Index

_

_jacobian_raw() _jacobianraw (diffpy.srmise.basefunction.BaseFunction attribute) _transform_derivatives (diffpy.srmise.basefunction.BaseFunction attribute) _transform_derivativesraw()

_transform_parametersraw (diffpy.srmise.basefunction.BaseFunction attribute) _transform_parametersraw() _valueraw (diffpy.srmise.basefunction.BaseFunction attribute) _valueraw()

A

actualize (diffpy.srmise.basefunction.BaseFunction attribute) actualize() (diffpy.srmise.basefunction.BaseFunction method) (diffpy.srmise.baselines.base.BaselineFunction method) (diffpy.srmise.peaks.base.PeakFunction method) add_peaks() (diffpy.srmise.peakextraction.PeakExtraction method) addexternalpeaks() (diffpy.srmise.modelcluster.ModelCluster method) addfilelog() (in module diffpy.srmise.srmiselog) AIC (class in diffpy.srmise.modelevaluators.aic) AICc (class in diffpy.srmise.modelevaluators.aicc) akaikeprobs() (diffpy.srmise.modelevaluators.aic.AIC static method) (diffpy.srmise.modelevaluators.aicc.AICc static method)

akaikeweights() (diffpy.srmise.modelevaluators.aic.AIC static method) (diffpy.srmise.modelevaluators.aicc.AICc static method) animate() (diffpy.srmise.dataclusters.DataClusters method) (diffpy.srmise.peakstability.PeakStability method) animate_classprobs() (diffpy.srmise.multimodelselection.MultimodelSelection method) animate_probs() (diffpy.srmise.multimodelselection.MultimodelSelection method) Arbitrary (class in diffpy.srmise.baselines.arbitrary) argsort() (diffpy.srmise.peaks.base.Peaks method) augment() (diffpy.srmise.modelcluster.ModelCluster method)

B

base (diffpy.srmise.basefunction.BaseFunction attribute) BaseFunction (built-in class) (class in diffpy.srmise.basefunction) BaseFunction.BaselineFunction (built-in class) BaseFunction.BaselineFunction.FromSequence (built-in class) BaseFunction.BaselineFunction.NanoSpherical (built-in class) BaseFunction.BaselineFunction.Polynomial (built-in class)

BaseFunction.PeakFunction (built-in class) BaseFunction.PeakFunction.Gaussian (built-in class) BaseFunction.PeakFunction.GaussianOverR (built-in class) Baseline (class in diffpy.srmise.baselines.base) BaselineFunction (class in diffpy.srmise.baselines.base) bestclasses() (diffpy.srmise.multimodelselection.MultimodelSelection method) bestmodels() (diffpy.srmise.multimodelselection.MultimodelSelection method)

C

change_slice() (diffpy.srmise.modelcluster.ModelCluster method) changeowner() (diffpy.srmise.modelparts.ModelPart method), [1] chi_squared() (diffpy.srmise.modelevaluators.base.ModelEvaluator method) classbestdgs() (diffpy.srmise.multimodelselection.MultimodelSelection method) classify() (diffpy.srmise.multimodelselection.MultimodelSelection method) cleanfit() (diffpy.srmise.modelcluster.ModelCluster method) clear() (diffpy.srmise.modelcluster.ModelCovariance method) (diffpy.srmise.pdfdataset.PDFDataSet method) (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) (diffpy.srmise.peakextraction.PeakExtraction method) clearcalc() (diffpy.srmise.peakextraction.PeakExtraction method) close() (diffpy.srmise.pdfdataset.PDFComponent method) cluster_boundaries() (diffpy.srmise.dataclusters.DataClusters method)

cluster_is_full() (diffpy.srmise.dataclusters.DataClusters method) combine_clusters() (diffpy.srmise.dataclusters.DataClusters method) comparepositions() (in module diffpy.srmise.applications.plot) compress() (diffpy.srmise.modelparts.ModelPart method), [1] contingent_fit() (diffpy.srmise.modelcluster.ModelCluster method) copy() (diffpy.srmise.modelcluster.ModelCluster method) (diffpy.srmise.modelparts.ModelPart method), [1] (diffpy.srmise.modelparts.ModelParts method) (diffpy.srmise.pdfdataset.PDFDataSet method) correlationwarning() (diffpy.srmise.modelcluster.ModelCovariance method) covariance() (diffpy.srmise.modelparts.ModelParts method) cut() (diffpy.srmise.dataclusters.DataClusters method) cut_freq() (diffpy.srmise.peaks.terminationripples.TerminationRipples method)

D

DataClusters (class in diffpy.srmise.dataclusters) default_formats (diffpy.srmise.basefunction.BaseFunction attribute) defaultvars() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) (diffpy.srmise.peakextraction.PeakExtraction method) deletepeak() (diffpy.srmise.modelcluster.ModelCluster method) dg_key() (diffpy.srmise.multimodelselection.MultimodelSelection method) dGobs (diffpy.srmise.pdfdataset.PDFDataSet attribute) dgseries() (in module diffpy.srmise.applications.plot) diffpy.srmise module diffpy.srmise.applications module diffpy.srmise.applications.extract module diffpy.srmise.applications.plot module diffpy.srmise.basefunction module diffpy.srmise.baselines module diffpy.srmise.baselines.arbitrary module diffpy.srmise.baselines.base module diffpy.srmise.baselines.fromsequence module diffpy.srmise.baselines.nanospherical module diffpy.srmise.baselines.polynomial module diffpy.srmise.dataclusters module diffpy.srmise.modelcluster module diffpy.srmise.modelevaluators module

diffpy.srmise.modelevaluators.aic module diffpy.srmise.modelevaluators.aicc module diffpy.srmise.modelevaluators.base module diffpy.srmise.modelparts module diffpy.srmise.multimodelselection module diffpy.srmise.pdfdataset module diffpy.srmise.pdfpeakextraction module diffpy.srmise.peakextraction module diffpy.srmise.peaks module diffpy.srmise.peaks.base module diffpy.srmise.peaks.gaussian module diffpy.srmise.peaks.gaussianoverr module diffpy.srmise.peaks.terminationripples module diffpy.srmise.peakstability module diffpy.srmise.srmiseerrors module diffpy.srmise.srmiselog module drobs (diffpy.srmise.pdfdataset.PDFDataSet attribute) dscale (diffpy.srmise.pdfdataset.PDFDataSet attribute)

E

eatkwds() (in module diffpy.srmise.multimodelselection) emit() (diffpy.srmise.srmiselog.TracePeaks method) errorscale() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) estimate_parameters (diffpy.srmise.basefunction.BaseFunction attribute) estimate_parameters() (diffpy.srmise.basefunction.BaseFunction method) (diffpy.srmise.baselines.arbitrary.Arbitrary method) (diffpy.srmise.baselines.fromsequence.FromSequence method) (diffpy.srmise.baselines.polynomial.Polynomial method) (diffpy.srmise.peaks.gaussian.Gaussian method) (diffpy.srmise.peaks.gaussianoverr.GaussianOverR method) (diffpy.srmise.peaks.terminationripples.TerminationRipples method)

estimate_peak() (diffpy.srmise.peakextraction.PeakExtraction method) estimatepeak() (diffpy.srmise.modelcluster.ModelCluster method) evaluate() (diffpy.srmise.modelevaluators.aic.AIC method) (diffpy.srmise.modelevaluators.aicc.AICc method) extend_grid() (diffpy.srmise.peaks.terminationripples.TerminationRipples method) extending-srmise extract() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) extract_single() (diffpy.srmise.peakextraction.PeakExtraction method)

F

factory() (diffpy.srmise.basefunction.BaseFunction static method) (diffpy.srmise.baselines.base.Baseline static method) (diffpy.srmise.modelcluster.ModelCluster static method) (diffpy.srmise.peaks.base.Peak static method) filename (diffpy.srmise.pdfdataset.PDFDataSet attribute) filter (diffpy.srmise.srmiselog.TracePeaks property) find_adjacent_clusters() (diffpy.srmise.dataclusters.DataClusters method) find_nearest_cluster() (diffpy.srmise.dataclusters.DataClusters method)

find_nearest_cluster2() (diffpy.srmise.dataclusters.DataClusters method) find_qmax() (in module diffpy.srmise.pdfpeakextraction) fit() (diffpy.srmise.modelcluster.ModelCluster method) (diffpy.srmise.modelparts.ModelParts method) (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) fit_single() (diffpy.srmise.peakextraction.PeakExtraction method) format_option() (diffpy.srmise.applications.extract.IndentedHelpFormatterWithNL method) free (diffpy.srmise.modelparts.ModelPart attribute) FromSequence (class in diffpy.srmise.baselines.fromsequence)

G

Gaussian (class in diffpy.srmise.peaks.gaussian) GaussianOverR (class in diffpy.srmise.peaks.gaussianoverr) get() (diffpy.srmise.modelcluster.ModelCovariance method) (diffpy.srmise.multimodelselection.MultimodelSelection method) get_aic() (diffpy.srmise.multimodelselection.MultimodelSelection method) get_class() (diffpy.srmise.multimodelselection.MultimodelSelection method) get_model() (diffpy.srmise.multimodelselection.MultimodelSelection method) get_nfree() (diffpy.srmise.multimodelselection.MultimodelSelection method) get_prob() (diffpy.srmise.multimodelselection.MultimodelSelection method) getcorrelation() (diffpy.srmise.modelcluster.ModelCovariance method) getcovariance() (diffpy.srmise.modelcluster.ModelCovariance method) getfilter() (diffpy.srmise.srmiselog.TracePeaks method) getfree() (diffpy.srmise.modelparts.ModelPart method), [1] getmodule() (diffpy.srmise.basefunction.BaseFunction method) (diffpy.srmise.baselines.arbitrary.Arbitrary method) (diffpy.srmise.baselines.base.BaselineFunction method) (diffpy.srmise.baselines.fromsequence.FromSequence method) (diffpy.srmise.baselines.nanospherical.NanoSpherical method) (diffpy.srmise.baselines.polynomial.Polynomial method) (diffpy.srmise.peaks.base.PeakFunction method) (diffpy.srmise.peaks.gaussian.Gaussian method) (diffpy.srmise.peaks.gaussianoverr.GaussianOverR method) (diffpy.srmise.peaks.terminationripples.TerminationRipples method)

getrangeslice() (diffpy.srmise.peakextraction.PeakExtraction method) getuncertainty() (diffpy.srmise.modelcluster.ModelCovariance method) getvalue() (diffpy.srmise.modelcluster.ModelCovariance method) getvar() (diffpy.srmise.pdfdataset.PDFDataSet method) Gobs (diffpy.srmise.pdfdataset.PDFDataSet attribute) gr_formataxis() (in module diffpy.srmise.applications.plot) growth_justified() (diffpy.srmise.modelevaluators.aic.AIC method) (diffpy.srmise.modelevaluators.aicc.AICc method)

I

IndentedHelpFormatterWithNL (class in diffpy.srmise.applications.extract)

J

jacobian (diffpy.srmise.basefunction.BaseFunction attribute) jacobian() (diffpy.srmise.basefunction.BaseFunction method) (diffpy.srmise.modelparts.ModelPart method), [1] (diffpy.srmise.peaks.terminationripples.TerminationRipples method)

join_adjacent() (diffpy.srmise.modelcluster.ModelCluster static method)

L

labelallsubplots() (in module diffpy.srmise.applications.plot) license liveplotting() (in module diffpy.srmise.srmiselog)

load() (diffpy.srmise.peakstability.PeakStability method) loadaics() (diffpy.srmise.multimodelselection.MultimodelSelection method) loadpdf() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method)

M

main() (in module diffpy.srmise.applications.extract) (in module diffpy.srmise.applications.plot) makeaicprobs() (diffpy.srmise.multimodelselection.MultimodelSelection method) makeaics() (diffpy.srmise.multimodelselection.MultimodelSelection method) makeaicweights() (diffpy.srmise.multimodelselection.MultimodelSelection method) makeclassprobs() (diffpy.srmise.multimodelselection.MultimodelSelection method) makeclassweights() (diffpy.srmise.multimodelselection.MultimodelSelection method) makeclusters() (diffpy.srmise.dataclusters.DataClusters method) makeplot() (in module diffpy.srmise.applications.plot) makesortedclasses() (diffpy.srmise.multimodelselection.MultimodelSelection method) makesortedclassprobs() (diffpy.srmise.multimodelselection.MultimodelSelection method) makesortedprobs() (diffpy.srmise.multimodelselection.MultimodelSelection method) maketrace() (diffpy.srmise.srmiselog.TracePeaks method) match_at() (diffpy.srmise.peaks.base.Peaks method) max() (diffpy.srmise.peaks.gaussian.Gaussian method) (diffpy.srmise.peaks.gaussianoverr.GaussianOverR method) maxprobdG_byclass() (diffpy.srmise.multimodelselection.MultimodelSelection method) maxprobdG_bymodel() (diffpy.srmise.multimodelselection.MultimodelSelection method) maxprobmodel_byclass() (diffpy.srmise.multimodelselection.MultimodelSelection method) maxprobmodel_bymodel() (diffpy.srmise.multimodelselection.MultimodelSelection method) metadata (diffpy.srmise.pdfdataset.PDFDataSet attribute) metadict (diffpy.srmise.basefunction.BaseFunction attribute) minpoints() (diffpy.srmise.modelevaluators.aic.AIC method) (diffpy.srmise.modelevaluators.aicc.AICc method) modelbestdgs() (diffpy.srmise.multimodelselection.MultimodelSelection method) ModelCluster (class in diffpy.srmise.modelcluster) ModelCovariance (class in diffpy.srmise.modelcluster) ModelEvaluator (class in diffpy.srmise.modelevaluators.base) ModelPart (class in diffpy.srmise.modelparts) ModelParts (class in diffpy.srmise.modelparts) module diffpy.srmise diffpy.srmise.applications diffpy.srmise.applications.extract diffpy.srmise.applications.plot diffpy.srmise.basefunction diffpy.srmise.baselines diffpy.srmise.baselines.arbitrary diffpy.srmise.baselines.base diffpy.srmise.baselines.fromsequence diffpy.srmise.baselines.nanospherical diffpy.srmise.baselines.polynomial diffpy.srmise.dataclusters diffpy.srmise.modelcluster diffpy.srmise.modelevaluators diffpy.srmise.modelevaluators.aic diffpy.srmise.modelevaluators.aicc diffpy.srmise.modelevaluators.base diffpy.srmise.modelparts diffpy.srmise.multimodelselection diffpy.srmise.pdfdataset diffpy.srmise.pdfpeakextraction diffpy.srmise.peakextraction diffpy.srmise.peaks diffpy.srmise.peaks.base diffpy.srmise.peaks.gaussian diffpy.srmise.peaks.gaussianoverr diffpy.srmise.peaks.terminationripples diffpy.srmise.peakstability diffpy.srmise.srmiseerrors diffpy.srmise.srmiselog

MultimodelSelection (class in diffpy.srmise.multimodelselection)

N

NanoSpherical (class in diffpy.srmise.baselines.nanospherical) npars() (diffpy.srmise.modelcluster.ModelCluster method) (diffpy.srmise.modelparts.ModelPart method), [1] (diffpy.srmise.modelparts.ModelParts method)

O

on_draw() (in module diffpy.srmise.applications.plot)

owner() (diffpy.srmise.modelparts.ModelPart method), [1]

P

pack_freepars() (diffpy.srmise.modelparts.ModelParts method) parameterdict (diffpy.srmise.basefunction.BaseFunction attribute) parformats (diffpy.srmise.basefunction.BaseFunction attribute) parpenalty() (diffpy.srmise.modelevaluators.aic.AIC method) (diffpy.srmise.modelevaluators.aicc.AICc method) pars (diffpy.srmise.modelparts.ModelPart attribute) parsepars() (in module diffpy.srmise.applications.extract) PDFComponent (class in diffpy.srmise.pdfdataset) PDFDataFormatError PDFDataSet (class in diffpy.srmise.pdfdataset) PDFPeakExtraction (class in diffpy.srmise.pdfpeakextraction) Peak (class in diffpy.srmise.peaks.base) PeakExtraction (class in diffpy.srmise.peakextraction) PeakFunction (class in diffpy.srmise.peaks.base) Peaks (class in diffpy.srmise.peaks.base) PeakStability (class in diffpy.srmise.peakstability)

persistentItems (diffpy.srmise.pdfdataset.PDFDataSet attribute), [1] pgradient() (diffpy.srmise.basefunction.BaseFunction method) plot() (diffpy.srmise.dataclusters.DataClusters method) (diffpy.srmise.peakextraction.PeakExtraction method) (diffpy.srmise.peakstability.PeakStability method) plot3dclassprobs() (diffpy.srmise.multimodelselection.MultimodelSelection method) plotseries() (diffpy.srmise.peakstability.PeakStability method) plottable() (diffpy.srmise.modelcluster.ModelCluster method) plottable_residual() (diffpy.srmise.modelcluster.ModelCluster method) Polynomial (class in diffpy.srmise.baselines.polynomial) popc() (diffpy.srmise.srmiselog.TracePeaks method) popr() (diffpy.srmise.srmiselog.TracePeaks method) prettypar() (diffpy.srmise.modelcluster.ModelCovariance method) prune() (diffpy.srmise.modelcluster.ModelCluster method) pushc() (diffpy.srmise.srmiselog.TracePeaks method) pushr() (diffpy.srmise.srmiselog.TracePeaks method)

Q

qbroad (diffpy.srmise.pdfdataset.PDFDataSet attribute) qdamp (diffpy.srmise.pdfdataset.PDFDataSet attribute)

qmax (diffpy.srmise.pdfdataset.PDFDataSet attribute) quality() (diffpy.srmise.modelcluster.ModelCluster method)

R

read() (diffpy.srmise.pdfdataset.PDFDataSet method) (diffpy.srmise.peakextraction.PeakExtraction method) (diffpy.srmise.srmiselog.TracePeaks method) readcompare() (in module diffpy.srmise.applications.plot) readmetadata() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) (diffpy.srmise.peakextraction.PeakExtraction method) readStr() (diffpy.srmise.pdfdataset.PDFDataSet method) readstr() (diffpy.srmise.peakextraction.PeakExtraction method) (diffpy.srmise.srmiselog.TracePeaks method) readxy() (diffpy.srmise.baselines.fromsequence.FromSequence method) reduce_to() (diffpy.srmise.modelcluster.ModelCluster method) refinableVars (diffpy.srmise.pdfdataset.PDFDataSet attribute), [1] release notes

removable (diffpy.srmise.modelparts.ModelPart attribute) replacepeaks() (diffpy.srmise.modelcluster.ModelCluster method) resample() (in module diffpy.srmise.pdfpeakextraction) resampledata() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) reset_clusters() (diffpy.srmise.dataclusters.DataClusters method) reset_trace() (diffpy.srmise.srmiselog.TracePeaks method) residual() (diffpy.srmise.modelcluster.ModelCluster method) (diffpy.srmise.modelparts.ModelParts method) residual_jacobian() (diffpy.srmise.modelparts.ModelParts method) rmax (diffpy.srmise.pdfdataset.PDFDataSet attribute) rmin (diffpy.srmise.pdfdataset.PDFDataSet attribute) robs (diffpy.srmise.pdfdataset.PDFDataSet attribute) run() (diffpy.srmise.peakstability.PeakStability method)

S

safefunction() (diffpy.srmise.basefunction.BaseFunction static method) safefunctionlist() (diffpy.srmise.basefunction.BaseFunction static method) save() (diffpy.srmise.peakstability.PeakStability method) scale_at() (diffpy.srmise.peaks.base.Peak method) (diffpy.srmise.peaks.base.PeakFunction method) (diffpy.srmise.peaks.gaussian.Gaussian method) (diffpy.srmise.peaks.gaussianoverr.GaussianOverR method) (diffpy.srmise.peaks.terminationripples.TerminationRipples method) setcovariance() (diffpy.srmise.modelcluster.ModelCovariance method) setcurrent() (diffpy.srmise.peakstability.PeakStability method) setdata() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) (diffpy.srmise.peakextraction.PeakExtraction method) setfigformat() (in module diffpy.srmise.applications.plot) setfilelevel() (in module diffpy.srmise.srmiselog) setfilter() (diffpy.srmise.srmiselog.TracePeaks method) setfree() (diffpy.srmise.modelparts.ModelPart method), [1] setlevel() (in module diffpy.srmise.srmiselog) setppe() (diffpy.srmise.peakstability.PeakStability method) settracer() (in module diffpy.srmise.srmiselog)

setvar() (diffpy.srmise.pdfdataset.PDFDataSet method) setvars() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) (diffpy.srmise.peakextraction.PeakExtraction method) sort() (diffpy.srmise.peaks.base.Peaks method) spdiameter (diffpy.srmise.pdfdataset.PDFDataSet attribute) SrMiseDataFormatError SrMiseError SrMiseEstimationError SrMiseFileError SrMiseFitError SrMiseLogError SrMiseModelEvaluatorError SrMisePDFKeyError SrMiseQmaxError SrMiseScalingError SrMiseStaticOwnerError SrMiseTransformationError SrMiseUndefinedCovarianceError static_owner (diffpy.srmise.modelparts.ModelPart attribute) stdratio() (in module diffpy.srmise.pdfpeakextraction) stype (diffpy.srmise.pdfdataset.PDFDataSet attribute)

T

TerminationRipples (class in diffpy.srmise.peaks.terminationripples) TracePeaks (class in diffpy.srmise.srmiselog) transform() (diffpy.srmise.modelcluster.ModelCovariance method) (diffpy.srmise.modelparts.ModelParts method)

transform_derivatives (diffpy.srmise.basefunction.BaseFunction attribute) transform_derivatives() (diffpy.srmise.basefunction.BaseFunction method) transform_parameters (diffpy.srmise.basefunction.BaseFunction attribute) transform_parameters() (diffpy.srmise.basefunction.BaseFunction method)

U

unpack_freepars() (diffpy.srmise.modelparts.ModelParts method)

update() (diffpy.srmise.modelparts.ModelPart method), [1]

V

value (diffpy.srmise.basefunction.BaseFunction attribute) value() (diffpy.srmise.basefunction.BaseFunction method) (diffpy.srmise.modelcluster.ModelCluster method) (diffpy.srmise.modelparts.ModelPart method), [1] (diffpy.srmise.modelparts.ModelParts method) (diffpy.srmise.peaks.terminationripples.TerminationRipples method)

valuebl() (diffpy.srmise.modelcluster.ModelCluster method)

W

write() (diffpy.srmise.pdfdataset.PDFDataSet method) (diffpy.srmise.peakextraction.PeakExtraction method) (diffpy.srmise.srmiselog.TracePeaks method) writemetadata() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) (diffpy.srmise.peakextraction.PeakExtraction method) writepwa() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method) writepwastr() (diffpy.srmise.pdfpeakextraction.PDFPeakExtraction method)

writestr() (diffpy.srmise.basefunction.BaseFunction method) (diffpy.srmise.modelcluster.ModelCluster method) (diffpy.srmise.modelparts.ModelPart method), [1] writeStr() (diffpy.srmise.pdfdataset.PDFDataSet method) writestr() (diffpy.srmise.peakextraction.PeakExtraction method) (diffpy.srmise.srmiselog.TracePeaks method) writesummary() (diffpy.srmise.peakextraction.PeakExtraction method)

X

xyrepr() (diffpy.srmise.baselines.fromsequence.FromSequence method)