 57520.3 0 30.4057 11653.4\n0.51 63990.9 0 32.8044 11653.4\n0.52 69313.7 0 34.886 11653.4\n0.53 73330.8 0 36.3811 11653.4\n0.54 75929.5 0 37.131 11653.4\n0.55 77044.7 0 37.0761 11653.4\n0.56 76660.3 0 36.2478 11653.4\n0.57 74808.1 0 34.7652 11653.4\n0.58 71565.9 0 32.8355 11653.4\n0.59 67053.6 0 30.7514 11653.4\n0.6 61428.1 0 28.8765 11653.4\n0.61 54877.1 0 27.5925 11653.4\n0.62 47611.7 0 27.1928 11653.4\n0.63 39858.8 0 27.7571 11653.4\n0.64 31853 0 29.1121 11653.4\n0.65 23828 0 30.9201 11653.4\n0.66 16008.6 0 32.8095 11653.4\n0.67 8603.69 0 34.4622 11653.4\n0.68 1798.99 0 35.646 11653.4\n0.69 -4248.35 0 36.2199 11653.4\n0.7 -9414.3 0 36.1298 11653.4\n0.71 -13611.1 0 35.4048 11653.4\n0.72 -16789.1 0 34.1541 11653.4\n0.73 -18936.8 0 32.5637 11653.4\n0.74 -20079.9 0 30.8888 11653.4\n0.75 -20278.6 0 29.4309 11653.4\n0.76 -19624.1 0 28.4858 11653.4\n0.77 -18233.7 0 28.2603 11653.4\n0.78 -16245 0 28.7926 11653.4\n0.79 -13810.2 0 29.9374 11653.4\n0.8 -11089.1 0 31.4287 11653.4\n0.81 -8242.85 0 32.9701 11653.4\n0.82 -5427.21 0 34.3007 11653.4\n0.83 -2786.99 0 35.2261 11653.4\n0.84 -450.548 0 35.6277 11653.4\n0.85 1474.5 0 35.4644 11653.4\n0.86 2904.71 0 34.7693 11653.4\n0.87 3783.01 0 33.6482 11653.4\n0.88 4079.74 0 32.2736 11653.4\n0.89 3792.54 0 30.8738 11653.4\n0.9 2944.99 0 29.7056 11653.4\n0.91 1584.28 0 29.0051 11653.4\n0.92 -222.159 0 28.9205 11653.4\n0.93 -2390.68 0 29.4595 11653.4\n0.94 -4826.07 0 30.4869 11653.4\n0.95 -7426.55 0 31.7771 11653.4\n0.96 -10088.8 0 33.0821 11653.4\n0.97 -12713 0 34.1826 11653.4\n0.98 -15207.3 0 34.9156 11653.4\n0.99 -17492 0 35.1842 11653.4\n1 -19503 0 34.9606 11653.4\n1.01 -21193.7 0 34.2847 11653.4\n1.02 -22537 0 33.2613 11653.4\n1.03 -23525.9 0 32.053 11653.4\n1.04 -24172 0 30.8661 11653.4\n1.05 -24504.7 0 29.9216 11653.4\n1.06 -24568.6 0 29.4096 11653.4\n1.07 -24419.8 0 29.435 11653.4\n1.08 -24122.2 0 29.9825 11653.4\n1.09 -23743.2 0 30.9231 11653.4\n1.1 -23349 0 32.0586 11653.4\n1.11 -23000.1 0 33.1763 11653.4\n1.12 -22747 0 34.0897 11653.4\n1.13 -22626 0 34.6619 11653.4\n1.14 -22656.6 0 34.8154 11653.4\n1.15 -22838.5 0 34.5356 11653.4\n1.16 -23150.5 0 33.8694 11653.4\n1.17 -23550 0 32.922 11653.4\n1.18 -23973.8 0 31.8483 11653.4\n1.19 -24339.8 0 30.8363 11653.4\n1.2 -24550.2 0 30.0775 11653.4\n1.21 -24495 0 29.7246 11653.4\n1.22 -24056.8 0 29.8486 11653.4\n1.23 -23116.2 0 30.4155 11653.4\n1.24 -21557.6 0 31.2994 11653.4\n1.25 -19274.7 0 32.3219 11653.4\n1.26 -16176.8 0 33.2965 11653.4\n1.27 -12193.8 0 34.0627 11653.4\n1.28 -7281.75 0 34.5058 11653.4\n1.29 -1426.42 0 34.5652 11653.4\n1.3 5353.3 0 34.2379 11653.4\n1.31 13003.6 0 33.5775 11653.4\n1.32 21435 0 32.6893 11653.4\n1.33 30523.3 0 31.7209 11653.4\n1.34 40111.4 0 30.8441 11653.4\n1.35 50013.2 0 30.225 11653.4\n1.36 60017.9 0 29.9866 11653.4\n1.37 69896.1 0 30.1742 11653.4\n1.38 79406.9 0 30.7413 11653.4\n1.39 88304.8 0 31.5659 11653.4\n1.4 96348 0 32.4856 11653.4\n1.41 103306 0 33.3355 11653.4\n1.42 108970 0 33.9764 11653.4\n1.43 113155 0 34.312 11653.4\n1.44 115713 0 34.2965 11653.4\n1.45 116534 0 33.9373 11653.4\n1.46 115552 0 33.2933 11653.4\n1.47 112750 0 32.4696 11653.4\n1.48 108158 0 31.6062 11653.4\n1.49 101857 0 30.8589 11653.4\n1.5 93973.5 0 30.3705 11653.4\n1.51 84679 0 30.2374 11653.4\n1.52 74183.6 0 30.4828 11653.4\n1.53 62730.5 0 31.0503 11653.4\n1.54 50588.5 0 31.8217 11653.4\n1.55 38044 0 32.6485 11653.4\n1.56 25391.8 0 33.3847 11653.4\n1.57 12926.4 0 33.9104 11653.4\n1.58 932.466 0 34.1461 11653.4\n1.59 -10323.7 0 34.0596 11653.4\n1.6 -20602.4 0 33.668 11653.4\n1.61 -29697.7 0 33.0355 11653.4\n1.62 -37443.6 0 32.2668 11653.4\n1.63 -43718.3 0 31.4948 11653.4\n1.64 -48447.8 0 30.8606 11653.4\n1.65 -51607 0 30.486 11653.4\n1.66 -53219.5 0 30.444 11653.4\n1.67 -53355.7 0 30.7394 11653.4\n1.68 -52129.5 0 31.3074 11653.4\n1.69 -49693 0 32.033 11653.4\n1.7 -46230.6 0 32.7797 11653.4\n1.71 -41951.5 0 33.4173 11653.4\n1.72 -37082.2 0 33.8426 11653.4\n1.73 -31857.8 0 33.9912 11653.4\n1.74 -26513.5 0 33.8433 11653.4\n1.75 -21276.4 0 33.4249 11653.4\n1.76 -16357.9 0 32.805 11653.4\n1.77 -11945.9 0 32.0878 11653.4\n1.78 -8199.74 0 31.3994 11653.4\n1.79 -5244.58 0 30.8672 11653.4\n1.8 -3168.44 0 30.5942 11653.4\n1.81 -2020.1 0 30.6332 11653.4\n1.82 -1808.73 0 30.9733 11653.4\n1.83 -2505.02 0 31.5432 11653.4\n1.84 -4043.73 0 32.2308 11653.4\n1.85 -6327.61 0 32.9098 11653.4\n1.86 -9232.41 0 33.464 11653.4\n1.87 -12612.9 0 33.8044 11653.4\n1.88 -16309.4 0 33.8798 11653.4\n1.89 -20154.9 0 33.6813 11653.4\n1.9 -23982.3 0 33.2426 11653.4\n1.91 -27631.4 0 32.6362 11653.4\n1.92 -30955 0 31.9652 11653.4\n1.93 -33825.5 0 31.3483 11653.4\n1.94 -36139.1 0 30.9002 11653.4\n1.95 -37819.9 0 30.7067 11653.4\n1.96 -38822.6 0 30.804 11653.4\n1.97 -39133.3 0 31.1691 11653.4\n1.98 -38769.7 0 31.7268 11653.4\n1.99 -37779.1 0 32.3689 11653.4\n2 -36236.3 0 32.979 11653.4\n2.01 -34239.2 0 33.4534 11653.4\n2.02 -31903.8 0 33.7162 11653.4\n2.03 -29358.9 0 33.7281 11653.4\n2.04 -26739.8 0 33.4898 11653.4\n2.05 -24181.7 0 33.0417 11653.4\n2.06 -21813.7 0 32.4591 11653.4\n2.07 -19752.2 0 31.8427 11653.4\n2.08 -18095.5 0 31.3035 11653.4\n2.09 -16919.2 0 30.943 11653.4\n2.1 -16272 0 30.8304 11653.4\n2.11 -16173 0 30.9862 11653.4\n2.12 -16610.4 0 31.3767 11653.4\n2.13 -17541.3 0 31.9234 11653.4\n2.14 -18892.7 0 32.5224 11653.4\n2.15 -20564 0 33.0666 11653.4\n2.16 -22430.5 0 33.4642 11653.4\n2.17 -24348.5 0 33.6515 11653.4\n2.18 -26160.4 0 33.6004 11653.4\n2.19 -27701.2 0 33.3208 11653.4\n2.2 -28804.8 0 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11653.4\n16.88 3724.52 0 32.2476 11653.4\n16.89 3923.38 0 32.3243 11653.4\n16.9 4127.8 0 32.3962 11653.4\n16.91 4330.1 0 32.4506 11653.4\n16.92 4522.83 0 32.4779 11653.4\n16.93 4699.11 0 32.4733 11653.4\n16.94 4852.94 0 32.4376 11653.4\n16.95 4979.41 0 32.3772 11653.4\n16.96 5074.99 0 32.3027 11653.4\n16.97 5137.62 0 32.2275 11653.4\n16.98 5166.82 0 32.165 11653.4\n16.99 5163.7 0 32.1265 11653.4\n17 5130.92 0 32.1189 11653.4\n17.01 5072.51 0 32.1435 11653.4\n17.02 4993.77 0 32.1959 11653.4\n17.03 4900.94 0 32.2666 11653.4\n17.04 4800.96 0 32.3428 11653.4\n17.05 4701.17 0 32.4109 11653.4\n17.06 4608.91 0 32.4589 11653.4\n17.07 4531.26 0 32.4783 11653.4\n17.08 4474.64 0 32.4657 11653.4\n17.09 4444.59 0 32.4234 11653.4\n17.1 4445.46 0 32.3589 11653.4\n17.11 4480.21 0 32.2836 11653.4\n17.12 4550.3 0 32.2109 11653.4\n17.13 4655.56 0 32.1539 11653.4\n17.14 4794.25 0 32.1229 11653.4\n17.15 4963.06 0 32.1234 11653.4\n17.16 5157.31 0 32.1553 11653.4\n17.17 5371.1 0 32.2128 11653.4\n17.18 5597.56 0 32.2855 11653.4\n17.19 5829.21 0 32.3604 11653.4\n17.2 6058.21 0 32.424 11653.4\n17.21 6276.74 0 32.4652 11653.4\n17.22 6477.37 0 32.4767 11653.4\n17.23 6653.33 0 32.4564 11653.4\n17.24 6798.86 0 32.4081 11653.4\n17.25 6909.46 0 32.3403 11653.4\n17.26 6982.07 0 32.265 11653.4\n17.27 7015.24 0 32.1957 11653.4\n17.28 7009.22 0 32.1448 11653.4\n17.29 6965.88 0 32.1215 11653.4\n17.3 6888.73 0 32.1299 11653.4\n17.31 6782.71 0 32.1686 11653.4\n17.32 6654.01 0 32.2305 11653.4\n17.33 6509.79 0 32.3044 11653.4\n17.34 6357.86 0 32.3771 11653.4\n17.35 6206.37 0 32.4355 11653.4\n17.36 6063.4 0 32.4695 11653.4\n17.37 5936.64 0 32.4731 11653.4\n17.38 5833.03 0 32.4455 11653.4\n17.39 5758.45 0 32.3918 11653.4\n17.4 5717.45 0 32.3215 11653.4\n17.41 5713.02 0 32.2471 11653.4\n17.42 5746.44 0 32.1818 11653.4\n17.43 5817.25 0 32.1375 11653.4\n17.44 5923.2 0 32.1221 11653.4\n17.45 6060.34 0 32.1384 11653.4\n17.46 6223.18 0 32.1834 11653.4\n17.47 6404.92 0 32.2489 11653.4\n17.48 6597.72 0 32.3231 11653.4\n17.49 6793 0 32.3928 11653.4\n17.5 6981.85 0 32.4456 11653.4\n17.51 7155.4 0 32.4721 11653.4\n17.52 7305.13 0 32.4678 11653.4\n17.53 7423.35 0 32.4333 11653.4\n17.54 7503.45 0 32.3749 11653.4\n17.55 7540.2 0 32.3029 11653.4\n17.56 7530.04 0 32.2301 11653.4\n17.57 7471.15 0 32.1696 11653.4\n17.58 7363.65 0 32.1322 11653.4\n17.59 7209.5 0 32.1246 11653.4\n17.6 7012.5 0 32.1483 11653.4\n17.61 6778.14 0 32.1989 11653.4\n17.62 6513.31 0 32.2672 11653.4\n17.63 6226.12 0 32.341 11653.4\n17.64 5925.47 0 32.407 11653.4\n17.65 5620.74 0 32.4536 11653.4\n17.66 5321.38 0 32.4726 11653.4\n17.67 5036.49 0 32.4606 11653.4\n17.68 4774.49 0 32.4199 11653.4\n17.69 4542.73 0 32.3576 11653.4\n17.7 4347.18 0 32.2848 11653.4\n17.71 4192.2 0 32.2145 11653.4\n17.72 4080.32 0 32.1593 11653.4\n17.73 4012.21 0 32.1291 11653.4\n17.74 3986.57 0 32.1294 11653.4\n17.75 4000.26 0 32.1601 11653.4\n17.76 4048.38 0 32.2155 11653.4\n17.77 4124.56 0 32.2857 11653.4\n17.78 4221.17 0 32.358 11653.4\n17.79 4329.7 0 32.4195 11653.4\n17.8 4441.1 0 32.4594 11653.4\n17.81 4546.23 0 32.4706 11653.4\n17.82 4636.2 0 32.4513 11653.4\n17.83 4702.82 0 32.4048 11653.4\n17.84 4738.91 0 32.3394 11653.4\n17.85 4738.67 0 32.2667 11653.4\n17.86 4697.91 0 32.1998 11653.4\n17.87 4614.25 0 32.1506 11653.4\n17.88 4487.23 0 32.128 11653.4\n17.89 4318.34 0 32.1361 11653.4\n17.9 4110.96 0 32.1734 11653.4\n17.91 3870.24 0 32.2331 11653.4\n17.92 3602.85 0 32.3043 11653.4\n17.93 3316.7 0 32.3744 11653.4\n17.94 3020.63 0 32.4309 11653.4\n17.95 2723.97 0 32.4637 11653.4\n17.96 2436.18 0 32.4671 11653.4\n17.97 2166.41 0 32.4406 11653.4\n17.98 1923.05 0 32.3888 11653.4\n17.99 1713.45 0 32.321 11653.4\n18 1543.49 0 32.2492 11653.4\n18.01 1417.33 0 32.1863 11653.4\n18.02 1337.24 0 32.1436 11653.4\n18.03 1303.42 0 32.1288 11653.4\n18.04 1314.04 0 32.1445 11653.4\n18.05 1365.2 0 32.188 11653.4\n18.06 1451.16 0 32.2512 11653.4\n18.07 1564.51 0 32.3229 11653.4\n18.08 1696.51 0 32.3901 11653.4\n18.09 1837.41 0 32.4409 11653.4\n18.1 1976.88 0 32.4665 11653.4\n18.11 2104.46 0 32.4622 11653.4\n18.12 2209.97 0 32.4288 11653.4\n18.13 2284.02 0 32.3724 11653.4\n18.14 2318.33 0 32.3028 11653.4\n18.15 2306.2 0 32.2326 11653.4\n18.16 2242.75 0 32.1742 11653.4\n18.17 2125.18 0 32.1382 11653.4\n18.18 1952.94 0 32.1311 11653.4\n18.19 1727.77 0 32.1542 11653.4\n18.2 1453.66 0 32.2032 11653.4\n18.21 1136.76 0 32.2692 11653.4\n18.22 785.087 0 32.3405 11653.4\n18.23 408.306 0 32.4042 11653.4\n18.24 17.3 0 32.4491 11653.4\n18.25 -376.231 0 32.4673 11653.4\n18.26 -760.244 0 32.4555 11653.4\n18.27 -1122.84 0 32.4159 11653.4\n18.28 -1452.72 0 32.3556 11653.4\n18.29 -1739.72 0 32.2851 11653.4\n18.3 -1975.13 0 32.2172 11653.4\n18.31 -2152.17 0 32.1639 11653.4\n18.32 -2266.2 0 32.1349 11653.4\n18.33 -2314.98 0 32.1354 11653.4\n18.34 -2298.75 0 32.1652 11653.4\n18.35 -2220.3 0 32.219 11653.4\n18.36 -2084.82 0 32.287 11653.4\n18.37 -1899.76 0 32.3571 11653.4\n18.38 -1674.56 0 32.4166 11653.4\n18.39 -1420.26 0 32.4552 11653.4\n18.4 -1149.12 0 32.4659 11653.4\n18.41 -874.14 0 32.447 11653.4\n18.42 -608.556 0 32.4017 11653.4\n18.43 -365.325 0 32.3382 11653.4\n18.44 -156.631 0 32.2677 11653.4\n18.45 6.5947 0 32.2027 11653.4\n18.46 115.092 0 32.155 11653.4\n18.47 161.637 0 32.1331 11653.4\n18.48 141.321 0 32.141 11653.4\n18.49 51.7431 0 32.1772 11653.4\n18.5 -106.9 0 32.2351 11653.4\n18.51 -331.821 0 32.3043 11653.4\n18.52 -617.751 0 32.3723 11653.4\n18.53 -957.147 0 32.4272 11653.4\n18.54 -1340.49 0 32.4592 11653.4\n18.55 -1756.63 0 32.4626 11653.4\n18.56 -2193.27 0 32.437 11653.4\n18.57 -2637.39 0 32.3869 11653.4\n18.58 -3075.76 0 32.3212 11653.4\n18.59 -3495.46 0 32.2515 11653.4\n18.6 -3884.37 0 32.1903 11653.4\n18.61 -4231.6 0 32.1487 11653.4\n18.62 -4527.93 0 32.134 11653.4\n18.63 -4766.13 0 32.149 11653.4\n18.64 -4941.21 0 32.1908 11653.4\n18.65 -5050.61 0 32.2518 11653.4\n18.66 -5094.26 0 32.3211 11653.4\n18.67 -5074.55 0 32.3862 11653.4\n18.68 -4996.22 0 32.4357 11653.4\n18.69 -4866.15 0 32.4606 11653.4\n18.7 -4693.06 0 32.4567 11653.4\n18.71 -4487.17 0 32.4248 11653.4\n18.72 -4259.77 0 32.3704 11653.4\n18.73 -4022.79 0 32.3033 11653.4\n18.74 -3788.29 0 32.2355 11653.4\n18.75 -3568.06 0 32.1789 11653.4\n18.76 -3373.12 0 32.144 11653.4\n18.77 -3213.32 0 32.1369 11653.4\n18.78 -3097.01 0 32.1588 11653.4\n18.79 -3030.69 0 32.2058 11653.4\n18.8 -3018.83 0 32.2694 11653.4\n18.81 -3063.72 0 32.3381 11653.4\n18.82 -3165.45 0 32.3996 11653.4\n18.83 -3321.89 0 32.443 11653.4\n18.84 -3528.87 0 32.4607 11653.4\n18.85 -3780.35 0 32.4496 11653.4\n18.86 -4068.7 0 32.4116 11653.4\n18.87 -4385.04 0 32.3535 11653.4\n18.88 -4719.58 0 32.2857 11653.4\n18.89 -5062.05 0 32.2202 11653.4\n18.9 -5402.09 0 32.1688 11653.4\n18.91 -5729.65 0 32.1408 11653.4\n18.92 -6035.4 0 32.1412 11653.4\n18.93 -6311.02 0 32.1698 11653.4\n18.94 -6549.56 0 32.2215 11653.4\n18.95 -6745.62 0 32.2869 11653.4\n18.96 -6895.57 0 32.3543 11653.4\n18.97 -6997.59 0 32.4115 11653.4\n18.98 -7051.75 0 32.4486 11653.4\n18.99 -7059.89 0 32.459 11653.4\n19 -7025.57 0 32.4408 11653.4\n19.01 -6953.81 0 32.3973 11653.4\n19.02 -6850.9 0 32.3362 11653.4\n19.03 -6724.11 0 32.2685 11653.4\n19.04 -6581.35 0 32.2062 11653.4\n19.05 -6430.86 0 32.1605 11653.4\n19.06 -6280.88 0 32.1397 11653.4\n19.07 -6139.3 0 32.1474 11653.4\n19.08 -6013.41 0 32.1823 11653.4\n19.09 -5909.57 0 32.238 11653.4\n19.1 -5833.05 0 32.3045 11653.4\n19.11 -5787.81 0 32.3698 11653.4\n19.12 -5776.44 0 32.4223 11653.4\n19.13 -5800.06 0 32.4527 11653.4\n19.14 -5858.34 0 32.4556 11653.4\n19.15 -5949.59 0 32.4306 11653.4\n19.16 -6070.85 0 32.3822 11653.4\n19.17 -6218.05 0 32.3188 11653.4\n19.18 -6386.23 0 32.2518 11653.4\n19.19 -6569.75 0 32.1932 11653.4\n19.2 -6762.56 0 32.1536 11653.4\n19.21 -6958.4 0 32.14 11653.4\n19.22 -7151.1 0 32.155 11653.4\n19.23 -7334.79 0 32.1957 11653.4\n19.24 -7504.11 0 32.2548 11653.4\n19.25 -7654.38 0 32.3217 11653.4\n19.26 -7781.76 0 32.3843 11653.4\n19.27 -7883.34 0 32.4316 11653.4\n19.28 -7957.17 0 32.4551 11653.4\n19.29 -8002.34 0 32.4508 11653.4\n19.3 -8018.88 0 32.4194 11653.4\n19.31 -8007.73 0 32.3666 11653.4\n19.32 -7970.65 0 32.3016 11653.4\n19.33 -7910.05 0 32.2361 11653.4\n19.34 -7828.9 0 32.1818 11653.4\n19.35 -7730.54 0 32.1485 11653.4\n19.36 -7618.5 0 32.1423 11653.4\n19.37 -7496.39 0 32.1641 11653.4\n19.38 -7367.73 0 32.21 11653.4\n19.39 -7235.81 0 32.2718 11653.4\n19.4 -7103.58 0 32.3383 11653.4\n19.41 -6973.61 0 32.3976 11653.4\n19.42 -6847.96 0 32.4392 11653.4\n19.43 -6728.22 0 32.4557 11653.4\n19.44 -6615.48 0 32.4444 11653.4\n19.45 -6510.36 0 32.407 11653.4\n19.46 -6413.05 0 32.3505 11653.4\n19.47 -6323.38 0 32.2846 11653.4\n19.48 -6240.9 0 32.2213 11653.4\n19.49 -6164.97 0 32.1719 11653.4\n19.5 -6094.82 0 32.1452 11653.4\n19.51 -6029.64 0 32.1461 11653.4\n19.52 -5968.68 0 32.1745 11653.4\n19.53 -5911.26 0 32.225 11653.4\n19.54 -5856.84 0 32.2887 11653.4\n19.55 -5805.05 0 32.3541 11653.4\n19.56 -5755.67 0 32.4095 11653.4\n19.57 -5708.63 0 32.4451 11653.4\n19.58 -5663.99 0 32.4547 11653.4\n19.59 -5621.85 0 32.4365 11653.4\n19.6 -5582.34 0 32.3939 11653.4\n19.61 -5545.55 0 32.3343 11653.4\n19.62 -5511.44 0 32.2684 11653.4\n19.63 -5479.79 0 32.2079 11653.4\n19.64 -5450.16 0 32.1637 11653.4\n19.65 -5421.84 0 32.1438 11653.4\n19.66 -5393.8 0 32.1517 11653.4\n19.67 -5364.75 0 32.186 11653.4\n19.68 -5333.07 0 32.2404 11653.4\n19.69 -5296.92 0 32.3052 11653.4\n19.7 -5254.27 0 32.3687 11653.4\n19.71 -5202.97 0 32.4196 11653.4\n19.72 -5140.85 0 32.4489 11653.4\n19.73 -5065.84 0 32.4515 11653.4\n19.74 -4976.03 0 32.427 11653.4\n19.75 -4869.85 0 32.3796 11653.4\n19.76 -4746.15 0 32.3179 11653.4\n19.77 -4604.26 0 32.2528 11653.4\n19.78 -4444.13 0 32.1959 11653.4\n19.79 -4266.32 0 32.1575 11653.4\n19.8 -4072.09 0 32.1446 11653.4\n19.81 -3863.38 0 32.1593 11653.4\n19.82 -3642.76 0 32.1991 11653.4\n19.83 -3413.38 0 32.2566 11653.4\n19.84 -3178.89 0 32.3216 11653.4\n19.85 -2943.31 0 32.3824 11653.4\n19.86 -2710.89 0 32.4282 11653.4\n19.87 -2485.95 0 32.4509 11653.4\n19.88 -2272.7 0 32.4465 11653.4\n19.89 -2075.1 0 32.4158 11653.4\n19.9 -1896.62 0 32.3643 11653.4\n19.91 -1740.17 0 32.3011 11653.4\n19.92 -1607.88 0 32.2375 11653.4\n19.93 -1501.07 0 32.1849 11653.4\n19.94 -1420.09 0 32.1527 11653.4\n19.95 -1364.33 0 32.1469 11653.4\n19.96 -1332.23 0 32.1683 11653.4\n19.97 -1321.27 0 32.2131 11653.4\n19.98 -1328.11 0 32.2732 11653.4\n19.99 -1348.67 0 32.3378 11653.4\n##### Results\nextraction_type='extract'\n### ModelCluster\npeak_funcs=[0]\nModelEvaluator=AIC\nslice=slice(None, 43, None)\n# BaselineObject\nowner=0\npars=[]\nfree=[]\nremovable=False\nstatic_owner=False\n\n## ModelPeaks\n# ModelPeak\nowner=1\npars=[1.4409645574666863, -1.2021756542216779, 35834.779473125469]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[2.438834586729778, -0.96289415777140697, 76731.43020027288]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[2.8449631419404557, -1.377022811246666, 20948.656697077673]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[3.6144870375166058, -0.96713516256064158, 74286.823948562524]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[4.1107321734767162, -0.98410710936823842, 56269.955304768802]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[4.5494140399501193, -0.9756431127837496, 81698.18210463904]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[4.8398410449548992, -1.4491665751304479, 21235.583150621042]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[5.4143786805580305, -1.1127424167906164, 63603.398981811821]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[5.9241758314319366, 1.5695897461410588, 195215.74804049844]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n# ModelPeak\nowner=1\npars=[6.7383992196340667, 0.05697362691040269, 168818.12286746191]\nfree=[True, True, True]\nremovable=True\nstatic_owner=False\n\n### start data\n#L r y dy\n1 -19502.9 11653.4\n1.14749 -22788.9 11653.4\n1.29499 1852.19 11653.4\n1.44248 116074 11653.4\n1.58997 -10291.9 11653.4\n1.73746 -27861.6 11653.4\n1.88496 -18215.1 11653.4\n2.03245 -28714 11653.4\n2.17994 -26150.2 11653.4\n2.32743 34592.3 11653.4\n2.47493 94708.1 11653.4\n2.62242 -34046.8 11653.4\n2.76991 -6095.59 11653.4\n2.9174 -9022.01 11653.4\n3.0649 -47692.9 11653.4\n3.21239 -39823.5 11653.4\n3.35988 -45615.1 11653.4\n3.50737 13411.8 11653.4\n3.65487 42196.6 11653.4\n3.80236 -28611.3 11653.4\n3.94985 -21093.7 11653.4\n4.09735 22420.5 11653.4\n4.24484 -12021.5 11653.4\n4.39233 -17934.3 11653.4\n4.53982 45713.7 11653.4\n4.68732 -9106.12 11653.4\n4.83481 459.793 11653.4\n4.9823 -30024.4 11653.4\n5.12979 -6029.52 11653.4\n5.27729 -3788.41 11653.4\n5.42478 38601.6 11653.4\n5.57227 5401.92 11653.4\n5.71976 12241.1 11653.4\n5.86726 6715.96 11653.4\n6.01475 11253.1 11653.4\n6.16224 26161.1 11653.4\n6.30973 -15451.2 11653.4\n6.45723 -45.4651 11653.4\n6.60472 29243.8 11653.4\n6.75221 20789.5 11653.4\n6.8997 3686.4 11653.4\n7.0472 6321.19 11653.4\n7.19469 -14234.2 11653.4\n\n" p1340 -a. \ No newline at end of file +a. diff --git a/doc/examples/parameter_summary.py b/doc/examples/parameter_summary.py index 75ff502..2ba1ac1 100644 --- a/doc/examples/parameter_summary.py +++ b/doc/examples/parameter_summary.py @@ -30,16 +30,17 @@ import matplotlib.pyplot as plt from diffpy.srmise import PDFPeakExtraction +from diffpy.srmise.applications.plot import makeplot from diffpy.srmise.baselines import Polynomial from diffpy.srmise.peaks import GaussianOverR -from diffpy.srmise.applications.plot import makeplot + def run(plot=True): - + ## Initialize peak extraction # Create peak extraction object ppe = PDFPeakExtraction() - + # Load the PDF from a file ppe.loadpdf("data/TiO2_fine_qmax26.gr") @@ -48,12 +49,12 @@ def run(plot=True): # diffpy.srmise strives to provide reasonable default values for these # parameters. For normal use setting the range, baseline, and uncertainty # should be sufficient. - kwds = {} - + kwds = {} + ## Range # Range defaults to the entire PDF if not specified. - kwds["rng"] = [1.5, 10.] - + kwds["rng"] = [1.5, 10.0] + ## dg # diffpy.srmise selects model complexity based primarily on the uncertainty # of the PDF. Note that very small uncertainties (<1%) can make peak @@ -87,10 +88,9 @@ def run(plot=True): # rho0 is the number density. Nevertheless, imperfect normalization of the # PDF means the experimental baseline is proportional to that value. blfunc = Polynomial(degree=1) - slope = -.65 # Play with this value! - y_intercept = 0. - kwds["baseline"] = blfunc.actualize([slope, y_intercept], - free=[True, False]) + slope = -0.65 # Play with this value! + y_intercept = 0.0 + kwds["baseline"] = blfunc.actualize([slope, y_intercept], free=[True, False]) ## pf # The pf (peakfunction) parameter allows setting the shape of peaks to be # extracted. Termination effects are added automatically to the peak @@ -107,7 +107,7 @@ def run(plot=True): # are strong signs that diffpy.srmise is having difficulty finding peaks # which are sufficiently constrained by the data. pf = GaussianOverR(0.7) - kwds["pf"] = [pf] # Despite the list, only one entry is currently supported. + kwds["pf"] = [pf] # Despite the list, only one entry is currently supported. ## qmax # PDFs typically report the value of qmax (i.e. the maximum momentum @@ -117,7 +117,7 @@ def run(plot=True): # to "automatic". An infinite qmax can be specified by setting qmax to 0, # In that case the Nyquist rate is 0 (infinite resolution), and # diffpy.srmise does not consider Nyquist sampling or termination effects. - kwds["qmax"] = 26.0 + kwds["qmax"] = 26.0 ## nyquist # This parameter governs whether diffpy.srmise attempts to find a model @@ -131,7 +131,7 @@ def run(plot=True): # [4] Farrow et al. (2011). Physical Review B, 84(13), 134105. # doi:10.1103/PhysRevB.84.134105 kwds["nyquist"] = True - + ## supersample # This parameter dictates the data be oversampled by at least this factor # (relative to the Nyquist rate) during the early stages of peak @@ -140,7 +140,7 @@ def run(plot=True): # been empirically sufficient. Increasing this value may help the peak- # finding and clustering process, but reduces speed. kwds["supersample"] = 4.0 - + ## cres # The cres (clustering resolution) parameter governs the sensitivity of the # clustering method used by diffpy.srmise. In short, when the data are @@ -152,7 +152,7 @@ def run(plot=True): # help the peak-finding process. Here it is roughly half the Nyquist # interval. kwds["cres"] = 0.05 - + # Apply peak extraction parameters. ppe.setvars(**kwds) @@ -175,7 +175,7 @@ def run(plot=True): # existing initial peaks into account during estimation. positions = [2.0, 4.5] for p in positions: - ppe.estimate_peak(p) # adds to initial_peaks + ppe.estimate_peak(p) # adds to initial_peaks ## Initial peaks from explicit parameters. # Adding initial peaks explicitly is similar to defining a baseline. @@ -188,11 +188,11 @@ def run(plot=True): # internal parameterization. Here two peaks are added in a region of # overlap, and the width parameter is fixed at a reasonable value to aid # convergence in this region. - pars = [[6.2, 0.25, 2.6],[6.45, 0.25, 2.7],[7.15, 0.25, 5]] + pars = [[6.2, 0.25, 2.6], [6.45, 0.25, 2.7], [7.15, 0.25, 5]] peaks = [] for p in pars: peaks.append(pf.actualize(p, free=[True, False, True], in_format="pwa")) - ppe.add_peaks(peaks) # adds to initial_peaks + ppe.add_peaks(peaks) # adds to initial_peaks ## Initial peaks and pruning # While initial peaks condition what other peaks can be extracted, by @@ -206,11 +206,9 @@ def run(plot=True): makeplot(ppe) plt.title("Initial Peaks") - ###### Perform peak extraction ppe.extract() - ## Save output # The write() method saves a file which preserves all aspects of peak # extraction and its results, by convention using the .srmise extension, @@ -233,5 +231,6 @@ def run(plot=True): makeplot(ppe) plt.show() -if __name__ == '__main__': + +if __name__ == "__main__": run() diff --git a/doc/examples/query_results.py b/doc/examples/query_results.py index 105fb14..c861ee5 100644 --- a/doc/examples/query_results.py +++ b/doc/examples/query_results.py @@ -26,22 +26,22 @@ at the command line. """ -import numpy as np import matplotlib.pyplot as plt +import numpy as np -from diffpy.srmise import PDFPeakExtraction -from diffpy.srmise import ModelCovariance +from diffpy.srmise import ModelCovariance, PDFPeakExtraction from diffpy.srmise.applications.plot import makeplot + def run(plot=True): - + ## Initialize peak extraction # Create peak extraction object ppe = PDFPeakExtraction() - + # Load the PDF from a file ppe.loadpdf("data/Ag_nyquist_qmax30.gr") - + # Obtain baseline from a saved diffpy.srmise trial. This is not the # initial baseline estimate from the previous example, but the baseline # after both it and the extracted peaks have been fit to the data. @@ -52,17 +52,17 @@ def run(plot=True): ## Set up extraction parameters. # Peaks are extracted between 2 and 10 angstroms, using the baseline # from the isolated peak example. - kwds = {} + kwds = {} kwds["rng"] = [2.0, 10.] kwds["baseline"] = baseline - + # Apply peak extraction parameters. ppe.setvars(**kwds) ## Perform peak extraction, and retain object containing a copy of the # model and the full covariance matrix. cov = ppe.extract() - + print "\n======= Accessing SrMise Results ========" ## Accessing results of extraction @@ -89,7 +89,7 @@ def run(plot=True): # above is the area (index = 2) of the next nearest neighbor (index = 1) # peak. Thus, this parameter can be referenced as (1,2). Several examples # are presented below. - + print "\n------ Parameter values and uncertainties ------" # ModelCovariance.get() returns a (value, uncertainty) tuple for a given @@ -175,7 +175,7 @@ def run(plot=True): # Reference for number of atoms in coordination shells for FCC. # http://chem-faculty.lsu.edu/watkins/MERLOT/cubic_neighbors/cubic_near_neighbors.html ideal_intensity = [12, 6, 24, 12, 24, 8, 48, 6, 36, 24, 24, 24] - + # Calculated the scaled intensities and uncertainties. intensity = [] for i in range(0, len(cov.model)-1): @@ -183,7 +183,7 @@ def run(plot=True): area *= scale darea = area*np.sqrt((dscale/scale)**2 + (darea/area)**2) intensity.append((ideal_intensity[i], area, darea)) - + print "\nIntensity" print "Ideal: Estimated" for i in intensity: diff --git a/doc/manual/source/conf.py b/doc/manual/source/conf.py index 367034b..965010c 100644 --- a/doc/manual/source/conf.py +++ b/doc/manual/source/conf.py @@ -12,237 +12,241 @@ # All configuration values have a default; values that are commented out # serve to show the default. -import sys, os +import os +import sys import time # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. -#sys.path.insert(0, os.path.abspath('.')) -#sys.path.insert(0, os.path.abspath('../../..')) +# sys.path.insert(0, os.path.abspath('.')) +# sys.path.insert(0, os.path.abspath('../../..')) # abbreviations -ab_authors = u'Luke Granlund' +ab_authors = "Luke Granlund" # -- General configuration ----------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' +# needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ['sphinx.ext.ifconfig', 'sphinx.ext.autodoc', - 'sphinx.ext.intersphinx', 'sphinx.ext.extlinks'] +extensions = [ + "sphinx.ext.ifconfig", + "sphinx.ext.autodoc", + "sphinx.ext.intersphinx", + "sphinx.ext.extlinks", +] # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # The suffix of source filenames. -source_suffix = '.rst' +source_suffix = ".rst" # The encoding of source files. -#source_encoding = 'utf-8-sig' +# source_encoding = 'utf-8-sig' # The master toctree document. -master_doc = 'index' +master_doc = "index" # General information about the project. -project = u'SrMise' -copyright = u'%Y, Board of Trustees of Michigan State University' +project = "SrMise" +copyright = "%Y, Board of Trustees of Michigan State University" # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. -sys.path.insert(0, os.path.abspath('../../..')) +sys.path.insert(0, os.path.abspath("../../..")) from setup import versiondata -fullversion = versiondata.get('DEFAULT', 'version') + +fullversion = versiondata.get("DEFAULT", "version") # The short X.Y version. -version = '.'.join(fullversion.split('.')[:2]) +version = ".".join(fullversion.split(".")[:2]) # The full version, including alpha/beta/rc tags. release = fullversion # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. -#language = None +# language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: -#today = '' -today_seconds = versiondata.getint('DEFAULT', 'timestamp') -today = time.strftime('%B %d, %Y', time.localtime(today_seconds)) +# today = '' +today_seconds = versiondata.getint("DEFAULT", "timestamp") +today = time.strftime("%B %d, %Y", time.localtime(today_seconds)) year = today.split()[-1] # Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' +# today_fmt = '%B %d, %Y' # substitute YEAR in the copyright string -copyright = copyright.replace('%Y', year) +copyright = copyright.replace("%Y", year) # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. exclude_patterns = [] # The reST default role (used for this markup: `text`) to use for all documents. -#default_role = None +# default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True +# add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). -#add_module_names = True +# add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. -#show_authors = False +# show_authors = False # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = "sphinx" # A list of ignored prefixes for module index sorting. -modindex_common_prefix = ['diffpy.srmise.'] +modindex_common_prefix = ["diffpy.srmise."] # Display all warnings for missing links. nitpicky = True # Define :source-release:`zip` and :source-release:`tar.gz` to point to the # GitHub source archive corresponding to the most recent release. -lasttag = release.split("-")[0] # Drop post-release git version increment. -extlinks = {'source-release': \ - ('https://github.com/diffpy/diffpy.srmise/archive/v%s' %lasttag + '.%s','')} +lasttag = release.split("-")[0] # Drop post-release git version increment. +extlinks = { + "source-release": ( + "https://github.com/diffpy/diffpy.srmise/archive/v%s" % lasttag + ".%s", + "", + ) +} # -- Options for HTML output --------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -#html_theme = 'classic' -html_theme = 'nature' +# html_theme = 'classic' +html_theme = "nature" # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. -#html_theme_options = {'collapsiblesidebar' : 'true'} #classic -html_theme_options = {} # nature +# html_theme_options = {'collapsiblesidebar' : 'true'} #classic +html_theme_options = {} # nature # Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] +# html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". -#html_title = None +# html_title = None # A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None +# html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. -#html_logo = None +# html_logo = None # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. -#html_favicon = None +# html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -#html_static_path = ['_static'] +# html_static_path = ['_static'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' +# html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. -#html_use_smartypants = True +# html_use_smartypants = True # Custom sidebar templates, maps document names to template names. -#html_sidebars = {} +# html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. -#html_additional_pages = {} +# html_additional_pages = {} # If false, no module index is generated. -#html_domain_indices = True +# html_domain_indices = True # If false, no index is generated. -#html_use_index = True +# html_use_index = True # If true, the index is split into individual pages for each letter. html_split_index = True # If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True +# html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -#html_show_sphinx = True +# html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True +# html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. -#html_use_opensearch = '' +# html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None +# html_file_suffix = None # Output file base name for HTML help builder. -htmlhelp_basename = 'SrMisedoc' +htmlhelp_basename = "SrMisedoc" # -- Options for LaTeX output -------------------------------------------------- latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', + # The paper size ('letterpaper' or 'a4paper'). + #'papersize': 'letterpaper', + # The font size ('10pt', '11pt' or '12pt'). + #'pointsize': '10pt', + # Additional stuff for the LaTeX preamble. + #'preamble': '', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('index', 'SrMise_manual.tex', u'SrMise Documentation', - ab_authors, 'manual'), + ("index", "SrMise_manual.tex", "SrMise Documentation", ab_authors, "manual"), ] # The name of an image file (relative to this directory) to place at the top of # the title page. -#latex_logo = None +# latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. -#latex_use_parts = False +# latex_use_parts = False # If true, show page references after internal links. -#latex_show_pagerefs = False +# latex_show_pagerefs = False # If true, show URL addresses after external links. -#latex_show_urls = False +# latex_show_urls = False # Documents to append as an appendix to all manuals. -#latex_appendices = [] +# latex_appendices = [] # If false, no module index is generated. -#latex_domain_indices = True +# latex_domain_indices = True # -- Options for manual page output -------------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'srmise', u'SrMise Documentation', - ab_authors, 1) -] +man_pages = [("index", "srmise", "SrMise Documentation", ab_authors, 1)] # If true, show URL addresses after external links. -#man_show_urls = False +# man_show_urls = False # -- Options for Texinfo output ------------------------------------------------ @@ -251,19 +255,25 @@ # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - ('index', 'SrMise', u'SrMise Documentation', - ab_authors, 'SrMise', 'One line description of project.', - 'Miscellaneous'), + ( + "index", + "SrMise", + "SrMise Documentation", + ab_authors, + "SrMise", + "One line description of project.", + "Miscellaneous", + ), ] # Documents to append as an appendix to all manuals. -#texinfo_appendices = [] +# texinfo_appendices = [] # If false, no module index is generated. -#texinfo_domain_indices = True +# texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' +# texinfo_show_urls = 'footnote' # Example configuration for intersphinx: refer to the Python standard library. diff --git a/doc/manual/source/extending.rst b/doc/manual/source/extending.rst index 9404c31..202c6cf 100644 --- a/doc/manual/source/extending.rst +++ b/doc/manual/source/extending.rst @@ -144,4 +144,3 @@ following differences: :type scale: `float` :returns: The adjusted peak parameters. :rtype: `numpy.ndarray(float)`. - diff --git a/doc/manual/source/tutorial/index.rst b/doc/manual/source/tutorial/index.rst index bfb9ea1..ec7f646 100644 --- a/doc/manual/source/tutorial/index.rst +++ b/doc/manual/source/tutorial/index.rst @@ -31,5 +31,3 @@ Examples .. include:: ../../../examples/README :start-after: ~PDF Info~ - - diff --git a/setup.py b/setup.py index 0d48217..e0e9b14 100755 --- a/setup.py +++ b/setup.py @@ -8,96 +8,101 @@ """ import os -from setuptools import setup, find_packages + +from setuptools import find_packages, setup # versioncfgfile holds version data for git commit hash and date. # It must reside in the same directory as version.py. MYDIR = os.path.dirname(os.path.abspath(__file__)) -versioncfgfile = os.path.join(MYDIR, 'diffpy/srmise/version.cfg') +versioncfgfile = os.path.join(MYDIR, "diffpy/srmise/version.cfg") + def gitinfo(): - from subprocess import Popen, PIPE + from subprocess import PIPE, Popen + kw = dict(stdout=PIPE, cwd=MYDIR) - proc = Popen(['git', 'describe', '--match=v[[:digit:]]*'], **kw) + proc = Popen(["git", "describe", "--match=v[[:digit:]]*"], **kw) desc = proc.stdout.read() - proc = Popen(['git', 'log', '-1', '--format=%H %at %ai'], **kw) + proc = Popen(["git", "log", "-1", "--format=%H %at %ai"], **kw) glog = proc.stdout.read() rv = {} - rv['version'] = '-'.join(desc.strip().split('-')[:2]).lstrip('v') - rv['commit'], rv['timestamp'], rv['date'] = glog.strip().split(None, 2) + rv["version"] = "-".join(desc.strip().split("-")[:2]).lstrip("v") + rv["commit"], rv["timestamp"], rv["date"] = glog.strip().split(None, 2) return rv def getversioncfg(): from ConfigParser import SafeConfigParser + cp = SafeConfigParser() cp.read(versioncfgfile) - gitdir = os.path.join(MYDIR, '.git') - if not os.path.isdir(gitdir): return cp + gitdir = os.path.join(MYDIR, ".git") + if not os.path.isdir(gitdir): + return cp try: g = gitinfo() except OSError: return cp d = cp.defaults() - if g['version'] != d.get('version') or g['commit'] != d.get('commit'): - cp.set('DEFAULT', 'version', g['version']) - cp.set('DEFAULT', 'commit', g['commit']) - cp.set('DEFAULT', 'date', g['date']) - cp.set('DEFAULT', 'timestamp', g['timestamp']) - cp.write(open(versioncfgfile, 'w')) + if g["version"] != d.get("version") or g["commit"] != d.get("commit"): + cp.set("DEFAULT", "version", g["version"]) + cp.set("DEFAULT", "commit", g["commit"]) + cp.set("DEFAULT", "date", g["date"]) + cp.set("DEFAULT", "timestamp", g["timestamp"]) + cp.write(open(versioncfgfile, "w")) return cp + versiondata = getversioncfg() # define distribution, but make this module importable setup_args = dict( - name = "diffpy.srmise", - version = versiondata.get('DEFAULT', 'version'), - namespace_packages = ['diffpy'], - packages = find_packages(), - include_package_data = True, - zip_safe = False, - + name="diffpy.srmise", + version=versiondata.get("DEFAULT", "version"), + namespace_packages=["diffpy"], + packages=find_packages(), + include_package_data=True, + zip_safe=False, # Dependencies # numpy # scipy # matplotlib >= 1.1.0 - install_requires = ['matplotlib >= 1.1.0', 'numpy', 'scipy'], - + install_requires=["matplotlib >= 1.1.0", "numpy", "scipy"], # other arguments here... - entry_points = { - 'console_scripts' : [ - 'srmise = diffpy.srmise.applications.extract:main', - 'srmiseplot = diffpy.srmise.applications.plot:main', - ] + entry_points={ + "console_scripts": [ + "srmise = diffpy.srmise.applications.extract:main", + "srmiseplot = diffpy.srmise.applications.plot:main", + ] }, - - author = "Luke Granlund", - author_email = "luke.r.granlund@gmail.com", - description = ("Peak extraction and peak fitting tool for atomic " - "pair distribution functions."), - license = 'BSD-style license', - url = "https://github.com/diffpy/diffpy.srmise/", - keywords = "peak extraction fitting PDF AIC multimodeling", - classifiers = [ + author="Luke Granlund", + author_email="luke.r.granlund@gmail.com", + description=( + "Peak extraction and peak fitting tool for atomic " + "pair distribution functions." + ), + license="BSD-style license", + url="https://github.com/diffpy/diffpy.srmise/", + keywords="peak extraction fitting PDF AIC multimodeling", + classifiers=[ # List of possible values at # http://pypi.python.org/pypi?:action=list_classifiers - 'Development Status :: 3 - Alpha', - 'Environment :: Console', - 'Intended Audience :: Developers', - 'Intended Audience :: Education', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: BSD License', - 'Operating System :: MacOS', - 'Operating System :: POSIX', - 'Operating System :: Microsoft :: Windows', - 'Programming Language :: Python :: 2.6', - 'Programming Language :: Python :: 2.7', - 'Topic :: Scientific/Engineering :: Chemistry', - 'Topic :: Scientific/Engineering :: Physics', - 'Topic :: Software Development :: Libraries', + "Development Status :: 3 - Alpha", + "Environment :: Console", + "Intended Audience :: Developers", + "Intended Audience :: Education", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: BSD License", + "Operating System :: MacOS", + "Operating System :: POSIX", + "Operating System :: Microsoft :: Windows", + "Programming Language :: Python :: 2.6", + "Programming Language :: Python :: 2.7", + "Topic :: Scientific/Engineering :: Chemistry", + "Topic :: Scientific/Engineering :: Physics", + "Topic :: Software Development :: Libraries", ], ) -if __name__ == '__main__': +if __name__ == "__main__": setup(**setup_args)