Module Expr Str ImportFrom alias Import alias Import alias Assign NameStore Call AttributeLoad NameLoad attr NameLoad ImportFrom alias Import alias identifier ImportFrom alias ImportFrom alias alias alias Import alias identifier Import alias identifier ImportFrom alias ImportFrom alias ImportFrom alias FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad For NameStore Call NameLoad NameLoad body For NameStore Call NameLoad NameLoad body If CompareEq NameLoad NameLoad body Assign SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad Num orelse Assign SubscriptStore NameLoad Index TupleLoad NameLoad NameLoad BinOpDiv Num BinOpMult NameLoad BinOpSub NameLoad NameLoad Return NameLoad decorator_list ClassDef bases NameLoad body Expr Str decorator_list ClassDef bases NameLoad body Expr Str decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam defaults vararg kwarg body Expr Str Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Str Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Str Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults vararg kwarg body Expr Str Assign NameStore Call NameLoad NameLoad keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr NameLoad NameLoad Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body If CompareIs AttributeLoad NameLoad attr NameLoad body Return Str Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr Return Call AttributeLoad NameLoad attr NameLoad keyword NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str Assign NameStore BinOpMod Str TupleLoad NameLoad NameLoad AttributeLoad NameLoad attr Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str Assign NameStore Call AttributeLoad NameLoad attr NameLoad Str If CompareGt AttributeLoad NameLoad attr Num body Assign TupleStore NameStore NameStore AttributeLoad NameLoad attr Assign NameStore BinOpMod Str TupleLoad NameLoad NameLoad NameLoad NameLoad orelse Assign NameStore BinOpMod Str AttributeLoad NameLoad attr Assign NameStore BinOpMod Str AttributeLoad NameLoad attr Assign NameStore BinOpMod Str AttributeLoad NameLoad attr Assign NameStore BinOpMod Str TupleLoad AttributeLoad NameLoad attr NameLoad NameLoad NameLoad NameLoad NameLoad Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults Str kwarg body Expr Str Expr Call AttributeLoad NameLoad attr Str BinOpMod Str TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr If CompareNotIn NameLoad ListLoad Str Str body Return Call AttributeLoad Call NameLoad NameLoad NameLoad attr keyword NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr If CompareEq NameLoad Str body If BoolOpAnd CompareNotIn Str NameLoad CompareNotIn Str NameLoad CompareNotIn Str NameLoad body Assign SubscriptStore NameLoad Index Str AttributeLoad NameLoad attr If CompareGt SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num body Assign SubscriptStore NameLoad Index Str NameLoad Return Call NameLoad NameLoad NameLoad orelse If CompareEq NameLoad Str body Return Call NameLoad NameLoad NameLoad decorator_list decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str If CompareNotEq AttributeLoad NameLoad attr Num body Raise Call NameLoad Str If UnaryOpNot Call NameLoad NameLoad NameLoad body Raise BinOpMod Call NameLoad Str Call NameLoad NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call NameLoad AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr Num Assign AttributeStore NameLoad attr NameLoad If CompareIsNot NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr NameLoad If CompareNotEq AttributeLoad NameLoad attr AttributeLoad AttributeLoad NameLoad attr attr body Raise Call NameLoad BinOpMod Str TupleLoad AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad Assign AttributeStore NameLoad attr Str Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr keyword Num orelse Expr Call AttributeLoad NameLoad attr Str decorator_list FunctionDef arguments args NameParam defaults body Expr Str If AttributeLoad NameLoad attr body Return BinOpMod Str TupleLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr Return Str decorator_list NameLoad FunctionDef arguments args NameParam defaults vararg kwarg body Expr Str If NameLoad body If CompareGt Call NameLoad NameLoad Num body Raise Call NameLoad Str If CompareEq SubscriptLoad NameLoad Index Num NameLoad body If CompareEq AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad NameLoad attr Str Assign AttributeStore NameLoad attr NameLoad orelse If CompareEq SubscriptLoad NameLoad Index Num NameLoad body If CompareEq AttributeLoad NameLoad attr NameLoad body Expr Call AttributeLoad NameLoad attr Str Assign AttributeStore NameLoad attr NameLoad orelse Raise Call NameLoad Str orelse Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str AttributeLoad NameLoad attr If BoolOpOr CompareGt AttributeLoad NameLoad attr Num CompareGt AttributeLoad NameLoad attr Num body Expr Call AttributeLoad NameLoad attr Str decorator_list FunctionDef arguments args NameParam defaults body Return AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults vararg kwarg body Expr Str TryExcept body If UnaryOpNot NameLoad body Assign AttributeStore NameLoad attr NameLoad Assign NameStore BinOpMult SubscriptLoad AttributeLoad NameLoad attr Index Num Num orelse If CompareEq NameLoad Str body Assign AttributeStore NameLoad attr Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Num orelse Assign AttributeStore NameLoad attr Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr NameLoad NameLoad handlers ExceptHandler type NameLoad body Raise Call NameLoad BinOpMod Str NameLoad Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Num body Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num Call NameLoad AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr keyword Num decorator_list FunctionDef arguments args NameParam defaults body Return AttributeLoad AttributeLoad NameLoad attr attr decorator_list NameLoad FunctionDef arguments args NameParam defaults body Return SubscriptLoad AttributeLoad NameLoad attr Index Num decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return BinOpDiv Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr BinOpSub AttributeLoad NameLoad attr Num decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return BinOpDiv Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr BinOpSub AttributeLoad NameLoad attr Num decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Num Return Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return Call AttributeLoad Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr attr decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str If AttributeLoad NameLoad attr body Assign NameStore BinOpMult BinOpMult AttributeLoad NameLoad attr BinOpPow AttributeLoad NameLoad attr BinOpMult Num AttributeLoad NameLoad attr BinOpPow Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse Assign NameStore AttributeLoad NameLoad attr Return Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword Str keyword Str decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str If AttributeLoad NameLoad attr body Assign NameStore BinOpMult BinOpMult AttributeLoad NameLoad attr BinOpPow AttributeLoad NameLoad attr BinOpMult Num AttributeLoad NameLoad attr BinOpPow Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse Assign NameStore AttributeLoad NameLoad attr Return Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword Str keyword Str decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr BinOpDiv AttributeLoad NameLoad attr AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Str Assign AttributeStore NameLoad attr Str Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr BinOpAdd BinOpPow AttributeLoad NameLoad attr Num BinOpPow AttributeLoad NameLoad attr Num Assign AttributeStore NameLoad attr Str Assign AttributeStore NameLoad attr Str Return NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword NameLoad keyword Str keyword Str decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Return Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr keyword NameLoad keyword Str keyword Str decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore AttributeLoad NameLoad attr If CompareEq Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Num body Raise Call NameLoad Str Assign NameStore BinOpDiv Num BinOpMult NameLoad AttributeLoad NameLoad attr Assign NameStore Num Assign NameStore Call AttributeLoad NameLoad attr NameLoad For NameStore Call NameLoad Num BinOpAdd NameLoad Num body Expr Call AttributeLoad NameLoad attr NameLoad AugAssignAdd NameStore BinOpAdd Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad BinOpDiv BinOpAdd NameLoad Num Num Return BinOpMult NameLoad NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore AttributeLoad NameLoad attr Return BinOpAdd BinOpMult BinOpSub NameLoad NameLoad BinOpDiv BinOpSub NameLoad Num BinOpSub AttributeLoad NameLoad attr Num NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad Assign TupleStore NameStore NameStore TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore AttributeLoad NameLoad attr For NameStore Call NameLoad NameLoad body For NameStore Call NameLoad NameLoad body Assign NameStore BinOpDiv BinOpSub SubscriptLoad NameLoad Index NameLoad SubscriptLoad NameLoad Index NameLoad BinOpSub NameLoad NameLoad Assign SubscriptStore SubscriptLoad NameLoad Index NameLoad Index NameLoad BinOpMult NameLoad SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad Return Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword Str keyword Str decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore Call AttributeLoad NameLoad attr TupleLoad NameLoad NameLoad For NameStore Call NameLoad NameLoad body For NameStore Call NameLoad NameLoad body Assign SubscriptStore SubscriptLoad NameLoad Index NameLoad Index NameLoad Call AttributeLoad NameLoad attr BinOpSub BinOpPow SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad Num BinOpPow SubscriptLoad NameLoad Index TupleLoad NameLoad NameLoad Num Return Call AttributeLoad NameLoad attr NameLoad keyword NameLoad keyword Str keyword Str decorator_list NameLoad FunctionDef arguments args NameParam defaults kwarg body Expr Str Return Call NameLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str If UnaryOpNot AttributeLoad NameLoad attr body Raise Call NameLoad BinOpMod Str AttributeLoad AttributeLoad NameLoad attr attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad NameLoad body Expr Str If AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Str Assign AttributeStore NameLoad attr Call NameLoad keyword NameLoad If NameLoad body Return Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr orelse Expr Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Expr Call AttributeLoad NameLoad attr Str Return AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr Str Return AttributeLoad AttributeLoad NameLoad attr attr decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr Str Return AttributeLoad AttributeLoad NameLoad attr attr decorator_list NameLoad FunctionDef arguments args NameParam NameParam defaults body Expr Str Expr Call AttributeLoad NameLoad attr Str If CompareGt NameLoad Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num body Raise Call NameLoad BinOpMod Str SubscriptLoad AttributeLoad NameLoad attr Index Num If AttributeLoad AttributeLoad NameLoad attr attr body If CompareGt NameLoad Call NameLoad AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr BinOpMod Str AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad Return SubscriptLoad AttributeLoad AttributeLoad NameLoad attr attr ExtSlice Slice Index NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad Call AttributeLoad SubscriptLoad Call AttributeLoad Call AttributeLoad Call NameLoad NameLoad NameLoad attr attr Index Num attr Str attr Str Assign NameStore BinOpMod Str TupleLoad AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad AugAssignAdd NameStore BinOpMod Str TupleLoad NameLoad AttributeLoad NameLoad attr If AttributeLoad NameLoad attr body AugAssignAdd NameStore BinOpMod Str TupleLoad NameLoad AttributeLoad NameLoad attr orelse AugAssignAdd NameStore BinOpMod Str TupleLoad NameLoad AttributeLoad NameLoad attr AugAssignAdd NameStore BinOpMod Str TupleLoad NameLoad Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad AttributeLoad NameLoad attr attr Return NameLoad decorator_list decorator_list If CompareEq NameLoad Str body ImportFrom alias alias alias Import alias identifier Import alias identifier Assign NameStore Call NameLoad Assign NameStore Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Str Print AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr keyword Num keyword Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr keyword Num keyword Str Expr Call AttributeLoad NameLoad attr
N/A N/A  Suite for 2-dimensional correlation analysis.  Decided to put it in, despite already
seeing a numpy-based version in paper "2D-correlation analysis applied to in situ and operando Mossbauer spectroscopy".
This would not be pandas friendly, so it wouldn't intgerate into skspec and I also want to build some tools from 
scratch to refamiliarize myself with the topic.

To remember/writeup eventually:

From page 32 Noda book,
Classical statistical cross correlation measures the dot product between spectral variables at different times.
For example, a pulse at t=0 and again at t=3, then the cross correlation would be max at tau=3.  If this experiment
went on for 50 minutes, then we average and integrate over all time.  If this pulse happed every 3 seconds, this correlation
would be 100% for exmaple.  If the pulse happed like only 5 times, the correlation would be diluted by the normalization factor.

The synchronous spectrum is the cross correlation at tau=0, summed and averaged over all times.  Basically, it measures the instantaneous
correlation of all spectral variables.  The asynchronous spectrum is the instantaneous orthogonal spectrum basically.  So whenever two things
are moving together at one instant, weight goes into the sync.  If not, weight goes into the async  Makes me think of an easy filter!  Can
just throw out regions where not much is happening right?  Maybe call it a 2dcs filter.


2d Codistriubtion Spectroscopy[2] is a more recent development and is also included.

References
----------

[1] Scaling techniques to enhance two-dimensional correlation spectra, Isao Noda,
    Journal of Molecular Structure.  2008. Volume: 883-884, Issue: 1-3, (216-227) 
[2] Isao Nodal. Journal of Molectul Structure. 2014.  Two-dimensional codistriubtion spectroscopy to
    determine the sequential order of distributed presence of species.  1069. 2014 (50-59)

 __future__ division N/A logging N/A pandas N/A logger N/A N/A logging getLogger __name__ math pi N/A numpy np skspec.core.anyspectra AnyFrame skspec.plotting.correlation_plot corr2d corr3d corr_multi N/A skspec.config pvconfig N/A skspec.core.utilities pvutils skspec.core.specindex SpecIndex skspec.pandas_utils.metadframe MetaDataFrame pca_lite PCA noda_matrix N/A N/A length N/A N/A N/A  Length is the number of timepoints/columns in the dataframe. 
       Returns the hilbert noda Transformation matrix. N/A Njk N/A N/A np empty N/A length length N/A j N/A range length N/A N/A k N/A range length N/A N/A N/A j k N/A N/A N/A Njk N/A N/A j k 0 N/A N/A N/A Njk N/A N/A j k N/A 1.0 N/A pi N/A k j N/A Njk N/A CorrError N/A Exception N/A N/A N/A Spec2dError N/A Exception N/A N/A N/A Spec2d N/A AnyFrame N/A N/A  Frame to hold synchronous, asynchronous and other 2D spectra objects.
    Custom output and plotting are main changes from AnyFrame.  
    
    Notes
    -----
    This class only stores limited units from the original data, including 
    specunit and varunit.  Otherwise, it is a generic AnyFrame, and we don't
    want users to access the original Spectra backwards through this class.
    
    Also overwrites Spectra.norm for 3dPlotting purposes.

    Will update active/spectral unit based on index/columns, but original
    datarange (like how much time synchronous corresponds to) is stored
    permanently in self._span_string
     __init__ N/A N/A self N/A args kwargs N/A N/A  Hack over norms for plotting API sake.  Stores metadata like
        scaling, spectral and variance range of spectra.  *args, **kwargs
        passed to AnyFrame constructor.

        kwargs
        ------

        spec: Optional (original dataset ie Spectra, TimeSpectra)
            Access the original data allows for more detailed output like
            sideplots in the plot calls and instructive headers.  
            
        scaled: str
            Status of scaling, ie "no scaling", "alpha=1" etc... just a string
            that is output in various plots.
            
        centered : str
            Status of centering (ie "mean", "no centering") just a string
            that is output in various plots.        
         N/A N/A self spec N/A N/A kwargs pop spec None N/A N/A self scaled N/A N/A kwargs pop scaled N/A N/A self centered N/A N/A kwargs pop centered N/A N/A N/A N/A super Spec2d self __init__ args kwargs N/A from_corr2d N/A N/A cls arrayout corr2d N/A args kwargs N/A N/A  From Corr2D, create Spec2d object (e.g. Synchronous Spectrum).
        Parameters
        ----------
        arrayout : matrix values (ie synchronous spectrum)
        
        corr2d : Corr2D calling object
        
        Notes
        -----

        Will store a reference to the original dataset, and also overwrite
        the index and columns, respectively.
        
         N/A specout N/A cls arrayout scaled N/A corr2d _scale_string centered N/A corr2d center spec N/A corr2d spec args kwargs N/A N/A specout index N/A corr2d index N/A N/A specout columns N/A corr2d index N/A specout N/A classmethod _var_span N/A N/A self N/A N/A N/A N/A N/A self spec None N/A N/A N/A cols N/A N/A self spec columns N/A N/A N/A pvutils _compute_span cols with_unit True N/A property _header N/A N/A self N/A N/A N/A  Header for string printout  N/A delim N/A pvconfig HEADERDELIM N/A name N/A N/A pvutils safe_lookup self name N/A ftunit N/A N/A pvutils safe_lookup self varunit N/A spunit N/A N/A pvutils safe_lookup self specunit N/A header N/A *%s*%sScaling:%s
 N/A name delim N/A self scaled N/A header N/A property _header_html N/A N/A self N/A N/A N/A  Header for html printout  N/A delim N/A pvconfig HEADERHTMLDELIM N/A ftunit N/A N/A pvutils safe_lookup self varunit N/A spunit N/A N/A pvutils safe_lookup self specunit N/A N/A N/A self ndim 1 N/A N/A N/A s1 s2 N/A self shape N/A colorshape N/A <font color="#0000CD">(%s%s X %s%s)</font> N/A s1 spunit s2 ftunit N/A N/A colorshape N/A <font color="#0000CD"> (%s)</font> N/A self shape N/A scale_string N/A Scaling: <font color="#197519">%s</font> N/A self scaled N/A span_string N/A Span:  <font color="#000000">%s</font> N/A self _var_span N/A header N/A %s:&nbsp%s%s%s%s%s
 N/A N/A self name colorshape delim scale_string delim span_string N/A header N/A property plot N/A N/A self kind N/A corr2d pltkwargs N/A N/A N/A N/A N/A pltkwargs setdefault title N/A %s (%s) N/A N/A self name N/A self _var_span N/A N/A kind N/A corr2d corr3d N/A N/A N/A N/A N/A super Spec2d self plot kind kind pltkwargs N/A N/A N/A pltkwargs setdefault xlabel N/A self full_specunit N/A N/A N/A pltkwargs setdefault ylabel N/A self full_varunit N/A N/A kind corr2d N/A N/A N/A N/A cmap pltkwargs N/A color pltkwargs N/A colors pltkwargs N/A N/A N/A pltkwargs N/A cmap N/A pvconfig CMAP_CONTOUR N/A N/A N/A N/A self index N/A 0 N/A N/A self index N/A -1 N/A N/A N/A pltkwargs N/A _reverse_axis True N/A N/A corr2d self pltkwargs N/A N/A N/A kind corr3d N/A N/A N/A corr3d self pltkwargs N/A N/A Corr2d N/A object N/A N/A  Computed 2d correlation spectra, including synchronous and asynchronus,
    correlation, disrelation and other spectra given a 2d data matrix, index
    and columns.  Index and columns are necessary for plotting, so made them
    a mandatory requirement. __init__ N/A N/A self spec refspec N/A None N/A N/A  refspec is if you want custom centering.   N/A N/A N/A spec ndim 2 N/A N/A N/A CorrError Data must be 2d! N/A N/A N/A isinstance spec MetaDataFrame N/A N/A N/A N/A CorrError Corr2d requires skspec data structures (Metadataframe,Spectra, etc... got %s N/A type data N/A N/A self spec N/A N/A spec deepcopy N/A N/A self index N/A spec index N/A N/A self columns N/A spec columns N/A N/A self specunit N/A spec specunit N/A N/A self varunit N/A spec varunit N/A N/A self _noda N/A noda_matrix N/A self M N/A N/A self _scaled False N/A N/A self alpha 0.8 N/A N/A self beta 0.0 N/A N/A self _PCA None N/A N/A refspec None N/A N/A refspec N/A N/A np array refspec N/A N/A N/A refspec shape N/A N/A self index shape N/A N/A N/A CorrError N/A Shape mismatch: spectral data index %s and reference spec shape %. N/A N/A N/A self index shape N/A refspec shape N/A N/A self ref_spectrum N/A N/A np array refspec N/A N/A self _center Pre-centered N/A N/A self dyn_spec N/A N/A N/A self spec subtract N/A self ref_spectrum axis 0 N/A N/A N/A N/A self set_center mean N/A _scale_string N/A N/A self N/A N/A N/A  Current state of scalling, used in __repr__ and plot  N/A N/A self _scaled N/A N/A N/A (a=%s, b=%s) N/A N/A self alpha N/A self beta N/A False N/A property scale N/A N/A self N/A args kwargs N/A N/A Scale the synchronous and asynchronous spectra via REF 2
        based on generalized exponential parameters.  Scaling alpha will enhance
        the fine detail of the correlations, but also the noise.  Enhancing beta
        can screen the fine details and enhance the primary correlations.  Alpha
        0.8 and beta 0.0 are suggested as optimal tradeoff between fine correlation
        enhancement and low noise.
         N/A args N/A N/A N/A N/A len args 1 N/A N/A N/A CorrError Please use keywords (alpha=..., beta=...) toavoid ambiguity. N/A N/A N/A args N/A 0 True N/A N/A N/A N/A self _scaled True N/A N/A N/A N/A logger warn Data already scaled! N/A N/A self _scaled True N/A N/A N/A N/A args N/A 0 False N/A N/A N/A N/A self _scaled False N/A N/A N/A N/A logger warn Data already unscaled! N/A N/A self _scaled False N/A N/A N/A CorrError Argument "%s" not understood; please use True or False. N/A N/A N/A self _scaled True N/A N/A self alpha N/A N/A kwargs pop alpha N/A self alpha N/A N/A self beta N/A N/A kwargs pop beta N/A self beta N/A N/A N/A N/A self alpha 1 N/A N/A self beta 1 N/A N/A N/A N/A logger warn Alpha/Beta lose meaning off of range 0-1. N/A center N/A N/A self N/A N/A N/A N/A self _center N/A property set_center N/A N/A self style N/A args kwargs N/A N/A  User sets centering, this updates the   N/A N/A N/A N/A style N/A N/A N/A self _center None N/A ref_spectrum N/A N/A N/A self spec N/A 0 0.0 N/A N/A N/A style mean N/A N/A N/A self _center mean N/A ref_spectrum N/A N/A N/A self spec mean axis 1 N/A N/A N/A self _center custom fcn. N/A ref_spectrum N/A style N/A self spec args kwargs N/A N/A N/A Exception N/A N/A N/A CorrError N/A Center requires style of "mean", None or a  a function, got "%s". style N/A N/A self ref_spectrum N/A N/A np array ref_spectrum N/A N/A N/A len N/A self ref_spectrum N/A N/A self shape N/A 0 N/A N/A N/A CorrError N/A ref. spectrum should be of spectral length (%s) got "%s". N/A N/A N/A self shape N/A 0 N/A len N/A self ref_spectrum N/A N/A self dyn_spec N/A N/A N/A self spec subtract N/A self ref_spectrum axis 0 N/A shape N/A N/A self N/A N/A N/A N/A N/A self spec shape N/A property M N/A N/A self N/A N/A N/A N/A N/A self shape N/A 1 N/A property sync_noscale N/A N/A self N/A N/A N/A  Return unscaled, synchronous spectrum as a numpy array.  N/A N/A N/A N/A np dot N/A self dyn_spec N/A self _dynconjtranspose N/A N/A self M 1.0 N/A property async_noscale N/A N/A self N/A N/A N/A N/A N/A N/A N/A np dot N/A self dyn_spec N/A N/A np dot N/A self _noda N/A self _dynconjtranspose N/A N/A self M 1.0 N/A property coeff_corr N/A N/A self N/A N/A N/A  Correlation coefficient (pg 78)  N/A N/A N/A np divide N/A self sync_noscale N/A self joint_var N/A property coeff_disr N/A N/A self N/A N/A N/A  Disrelation coefficient (pg 79)  N/A N/A N/A np divide N/A self async_noscale N/A self joint_var N/A property joint_var N/A N/A self N/A N/A N/A  Product of standard devations of dynamic spectrum. 
        s1 * s2 or sqrt(siag(sync*sync)).
         N/A std N/A N/A N/A self dyn_spec std axis 1 N/A N/A N/A np outer std std N/A property _dynconjtranspose N/A N/A self N/A N/A N/A  Dynamic spectrum conjugate transpose; helpful to be cached N/A N/A N/A N/A N/A np conj N/A self dyn_spec transpose N/A property sync N/A N/A self N/A N/A N/A N/A N/A self _scaled N/A N/A matrixout N/A N/A N/A self sync_noscale N/A N/A self joint_var N/A -1.0 N/A self alpha N/A N/A abs N/A self coeff_corr N/A self beta N/A N/A matrixout N/A self sync_noscale N/A N/A N/A Spec2d from_corr2d matrixout corr2d self name Synchronous Correlation iunit synchronicity N/A property async N/A N/A self N/A N/A N/A N/A N/A self _scaled N/A N/A matrixout N/A N/A N/A self async_noscale N/A N/A self joint_var N/A -1.0 N/A self alpha N/A N/A abs N/A self coeff_disr N/A self beta N/A N/A matrixout N/A self async_noscale N/A N/A N/A Spec2d from_corr2d matrixout corr2d self name Asynchronous Correlation iunit asynchronicity N/A property phase N/A N/A self N/A N/A N/A  Global phase angle (pg 79).  This will use scaled data. N/A phase N/A N/A np arctan N/A N/A self async N/A self sync N/A N/A phase name Phase Map N/A N/A phase iunit phase angle N/A phase N/A property modulous N/A N/A self N/A N/A N/A  Effective lengh the vector with components Sync/Async N/A modulous N/A N/A np sqrt N/A N/A N/A self sync 2 N/A N/A self async 2 N/A N/A modulous name Modulous N/A N/A modulous iunit mod N/A modulous N/A property correlation N/A N/A self N/A N/A N/A  2D Correlation Spectrum N/A N/A N/A Spec2d from_corr2d N/A self coeff_corr corr2d self name Correlation Coefficient iunit corr. coefficient N/A property disrelation N/A N/A self N/A N/A N/A  2D Disrelation Spectrum N/A N/A N/A Spec2d from_corr2d N/A self coeff_disr corr2d self name Disrelation Coefficient iunit disr. coefficient N/A property char_index N/A N/A self N/A N/A N/A  Characteristic index.  In Ref. [2], this is the 
        characteristic time, and is equation 6.

        Returns: Spectrum of length equivalent to spectral index.
         N/A m N/A self M N/A N/A N/A N/A np count_nonzero N/A self ref_spectrum 0 N/A N/A N/A CorrError CoDistribution divides by ref spectrum.  If not centring, the ref spec is 0 and you get infinities! N/A coeff N/A 1.0 N/A m N/A self ref_spectrum N/A summation 0 N/A k_matrix N/A N/A np empty m N/A k N/A range 1 N/A m 1 N/A N/A N/A N/A k_matrix fill k N/A summation N/A N/A N/A N/A self dyn_spec dot k_matrix N/A N/A m 1 2 N/A N/A coeff summation N/A property char_perturb N/A N/A self N/A N/A N/A  Characteristic index.  In Ref. [2], this is the 
        characteristic time, and is equation 6.

        Returns: Spectrum of length equivalent to spectral index.
         N/A N/A tm t1 N/A N/A N/A self columns N/A -1 N/A N/A self columns N/A 0 N/A Kj N/A self char_index N/A N/A N/A N/A tm t1 N/A N/A Kj 1 N/A N/A self M 1 t1 N/A property async_codist N/A N/A self N/A N/A N/A  Asynchronous codistribution  N/A numrows N/A N/A self shape N/A 0 N/A async N/A N/A np empty N/A numrows numrows N/A N/A tm t1 N/A N/A N/A self columns N/A -1 N/A N/A self columns N/A 0 N/A tbar N/A N/A self char_perturb values N/A var N/A self joint_var N/A i N/A range numrows N/A N/A j N/A range numrows N/A N/A coeff N/A N/A N/A tbar N/A j N/A tbar N/A i N/A tm t1 N/A N/A N/A async N/A i N/A j N/A coeff N/A var N/A N/A i j N/A N/A N/A Spec2d from_corr2d async corr2d self name Asynchronous Codistribution iunit asynchronicity N/A property sync_codist N/A N/A self N/A N/A N/A  Syncrhonous codistribution.  Computed from asyn_codist N/A numrows N/A N/A self shape N/A 0 N/A var N/A self joint_var N/A async_cod N/A N/A self async_codist values N/A sync N/A N/A np empty N/A numrows numrows N/A i N/A range numrows N/A N/A j N/A range numrows N/A N/A N/A N/A sync N/A i N/A j N/A N/A np sqrt N/A N/A N/A var N/A N/A i j 2 N/A N/A async_cod N/A N/A i j 2 N/A N/A N/A Spec2d from_corr2d sync corr2d self name Synchronous Codistribution iunit synchronicity N/A property plot N/A N/A self N/A pltkwargs N/A N/A  Quad plot shows several kinds of correlation plots. N/A N/A corr_multi self pltkwargs N/A _pcagate N/A N/A self attr N/A N/A N/A  Raise an error if use calls inaccessible PCA method. N/A N/A N/A self _PCA N/A N/A N/A CorrError N/A Please run .pca_fit() method before calling %s.%s N/A N/A self __class__ __name__ attr N/A pca_fit N/A N/A self n_components fit_transform N/A None True N/A N/A          
        Adaptation of Alexis Mignon's pca.py script

        Adapted to fit skspec 5/6/2013.  
        Original credit to Alexis Mignon:
        Module for Principal Component Analysis.

        Author: Alexis Mignon (c)
        Date: 10/01/2012
        e-mail: alexis.mignon@gmail.com
        (https://code.google.com/p/pypca/source/browse/trunk/PCA.py)

        Constructor arguments:
        * k: number of principal components to compute. 'None'
             (default) means that all components are computed.
        * kernel: perform PCA on kernel matrices (default is False)
        * extern: use extern product to perform PCA (default is 
               False). Use this option when the number of samples
               is much smaller than the number of features.            

        See pca.py constructor for more info.

        This will initialize PCA class and fit current values of timespectra.

        Notes:
        ------
        The pcakernel.py module is more modular.  These class methods
        make it easier to perform PCA on a timespectra, but are less 
        flexible than using the module functions directly.

        timespectra gets transposed as PCA module expects rows as 
        samples and columns as features.

        Changes to timespectra do not retrigger PCA refresh.  This 
        method should be called each time changes are made to the data.
         N/A N/A self center N/A N/A N/A N/A logger warn Builtin PCA will perform mean-centering on data.  Data is not mean centered yet. N/A N/A self _PCA N/A PCA n_components n_components N/A fit_transform N/A N/A N/A N/A N/A self _PCA fit_transform N/A self dyn_spec N/A N/A N/A N/A N/A self _PCA fit N/A self dyn_spec N/A PCA N/A N/A self N/A N/A N/A  Return the full PCA class object N/A N/A N/A self _pcagate pca N/A N/A self _PCA N/A property pca_evals N/A N/A self N/A N/A N/A N/A N/A self _pcagate eigen values N/A N/A N/A self _PCA eigen_values_ N/A property pca_evecs N/A N/A self N/A N/A N/A N/A N/A self _pcagate eigen vectors N/A N/A N/A self _PCA eigen_vectors_ N/A property load_vec N/A N/A self k N/A N/A N/A  Return loading vector series for k.  If k > number of components
            computed with runpca(), this raises an error rather than 
            recomputing.
         N/A N/A N/A self _pcagate load_vec N/A N/A k N/A len N/A N/A self shape N/A 1 N/A N/A N/A CorrError N/A Principle components must be <= numberof samples %s N/A N/A self shape N/A 1 N/A N/A N/A self _PCA _k N/A N/A N/A k N/A len N/A self pca_evals N/A N/A N/A N/A logger warn N/A Refitting, only %s components were computedoriginally N/A N/A self _PCA _k N/A N/A N/A self pca_fit n_components k fit_transform False N/A N/A N/A N/A self _PCA eigen_vectors_ N/A N/A N/A k N/A __repr__ N/A N/A self N/A N/A N/A  Aligned columns like pyparty.multicanvas  N/A pad N/A pvconfig PAD N/A address N/A N/A N/A N/A N/A N/A N/A N/A N/A N/A super Corr2d self __repr__ split N/A -1 strip ' strip > N/A outstring N/A %s (%s X %s) at %s:
 N/A N/A N/A self __class__ __name__ N/A N/A self shape N/A 0 N/A N/A self shape N/A 1 address N/A outstring N/A %sCentering -->  %s
 N/A pad N/A self center N/A N/A self _scaled N/A N/A outstring N/A %sScaled    -->  %s
 N/A pad N/A self _scale_string N/A N/A outstring N/A %sScaled    -->  %s
 N/A pad N/A self _scaled N/A outstring N/A %sUnits     -->  [%s X %s] N/A pad N/A N/A N/A self specunit lower N/A N/A N/A self varunit lower N/A outstring N/A N/A N/A N/A __name__ __main__ N/A skspec.data aunps_glass solvent_evap aunps_water N/A numpy np N/A matplotlib.pyplot plt N/A ts N/A solvent_evap N/A cd N/A Corr2d ts N/A N/A N/A cd set_center mean N/A N/A cd sync N/A N/A N/A cd scale alpha 0 beta 0 N/A N/A N/A N/A cd sync plot contours 20 kind corr3d N/A N/A N/A plt show