LALInference.h

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/*
 *
 *  LALInference:             Bayesian Followup
 *  include/LALInference.h:   main header file
 *
 *  Copyright (C) 2009,2012 Ilya Mandel, Vivien Raymond, Christian
 *  Roever, Marc van der Sluys, John Veitch, and Will M. Farr
 *
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 2 of the License, or
 *  (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with with program; see the file COPYING. If not, write to the
 *  Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 *  MA  02110-1301  USA
 */
#ifndef LALInference_h
#define LALInference_h
 
/**
 * \defgroup LALInference_h Header LALInference.h
 * \ingroup lalinference_general
 * \brief Main header file for LALInference common routines and structures
 *
 * LALInference is a Bayesian analysis toolkit for use with LAL. It contains
 * common requirements for Bayesian codes such as Likelihood functions, data
 * handling routines, MCMC and Nested Sampling algorithms and a template generation
 * interface to the LALInspiral package.
 *
 * This file contains the basic structures for the algorithm state, interferometer
 * data, manipulation of variables and type declarations for the standard function types.
 *
 */
/** @{ */
 
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_spline.h>
 
#define VARNAME_MAX 40
#define VARVALSTRINGSIZE_MAX 128
 
#include <lal/LALStdlib.h>
#include <lal/LALConstants.h>
#include <lal/SimulateCoherentGW.h>
#include <lal/GeneratePPNInspiral.h>
#include <lal/LIGOMetadataTables.h>
#include <lal/LALDatatypes.h>
#include <lal/FindChirp.h>
#include <lal/Window.h>
#include <lal/LALString.h>
#include <lal/StringInput.h>
#include <lal/StringVector.h>
#include <lal/LALSimInspiral.h>
#include <lal/LALSimInspiralWaveformCache.h>
#include <lal/LALSimNeutronStar.h>
#include <lal/LALHashTbl.h>
#include <lal/RealFFT.h>
#include <lal/LALDetectors.h>
 
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_min.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_eigen.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_statistics.h>
#include <gsl/gsl_complex_math.h>
#include <gsl/gsl_cdf.h>
 
#include <sys/time.h>
 
/*LIB imports*/
#include <lal/LALInferenceBurstRoutines.h>
 
//...other includes
 
struct tagLALInferenceRunState;
struct tagLALInferenceThreadState;
struct tagLALInferenceIFOData;
struct tagLALInferenceModel;
 
/*Data storage type definitions*/
 
/**
 * An enumerated type for denoting the type of a variable. Several LAL
 * types are supported as well as others.
 */
typedef enum tagLALInferenceVariableType {
  LALINFERENCE_INT4_t,
  LALINFERENCE_INT8_t,
  LALINFERENCE_UINT4_t,
  LALINFERENCE_REAL4_t,
  LALINFERENCE_REAL8_t,
  LALINFERENCE_COMPLEX8_t,
  LALINFERENCE_COMPLEX16_t,
  LALINFERENCE_gslMatrix_t,
  LALINFERENCE_REAL8Vector_t,
  LALINFERENCE_INT4Vector_t,
  LALINFERENCE_UINT4Vector_t,
  LALINFERENCE_COMPLEX16Vector_t,
  LALINFERENCE_string_t,
  LALINFERENCE_MCMCrunphase_ptr_t,
  LALINFERENCE_void_ptr_t
} LALInferenceVariableType;
 
/**
 * An enumerated type for denoting the topology of a parameter.
 * This information is used by the sampling routines when deciding
 * what to vary in a proposal, etc.
 */
typedef enum tagLALInferenceParamVaryType {
        LALINFERENCE_PARAM_LINEAR,   /** A parameter that simply has a maximum and a minimum */
        LALINFERENCE_PARAM_CIRCULAR, /** A parameter that is cyclic, such as an angle between 0 and 2pi */
        LALINFERENCE_PARAM_FIXED,    /** A parameter that never changes, functions should respect this */
        LALINFERENCE_PARAM_OUTPUT    /** A parameter changed by an inner code and passed out */
} LALInferenceParamVaryType;
 
extern size_t LALInferenceTypeSize[15];
 
/**
 * The LALInferenceVariableItem list node structure
 * This should only be accessed using the accessor functions below
 * Implementation may change to hash table so please use only the
 * accessor functions below.
 *
 * A note on memory ownership: each LALInferenceVariableItem() owns
 * the memory for its contents.  This means after calling
 * LALInferenceAddVariable() or LALInferenceSetVariable(), you should
 * not free the memory assoicated with the new variable's value.  In
 * fact, you should not access this memory through its original
 * pointer again (access through pointers returned by
 * LALInferenceGetVariable() is OK); the object may not be live in
 * memory if its variable has been overwritten through another call to
 * LALInferenceSetVariable().
 */
typedef struct
tagVariableItem
{
  char                    name[VARNAME_MAX];
  void                    *value;
  LALInferenceVariableType              type;
  LALInferenceParamVaryType             vary;
  struct tagVariableItem                *next;
} LALInferenceVariableItem;
 
 
/**
 * The LALInferenceVariables structure to contain a set of parameters
 * Implemented as a linked list of LALInferenceVariableItems.
 * Should only be accessed using the accessor functions below
 */
typedef struct
tagLALInferenceVariables
{
  LALInferenceVariableItem      *head;
  INT4                          dimension;
  LALHashTbl        *hash_table;
} LALInferenceVariables;
 
/**
 * Phase of MCMC run (depending on burn-in status, different actions
 * are performed during the run, and this tag controls the activity).
 */
typedef enum tagLALInferenceMCMCRunPhase {
        LALINFERENCE_ONLY_PT,          /** Run only parallel tempers. */
        LALINFERENCE_TEMP_PT,          /** In the parallel tempering phase of an annealed run */
        LALINFERENCE_ANNEALING,        /** In the annealing phase of an annealed run */
        LALINFERENCE_SINGLE_CHAIN,     /** In the single-chain sampling phase of an annealed run */
        LALINFERENCE_LADDER_UPDATE     /** Move all temperature chains to cold chains location (helpful for burnin) */
} LALInferenceMCMCRunPhase;
 
/** Returns an array of header strings (terminated by NULL) from a common-format output file */
char **LALInferenceGetHeaderLine(FILE *inp);
 
/** Converts between internally used parameter names and those external (e.g. in SimInspiralTable?) */
const char *LALInferenceTranslateInternalToExternalParamName(const char *inName);
 
/** Converts between externally used parameter names and those internal */
void LALInferenceTranslateExternalToInternalParamName(char *outName, const char *inName);
 
/**
 * Print the parameter names to a file as a tab-separated ASCII line
 * \param out [in] pointer to output file
 * \param params [in] LALInferenceVaraibles structure to print
 */
int LALInferenceFprintParameterHeaders(FILE *out, LALInferenceVariables *params);
 
/**
 * Print the parameters which do not vary to a file as a tab-separated ASCII line
 * \param out [in] pointer to output file
 * \param params [in] LALInferenceVaraibles structure to print
 */
INT4 LALInferenceFprintParameterNonFixedHeaders(FILE *out, LALInferenceVariables *params);
 
/**
 * Print the parameters which do not vary to a file as a tab-separated ASCII line, adding the given suffix
 * \param out [in] pointer to output file
 * \param params [in] LALInferenceVaraibles structure to print
 * \param suffix [in] Suffix string to add to each parameter name
 */
INT4 LALInferenceFprintParameterNonFixedHeadersWithSuffix(FILE *out, LALInferenceVariables *params, const char *suffix);
 
/** Prints a variable item to a string. Print at most N characters. Returns the number of characters actually required
 * to store the output (can be more or less than N) */
UINT4 LALInferencePrintNVariableItem(char *out, UINT4 N, const LALInferenceVariableItem *const ptr);
 
/**
 * Return a pointer to the memory the variable \c vars is stored in specified by \c name
 * User must cast this pointer to the expected type before dereferencing
 * it to get the value of the variable.
 */
void *LALInferenceGetVariable(const LALInferenceVariables * vars, const char * name);
 
/** Get number of dimensions in variable \c vars */
INT4 LALInferenceGetVariableDimension(LALInferenceVariables *vars);
 
/** Get number of dimensions in \c vars which are not fixed to a certain value */
INT4 LALInferenceGetVariableDimensionNonFixed(LALInferenceVariables *vars);
 
/** Get number of dimensions in \c vars which are not fixed to a certain value,
 *    with a flag for skipping counting vectors */
INT4 LALInferenceGetVariableDimensionNonFixedChooseVectors(LALInferenceVariables *vars, INT4 count_vectors);
 
/**
 * Get the LALInferenceVariableType of the \c idx -th item in the \c vars
 * Indexing starts at 1
 */
INT4 LALInferenceGetVariableTypeByIndex(LALInferenceVariables *vars, int idx);
 
/** Get the LALInferenceVariableType of the parameter named \c name in \c vars */
LALInferenceVariableType LALInferenceGetVariableType(const LALInferenceVariables *vars, const char *name);
 
/**
 * Get the LALInferenceParamVaryType of the parameter named \c name in \c vars
 * see the declaration of LALInferenceParamVaryType for possibilities
 */
LALInferenceParamVaryType LALInferenceGetVariableVaryType(LALInferenceVariables *vars, const char *name);
 
/**
 * Set the LALInferenceParamVaryType of the parameter named \c name in \c vars,
 * see the declaration of LALInferenceParamVaryType for possibilities
 */
void LALInferenceSetParamVaryType(LALInferenceVariables *vars, const char *name, LALInferenceParamVaryType vary);
 
/**
 * Get the name of the idx-th variable
 * Indexing starts at 1
 */
char *LALInferenceGetVariableName(LALInferenceVariables *vars, int idx);
 
/**
 * Set a variable named \c name in \c vars with a value.
 * Pass a void * in \c value to the value you wish to set,
 * i.e. LALInferenceSetVariable(vars, "mu", (void *)&mu);
 */
void LALInferenceSetVariable(LALInferenceVariables * vars, const char * name, const void * value);
 
/**
 * Add a variable named \c name to \c vars with initial value referenced by \c value
 * \param type is a LALInferenceVariableType (enumerated above)
 * \param vary is a LALInferenceParamVaryType (enumerated above)
 * \param vars UNDOCUMENTED
 * \param name UNDOCUMENTED
 * \param value UNDOCUMENTED
 * If the variable already exists it will be over-written UNLESS IT HAS A CONFLICTING TYPE
 */
void LALInferenceAddVariable(LALInferenceVariables * vars, const char * name, const void * value,
        LALInferenceVariableType type, LALInferenceParamVaryType vary);
 
/**
 * Remove \c name from \c vars
 * Frees the memory for the \c name structure and its contents
 */
void LALInferenceRemoveVariable(LALInferenceVariables *vars,const char *name);
 
/**
 * Checks for \c name being present in \c vars
 * returns 1(==true) or 0
 */
int  LALInferenceCheckVariable(LALInferenceVariables *vars,const char *name);
 
/**
 * Checks for \c name being present in \c vars and having type LINEAR or CIRCULAR.
 * returns 1 or 0
 */
int LALInferenceCheckVariableNonFixed(LALInferenceVariables *vars, const char *name);
int LALInferenceCheckVariableToPrint(LALInferenceVariables *vars, const char *name);
/**
 * Delete the variables in this structure.
 * Does not free the LALInferenceVariables itself
 * \param vars will have its dimension set to 0
 */
void LALInferenceClearVariables(LALInferenceVariables *vars);
 
/** Deep copy the variables from one to another LALInferenceVariables structure */
void LALInferenceCopyVariables(LALInferenceVariables *origin, LALInferenceVariables *target);
 
/*  Copy REAL8s from "origin" to "target" if they weren't set on the command line */
void LALInferenceCopyUnsetREAL8Variables(LALInferenceVariables *origin, LALInferenceVariables *target, ProcessParamsTable *commandLine);
 
/** Print variables to stdout */
void LALInferencePrintVariables(LALInferenceVariables *var);
 
/** Check for equality in two variables */
int LALInferenceCompareVariables(LALInferenceVariables *var1, LALInferenceVariables *var2);
 
/** Computes the factor relating the physical waveform to a measured
    waveform for a spline-fit calibration model in amplitude and
    phase.  The spline points can be arbitrary frequencies, and the
    values of the calibration offset at these points can be arbitary,
    too.  For amplitude offset, \f$\delta A\f$, and phase offset,
    \f$\delta \phi\f$, the measured waveform is related to the
    physical waveform via
 
    \f[
      h_\mathrm{meas} = h_\mathrm{phys} \left(1 + \delta A \right) \frac{2 + i \delta \phi}{2 - i \delta \phi}
    \f]
 
    The phase factor takes the form above rather than the more obvious
    \f$\exp(i \delta \phi)\f$ or \f$1 + \delta \phi\f$ because it is
    faster to compute than the former (but, for small \f$\phi\f$,
    equivalent through second order in \f$\delta \phi\f$) and, unlike
    the latter, it ensures that the complex amplitude of the
    correction is always 1.  (A similar technique is used when using
    finite-difference approximations to solve the multi-dimensional
    Schrodinger equation to ensure that the evolution remains
    unitary.)  Note that this implies that the phase calibration
    parameter ranges over \f$\delta \phi \in [-\infty, \infty]\f$.
 
    The values of \f$\delta A\f$ and \f$\delta \phi\f$ at arbitrary
    frequency are obtained by a spline curve that passes through the
    given values at the given frequencies.
 
*/
int LALInferenceSplineCalibrationFactor(REAL8Vector *freqs,
                                        REAL8Vector *deltaAmps,
                                        REAL8Vector *deltaPhases,
                                        COMPLEX16FrequencySeries *calFactor);
 
 /** Modified version of LALInferenceSplineCalibrationFactor to compute the 
 *      calibration factors for the specific frequency nodes used for 
 *      Reduced Order Quadrature likelihoods.
 */
 
int LALInferenceSplineCalibrationFactorROQ(REAL8Vector *logfreqs,
                                        REAL8Vector *deltaAmps,
                                        REAL8Vector *deltaPhases,
                                        REAL8Sequence *freqNodesLin,
                                        COMPLEX16Sequence **calFactorROQLin,
                                        REAL8Sequence *freqNodesQuad,
                                        COMPLEX16Sequence **calFactorROQQuad);
 
 
//Wrapper for template computation
//(relies on LAL libraries for implementation) <- could be a #DEFINE ?
//typedef void (LALTemplateFunction) (LALInferenceVariables *currentParams, struct tagLALInferenceIFOData *data); //Parameter Set is modelParams of LALInferenceIFOData
/**
 * Type declaration for template function, which operates on
 * a LALInferenceIFOData structure \c *data
 */
typedef void (*LALInferenceTemplateFunction) (struct tagLALInferenceModel *model);
 
 
/**
 * Jump proposal distribution
 * Computes \c proposedParams based on \c currentParams
 * and additional variables stored as proposalArgs inside \c runState,
 * which could include correlation matrix, etc.,
 * as well as forward and reverse proposal probability.  The log of the
 * Metropolis-Hasting proposal ratio is returned.
 * A jump proposal distribution function could call other jump proposal
 * distribution functions with various probabilities to allow for multiple
 * jump proposal distributions
 */
typedef REAL8 (*LALInferenceProposalFunction) (struct tagLALInferenceThreadState *thread,
        LALInferenceVariables *currentParams,
        LALInferenceVariables *proposedParams);
 
/**
 * Type declaration for prior function which returns p(\c params)
 * Can depend on \c runState ->priorArgs
 */
typedef REAL8 (*LALInferencePriorFunction) (struct tagLALInferenceRunState *runState,
        LALInferenceVariables *params, struct tagLALInferenceModel *model);
 
/**
 * Type declaration for CubeToPrior function which converts parameters in unit hypercube
 * to their corresponding physical values according to the prior.
 * Can depend on \c runState ->priorArgs
 */
typedef UINT4 (*LALInferenceCubeToPriorFunction) (struct tagLALInferenceRunState *runState,
  LALInferenceVariables *params, struct tagLALInferenceModel *model, double *cube, void *context);
 
/**
 * Detector-dependent buffers and parameters
 * A linked list meant for parameters and buffers that are separately specified for
 * each detector.  The list ordering should be the same as the IFO linked list.
 */
typedef struct
tagLALInferenceIFOModel
{
  LALInferenceVariables       *params; /** Parameters used when filling the buffers - template functions should copy to here */
 
  LALDetector                 *detector; /** LALDetector structure for where this data came from */
 
  void                        *extraData; /** Pointer to extra detector-dependent parameters, used by pulsar analyses */
 
  REAL8TimeSeries             *timehPlus, *timehCross; /** Time series model buffers */
  COMPLEX16FrequencySeries    *freqhPlus, *freqhCross; /** Freq series model buffers */
  COMPLEX16TimeSeries         *compTimeSignal; /** Complex time series signal buffer */
  REAL8TimeSeries             *timeData; /** Time series model buffer */
 
  struct tagLALInferenceIFOModel *next; /** A pointer to the next set of parameters for linked list */
} LALInferenceIFOModel;
 
/**
 * Structure to constain a model and its parameters.
 */
typedef struct tagLALInferenceModel
{
  LALInferenceVariables       *params; /** Parameters used when filling the buffers - template functions should copy to here */
  LALInferenceIFOModel        *ifo; /** IFO-dependent parameters and buffers */
  LALSimulationDomain          domain; /** Domain of model */
  LALInferenceTemplateFunction templt; /** The template generation function */
 
  REAL8                        logprior; /** Prior value at *params* */
  REAL8                        loglikelihood; /** Likelihood value at *params* */
  REAL8                        SNR; /** Network SNR at *params* */
  REAL8*                       ifo_loglikelihoods; /** Array of single-IFO likelihoods at *params* */
  REAL8*                       ifo_SNRs; /** Array of single-IFO SNRs at *params* */
 
  REAL8                        fLow;   /** Start frequency for waveform generation */
  REAL8                        fHigh;   /** End frequency for waveform generation */
  REAL8                        deltaT, deltaF;   /** Sampling rate information */
  INT4                         freqLength; /* Length of freq-domain buffer */
 
  REAL8TimeSeries             *timehPlus, *timehCross; /** Time series model buffers */
  COMPLEX16FrequencySeries    *freqhPlus, *freqhCross; /** Freq series model buffers */
  COMPLEX16FrequencySeries    **freqhs; /** Projected freq series model buffers */
 
  LALDict *LALpars;
  LALSimInspiralWaveformCache *waveformCache;   /** Waveform cache */
  LALSimBurstWaveformCache    *burstWaveformCache;   /** Burst Waveform cache for LIB*/
  REAL8FFTPlan                *timeToFreqFFTPlan, *freqToTimeFFTPlan; /** Pre-calculated FFT plans for forward and reverse FFTs */
  REAL8Window                 *window;        /** A window */
  REAL8                        padding; /** The padding of the above window */
  struct tagLALInferenceROQModel *roq; /** ROQ data */
  int roq_flag;               /** Is ROQ enabled */
  LALSimNeutronStarFamily     *eos_fam; /** Neutron Star equation of state family */
 
} LALInferenceModel;
 
 
/**
 * Type declaration for variables init function, can be user-declared.
 * The function returns a pointer to a new LALInferenceVariables instance
 * Reads \c runState->commandLine to get user config
 */
typedef LALInferenceModel* (*LALInferenceInitModelFunction) (struct tagLALInferenceRunState *runState);
 
 
//Likelihood calculator
//Should take care to perform expensive evaluation of h+ and hx
//only once if possible, unless necessary because different IFOs
//have different data lengths or sampling rates
/**
 * Type declaration for likelihood function
 * Computes p(\c data | \c currentParams, \c templt )
 * templt is a LALInferenceTemplateFunction defined below
 */
typedef REAL8 (*LALInferenceLikelihoodFunction) (LALInferenceVariables *currentParams,
        struct tagLALInferenceIFOData * data, LALInferenceModel *model);
 
/** Perform one step of an algorithm, replaces \c runState ->currentParams */
typedef INT4 (*LALInferenceEvolveOneStepFunction) (struct tagLALInferenceRunState *runState);
 
/** Propose a swap between chain locations */
typedef void (*LALInferenceSwapRoutine) (struct tagLALInferenceRunState *runState, FILE *);
 
/**
 * Type declaration for an algorithm function which is called by the driver code
 * The user must initialise runState before use. The Algorithm manipulates
 * \param runState to do its work
 */
typedef void (*LALInferenceAlgorithm) (struct tagLALInferenceRunState *runState);
 
/** Type declaration for output logging function, can be user-declared */
typedef void (*LALInferenceLogFunction) (LALInferenceVariables *algorithmParams, LALInferenceVariables *vars);
 
 
/**
 * Structure for holding a LALInference proposal, along with name and stats.
 */
typedef struct
tagLALInferenceProposal
{
    LALInferenceProposalFunction func;  /* The actual proposal function */
    char name[VARNAME_MAX]; /* The name of the proposal.  This is used for printing stats */
    INT4   weight;     // Weight of proposal function in cycle
    INT4   proposed;   // Number of times proposal has been called
    INT4   accepted;   // Number of times a proposal from this function has been accepted
    LALInferenceVariables *args; /** Local storage for arguments needed by the proposal (e.g. number of detectors) */
} LALInferenceProposal;
 
/**
 * Structure for holding a proposal cycle
 */
typedef struct
tagLALInferenceProposalCycle
{
    LALInferenceProposal **proposals;  /** Array of proposals (one per proposal function) */
    INT4 *order; /* Array of proposal orders, with each element giving the index of the funcion in *proposals* */
    INT4 length; /** Length of cycle */
    INT4 nProposals; /* The number of unique proposals in the cycle */
    INT4 counter; /** Counter for cycling through proposals */
    char last_proposal_name[VARNAME_MAX]; /** Name of current proposal */
    LALInferenceVariables *proposalArgs; /** Storage for arguments needed by proposal functions (e.g. number of detectors) */
} LALInferenceProposalCycle;
 
/**
 * Structure containing chain-specific variables
 */
typedef struct
tagLALInferenceThreadState
{
    INT4 id; /** Unique integer ID of this thread.  Handy of I/O. */
    char name[VARNAME_MAX];
    INT4 step; /** Step counter for this thread.  Negative numbers indicate burnin*/
    INT4 effective_sample_size; /** Step counter for this thread.  Negative numbers indicate burnin*/
    LALInferenceProposalFunction proposal; /** The proposal cycle */
    LALInferenceProposalCycle *cycle; /** Cycle of proposals to call */
    LALInferenceModel *model; /** Stucture containing model buffers and parameters */
    REAL8 currentPropDensity; /** Array containing multiple proposal densities */
    REAL8 temperature;
    LALInferenceVariables *proposalArgs, /** Arguments needed by proposals */
                          *algorithmParams, /** Stope things such as output arrays */
                          *priorArgs; /** Prior boundaries, etc.  This is
                                          stored at the thread level because proposals
                                          often need to know about prior boundaries */
    LALInferenceVariables *currentParams, /** The current parameters */
                          *preProposalParams, /** Current location going into jump proposal */
                          *proposedParams; /** Parameters proposed */
    LALInferenceVariables **differentialPoints; /** Array of points for differential evolution */
    size_t differentialPointsLength; /** Length of the current differential points stored in
                                         differentialPoints.  This should be removed can be given
                                         as an algorithmParams entry */
    size_t differentialPointsSize; /** Size of the differentialPoints memory block
                                       (must be >= length of differential points).
                                        Can also be removed. */
    size_t differentialPointsSkip; /** When the DE buffer gets too long, start storing
                                       only every n-th output point; this counter stores n */
    REAL8 *currentIFOSNRs; /** Array storing single-IFO SNRs of current sample */
    REAL8 *currentIFOLikelihoods; /** Array storing single-IFO likelihoods of current sample */
    REAL8 currentSNR; /** Array storing network SNR of current sample */
    REAL8 nullLikelihood;
    REAL8 currentLikelihood; /** This should be removed, can be given as an algorithmParams or proposalParams entry */
    REAL8 currentPrior; /** This should be removed, can be given as an algorithmParams entry */
    INT4 accepted;
    INT4 acceptanceCount;
    gsl_rng *GSLrandom;
    REAL8 creation_time;
    struct tagLALInferenceRunState *parent; /** Pointer to the parent RunState of the thread.  e.g., Useful for getting data */
    INT4 *temp_swap_accepts;
    INT4 temp_swap_window;
    INT4 temp_swap_counter;
} LALInferenceThreadState;
 
 
/**
 * Structure containing inference run state
 * This includes pointers to the function types required to run
 * the algorithm, and data structures as required
 */
typedef struct
tagLALInferenceRunState
{
  ProcessParamsTable        *commandLine; /** A ProcessParamsTable with command line arguments */
  LALInferenceInitModelFunction  initModel; /** A function that returns a new set of variables for the model */
  LALInferenceAlgorithm              algorithm; /** The algorithm function */
  LALInferenceEvolveOneStepFunction  evolve; /** The algorithm's single iteration function */
  LALInferencePriorFunction          prior; /** The prior for the parameters */
  LALInferenceCubeToPriorFunction    CubeToPrior; /** MultiNest prior for the parameters */
  LALInferenceLikelihoodFunction     likelihood; /** The likelihood function */
  LALInferenceLogFunction            logsample; /** Log sample, i.e. to disk */
  struct tagLALInferenceIFOData      *data; /** The data from the interferometers */
  LALInferenceVariables *proposalArgs; /** Common arguments needed by proposals, to be copied to thread->cycle */
  LALInferenceVariables              *priorArgs,     /** Any special arguments for the prior function */
    *algorithmParams;                                /** Parameters which control the running of the algorithm*/
  LALInferenceVariables                         **livePoints; /** Array of live points for Nested Sampling */
  INT4 nthreads; /** Number of threads stored in ``threads``. */
  LALInferenceSwapRoutine  parallelSwap;
  gsl_rng *GSLrandom;
  char *outFileName; /** Name for thread's output file */
  char *resumeOutFileName; /** Name for thread's resume file */
  char runID[VARNAME_MAX];
  LALInferenceThreadState          *threads; /** Array of chains for this run */
 
} LALInferenceRunState;
 
 
#define DETNAMELEN 8
 
/**
 * Structure to contain IFO data.
 * Some fields may be left empty if not needed
 */
typedef struct
tagLALInferenceIFOData
{
  char                       name[DETNAMELEN]; /** Detector name */
  REAL8TimeSeries           *timeData,         /** A time series from the detector */
                            *whiteTimeData, *windowedTimeData; /** white is not really white, but over-white. */
  REAL8TimeSeries           *varTimeData;    /** A time series of the data noise variance */
  /* Stores the log(L) for the model in presence of data.  These were
     added to allow for individual-detector log(L) output.  The
     convention is that loglikelihood always stores the log(L) for the
     model in freqModel... or timeModel....  When a jump is accepted,
     that value is copied into acceptedloglikelihood, which is the
     quantity that is actually output in the output files. */
  REAL8                      nullloglikelihood;
  REAL8                      fPlus, fCross; /** Detector responses */
  REAL8                      timeshift;     /** What is this? */
  COMPLEX16FrequencySeries  *freqData,      /** Buffer for frequency domain data */
                            *whiteFreqData; /* Over-white. */
  COMPLEX16TimeSeries       *compTimeData;  /** Complex time series data buffers */
  LALInferenceVariables     *dataParams;    /* Optional data parameters */
  REAL8FrequencySeries      *oneSidedNoisePowerSpectrum;  /** one-sided Noise Power Spectrum */
  REAL8FrequencySeries      *noiseASD;  /** (one-sided Noise Power Spectrum)^{-1/2} */
//  REAL8TimeSeries           *timeDomainNoiseWeights; /** Roughly, InvFFT(1/Noise PSD). */
  REAL8Window               *window;        /** A window */
  REAL8                      padding; /** Padding for the above window */
  REAL8FFTPlan              *timeToFreqFFTPlan, *freqToTimeFFTPlan; /** Pre-calculated FFT plans for forward and reverse FFTs */
  REAL8FFTPlan              *margFFTPlan; /** FFT plan needed for time/time-and-phase marginalisation */
  REAL8                     fLow, fHigh;        /** integration limits for overlap integral in F-domain */
  LALDetector               *detector;          /** LALDetector structure for where this data came from */
  LIGOTimeGPS               epoch;              /** The epoch of this observation (the time of the first sample) */
  REAL8                     SNR;                /** IF INJECTION ONLY, E(SNR) of the injection in the detector.*/
  REAL8                     STDOF;              /** Degrees of freedom for IFO to be used in Student-T Likelihood. */
  UINT4                     likeli_counter; /** counts how many time the likelihood has been calculated */
  UINT4                     templa_counter; /** counts how many time the template has been calculated */
  struct tagLALInferenceROQData *roq; /** ROQ data */
 
  struct tagLALInferenceIFOData      *next;     /** A pointer to the next set of data for linked list */
} LALInferenceIFOData;
 
typedef struct
tagLALInferenceROQData
{
  COMPLEX16 *weightsLinear; /** weights for <d|h>: NOTE: needs to be stored from data read from command line */
  REAL8 *weightsQuadratic; /** weights for calculating <h|h>*/
  REAL8 time_weights_width;
  REAL8 time_step_size;
  int n_time_steps;
  FILE *weightsFileLinear;
  FILE *weightsFileQuadratic;
 
 
  struct tagLALInferenceROQSplineWeightsLinear *weights_linear;
 
 
  /* Deprecated functions that should be removed at some point */ 
  gsl_matrix_complex *weights; /** weights for the likelihood: NOTE: needs to be stored from data read from command line */
  gsl_matrix_complex *mmweights; /** weights for calculating <h|h> if not using analytical formula */
  double int_f_7_over_3; /** /int_{fmin}^{fmax} df f^(-7/3)/psd...for <h|h> part of the likelihood */
  /* end deprecated function */
 
} LALInferenceROQData;
 
/**
 *  *  * Structure to contain spline of ROQ weights as a function of tc
 *   *   */
 
typedef struct
tagLALInferenceROQSplineWeightsLinear
{
  
 
  gsl_spline *spline_real_weight_linear;
  gsl_spline *spline_imag_weight_linear; 
  gsl_interp_accel *acc_real_weight_linear;
  gsl_interp_accel *acc_imag_weight_linear;
 
} LALInferenceROQSplineWeights;
/**
 *  * Structure to contain model-related Reduced Order Quadrature quantities
 *   */
typedef struct
tagLALInferenceROQModel
{
  COMPLEX16FrequencySeries *hptildeLinear;
  COMPLEX16FrequencySeries *hctildeLinear;
  COMPLEX16FrequencySeries *hptildeQuadratic;
  COMPLEX16FrequencySeries *hctildeQuadratic;
 
  COMPLEX16Sequence *calFactorLinear;
 
  COMPLEX16Sequence *calFactorQuadratic;
 
  REAL8Sequence  * frequencyNodesLinear; /** empirical frequency nodes for the likelihood. NOTE: needs to be stored from data read from command line */
  REAL8Sequence * frequencyNodesQuadratic;
  REAL8 trigtime;
  REAL8 ROQnullLikelihood;
  
  FILE *nodesFileLinear;
  FILE *nodesFileQuadratic;
   
  /* Deprecated functions that should be removed at some point */
  gsl_vector_complex *hplus; /** waveform at frequency nodes. */
  gsl_vector_complex *hcross;
  gsl_vector_complex *hstrain;
  gsl_vector         *frequencyNodes; /** empirical frequency nodes for the likelihood. NOTE: needs to be stored from data read from command line */
  REAL8* amp_squared;
  /* end Deprecated functions */
 
} LALInferenceROQModel;
 
/**
 * Structure to contain data-related Reduced Order Quadrature quantities
 */
/* Initialize an empty thread, saving a timestamp for benchmarking */
LALInferenceThreadState *LALInferenceInitThread(LALInferenceThreadState *thread);
 
/* Initialize a bunch of threads using LALInferenceInitThread */
LALInferenceThreadState *LALInferenceInitThreads(INT4 nthreads);
 
/** Returns the element of the process params table with "name" */
ProcessParamsTable *LALInferenceGetProcParamVal(ProcessParamsTable *procparams,const char *name);
 
/**
 * parses a character string (passed as one of the options) and decomposes
 * it into individual parameter character strings. \c input is of the form
 * input   :  \"[one,two,three]\"
 * and the resulting output \c strings is
 * strings :  {\"one\", \"two\", \"three\"}
 * length of parameter names is for now limited to 512 characters.
 * (should 'theoretically' (untested) be able to digest white space as well.
 * Irrelevant for command line options, though.)
 * \c n UNDOCUMENTED
 */
void LALInferenceParseCharacterOptionString(char *input, char **strings[], UINT4 *n);
 
/** Return a ProcessParamsTable from the command line arguments */
ProcessParamsTable *LALInferenceParseCommandLine(int argc, char **argv);
 
/** Return a ProcessParamsTrable from a string vector */
ProcessParamsTable *LALInferenceParseStringVector(LALStringVector *arglist);
 
/** Return a ProcessParamsTable from the command line arguments (SWIG version) */
ProcessParamsTable *LALInferenceParseCommandLineStringVector(LALStringVector *args);
 
/** Output the command line based on the ProcessParamsTable \c procparams */
char* LALInferencePrintCommandLine(ProcessParamsTable *procparams);
 
/** Execute FFT for data in \c IFOdata */
void LALInferenceExecuteFT(LALInferenceModel *model);
/** Execute Inverse FFT for data in \c IFOdata */
void LALInferenceExecuteInvFT(LALInferenceModel *model);
 
/** Return the list node for "name" - do not rely on this */
LALInferenceVariableItem *LALInferenceGetItem(const LALInferenceVariables *vars,const char *name);
 
/**
 * Return the list node for the idx-th item - do not rely on this
 * Indexing starts at 1
 */
LALInferenceVariableItem *LALInferenceGetItemNr(LALInferenceVariables *vars, int idx);
 
/**
 * Pop the list node for "name". Returns a pointer to the node, which is removed from vars
 */
LALInferenceVariableItem *LALInferencePopVariableItem(LALInferenceVariables *vars, const char *name);
 
/** Output the sample to file *fp, in ASCII format */
void LALInferencePrintSample(FILE *fp,LALInferenceVariables *sample);
 
/** Output only non-fixed parameters */
void LALInferencePrintSampleNonFixed(FILE *fp,LALInferenceVariables *sample);
 
/** Output spline calibration parameters */
void LALInferencePrintSplineCalibration(FILE *fp, LALInferenceThreadState *thread);
 
/** Read in the non-fixed parameters from the given file (position in
    the file must be arranged properly before calling this
    function). */
void LALInferenceReadSampleNonFixed(FILE *fp, LALInferenceVariables *sample);
 
/** Utility for readling in delimited ASCII files. */
REAL8 *LALInferenceParseDelimitedAscii(FILE *input, INT4 nCols, INT4 *wantedCols, INT4 *nLines);
 
/* Parse a single line of delimited ASCII. */
void parseLine(char *record, const char *delim, char arr[][VARNAME_MAX], INT4 *cnt);
 
/* Discard the standard header of a PTMCMC chain file. */
void LALInferenceDiscardPTMCMCHeader(FILE *filestream);
 
/* Burn-in a PTMCMC output file. */
void LALInferenceBurninPTMCMC(FILE *filestream, INT4 logl_idx, INT4 nPar);
 
/* Burn-in a generic ASCII stream. */
void LALInferenceBurninStream(FILE *filestream, INT4 burnin);
 
/* Read column names from an ASCII file. */
void LALInferenceReadAsciiHeader(FILE *input, char params[][VARNAME_MAX], INT4 *nCols);
 
/* Utility for selecting columns from an array, in the specified order. */
REAL8 **LALInferenceSelectColsFromArray(REAL8 **inarray, INT4 nRows, INT4 nCols, INT4 nSelCols, INT4 *selCols);
 
/** Output proposal statistics header to file *fp */
int LALInferencePrintProposalStatsHeader(FILE *fp, LALInferenceProposalCycle *cycle);
 
/** Output proposal statistics to file *fp */
void LALInferencePrintProposalStats(FILE *fp, LALInferenceProposalCycle *cycle);
 
/**
 * Reads one line from the given file and stores the values there into
 * the variable structure, using the given header array to name the
 * columns.  Returns 0 on success.
 */
void LALInferenceProcessParamLine(FILE *inp, char **headers, LALInferenceVariables *vars);
 
/** Sorts the variable structure by name */
void LALInferenceSortVariablesByName(LALInferenceVariables *vars);
 
/** LALInferenceVariable buffer to array and vica versa */
INT4 LALInferenceThinnedBufferToArray(LALInferenceThreadState *thread, REAL8** DEarray, INT4 step);
INT4 LALInferenceBufferToArray(LALInferenceThreadState *thread, REAL8** DEarray);
 
/** LALInference variables to an array, and vica versa */
void LALInferenceCopyVariablesToArray(LALInferenceVariables *origin, REAL8 *target);
 
void LALInferenceCopyArrayToVariables(REAL8 *origin, LALInferenceVariables *target);
 
/**
 * Append the sample to a file. file pointer is stored in state->algorithmParams as a
 * LALInferenceVariable called "outfile", as a void ptr.
 * Caller is responsible for opening and closing file.
 * Variables are alphabetically sorted before being written
 */
void LALInferenceLogSampleToFile(LALInferenceVariables *algorithmParams, LALInferenceVariables *vars);
 
/**
 * Append the sample to an array which can be later processed by the user.
 * Array is stored as a C array in a LALInferenceVariable in state->algorithmParams
 * called "outputarray". Number of items in the array is stored as "N_outputarray".
 * Will create the array and store it in this way if it does not exist.
 * DOES NOT FREE ARRAY, user must clean up after use.
 * Also outputs sample to disk if possible using LALInferenceLogSampleToFile()
 */
void LALInferenceLogSampleToArray(LALInferenceVariables *algorithmParams, LALInferenceVariables *vars);
 
/** Convert from Mc, eta space to m1, m2 space (note m1 > m2).*/
void LALInferenceMcEta2Masses(double mc, double eta, double *m1, double *m2);
 
/** Convert from Mc, q space to m1, m2 space (q = m2/m1, with m1 > m2). */
void LALInferenceMcQ2Masses(double mc, double q, double *m1, double *m2);
 
/** Convert from q to eta (q = m2/m1, with m1 > m2). */
void LALInferenceQ2Eta(double q, double *eta);
/** Convert from dQuadMonS, dQuadMonA to dQuadMon1, dQuadMon2. */
void LALInferencedQuadMonSdQuadMonA(REAL8 dQuadMonS, REAL8 dQuadMonA, REAL8 *dQuadMon1, REAL8 *dQuadMon2);
/** Convert from lambdaT, dLambdaT, and eta to lambda1 and lambda2. */
void LALInferenceLambdaTsEta2Lambdas(REAL8 lambdaT, REAL8 dLambdaT, REAL8 eta, REAL8 *lambda1, REAL8 *lambda2);
 
/** Calculate lambda1,2(m1,2|eos(logp1,gamma1,gamma2,gamma3)) */
void LALInferenceLogp1GammasMasses2Lambdas(REAL8 logp1, REAL8 gamma1, REAL8 gamma2, REAL8 gamma3, REAL8 mass1, REAL8 mass2, REAL8 *lambda1, REAL8 *lambda2);
 
/** Convert from spectral parameters to lambda1, lambda2 */
void LALInferenceSDGammasMasses2Lambdas(REAL8 gamma[], REAL8 mass1, REAL8 mass2, REAL8 *lambda1, REAL8 *lambda2, int size);
 
/** Check for causality violation and mass conflict given masses and eos */
int LALInferenceEOSPhysicalCheck(LALInferenceVariables *params, ProcessParamsTable *commandLine);
 
/** Specral decomposition of eos's adiabatic index */
double AdiabaticIndex(double gamma[],double x, int size);
 
/** Determine if the Adiabatic index is within 'prior' range */
int LALInferenceSDGammaCheck(double gamma[], int size);
 
/**
 * The kD trees in LALInference are composed of cells.  Each cell
 * represents a rectangular region in parameter space, defined by
 * \f$\mathrm{lowerLeft} <= x <= \mathrm{upperRight}\f$.  It also
 * contains two sub-cells, each of which represents rectangular
 * regions of half the size. The dimension along which a cell at a
 * particular level in the tree is split in half is given by its
 * level (mod the dimension of the space).
 *
 * Each cell contains some number (which may be zero) of points.
 * Periodically, the cell will compute the mean and covariance of its
 * points, and the eigenvectors of the covariance matrix (principal
 * axes) of an ellipse fitting the the points.  It will also compute
 * the (tight) bounds of a box enclosing the points in a coordinate
 * system aligned with the principal axes.  When this has been done,
 * the \c eigenFrameStale element will be set to zero.  If points are
 * subsequently added to the cell, the \c eigenFrameStale flag will
 * be set to a non-zero value until the next re-computation of the
 * principal axes.
 */
typedef struct tagLALInferenceKDTree {
  size_t npts; /** Stores the number of tree points that lie in the cell. */
  size_t ptsSize; /** Size of the pts buffer. */
  size_t dim; /** Dimension of the system. */
  REAL8 **pts;
  REAL8 *ptsMean; /** Mean of pts. */
  REAL8 *lowerLeft; /** Lower left (i.e. coordinate minimum) bound;
                         length is ndim from LALInferenceKDTree. */
  REAL8 *upperRight; /** Upper right (i.e. coordinate maximum) bound. */
  REAL8 **ptsCov; /** dim-by-dim covariance matrix. */
  REAL8 **ptsCovEigenVects; /** Eigenvectors of the covariance matrix:
                                [i][j] is the jth component of the ith
                                eigenvector. */
  REAL8 *eigenMin; /** Minimum coordinates of points in the eigen-frame. */
  REAL8 *eigenMax; /** Maximum coordinates of points in the eigen-frame. */
  int eigenFrameStale; /** == 1 when the mean, covariance, and
                           eigenvectors are out of date (i.e. more
                           points added). */
  struct tagLALInferenceKDTree *left; /** Left (i.e. lower-coordinate)
                                          sub-tree, may be NULL if
                                          empty.*/
  struct tagLALInferenceKDTree *right; /** Right
                                           (i.e. upper-coordinate)
                                           sub-tree, may be NULL if
                                           empty. */
} LALInferenceKDTree;
 
/** Delete a kD-tree.  Also deletes all contained cells, and points. */
void LALInferenceKDTreeDelete(LALInferenceKDTree *tree);
 
/**
 * Constructs a fresh, empty kD tree.  The top-level cell will get
 * the given bounds, which should enclose every point added by
 * LALInferenceKDAddPoint().
 */
LALInferenceKDTree *LALInferenceKDEmpty(REAL8 *lowerLeft, REAL8 *upperRight, size_t ndim);
 
/**
 * Adds a point to the kD-tree, returns 0 on successful exit.  The
 * memory for pt is owned by the tree, so should not be deallocated
 * or modified except by LALInferenceKDTreeDelete().
 */
int LALInferenceKDAddPoint(LALInferenceKDTree *tree, REAL8 *pt);
 
/**
 * Returns the first cell that contains the given point that also
 * contains fewer than Npts points, if possible.  If no cell
 * containing the given point has fewer than Npts points, then
 * returns the cell containing the fewest number of points and the
 * given point.  Non-positive Npts will give the fewest-point cell in
 * the tree containing the given point.  Returns NULL on error.
 */
LALInferenceKDTree *LALInferenceKDFindCell(LALInferenceKDTree *tree, REAL8 *pt, size_t Npts);
 
/**
 * Returns the log of the volume of the given cell, which is part of
 * the given tree.
 */
double LALInferenceKDLogCellVolume(LALInferenceKDTree *cell);
 
/**
 * Returns the log of the volume of the box aligned with the
 * principal axes of the points in the given cell that tightly
 * encloses those points.
 */
double LALInferenceKDLogCellEigenVolume(LALInferenceKDTree *cell);
 
/**
 * Fills in the given REAL8 array with the parameter values from
 * params; the ordering of the variables is taken from the order of
 * the non-fixed variables in \c templt.  It is an error if pt does
 * not point to enough storage to store all the non-fixed parameters
 * from \c templt and \c params.
 */
void LALInferenceKDVariablesToREAL8(LALInferenceVariables *params, REAL8 *pt, LALInferenceVariables *templt);
 
/**
 * Fills in the non-fixed variables in params from the given REAL8
 * array.  The ordering of variables is given by the order of the
 * non-fixed variables in \c templt.
 */
void LALInferenceKDREAL8ToVariables(LALInferenceVariables *params, REAL8 *pt, LALInferenceVariables *templt);
 
/**
 * Draws a \c pt uniformly from a randomly chosen cell of \c
 * tree. The chosen cell will be chosen to have (as nearly as
 * possible) \c Npts in it.
 */
void LALInferenceKDDrawEigenFrame(gsl_rng * rng, LALInferenceKDTree *tree, REAL8 *pt, size_t Npts);
 
/**
 * Returns the log of the jump proposal probability ratio for the
 * LALInferenceKDDrawEigenFrame() proposal to propose the point \c
 * proposed given the current position \c current , where \c Npts is
 * the parameter used to select the box to draw from in
 * LALInferenceKDDrawEigenFrame().
 */
REAL8 LALInferenceKDLogProposalRatio(LALInferenceKDTree *tree, REAL8 *current,
                                     REAL8 *proposed, size_t Npts);
 
/** Check matrix is positive definite. dim is matrix dimensions */
UINT4 LALInferenceCheckPositiveDefinite(
                          gsl_matrix       *matrix,
                          UINT4            dim
                          );
 
/** Draw a random multivariate vector from Gaussian distr given covariance matrix */
void
XLALMultiNormalDeviates(
                        REAL4Vector *vector,
                        gsl_matrix *matrix,
                        UINT4 dim,
                        RandomParams *randParam
                        );
/** Draw a random multivariate vector from student-t distr given covariance matrix */
void
XLALMultiStudentDeviates(
                         REAL4Vector  *vector,
                         gsl_matrix   *matrix,
                         UINT4         dim,
                         UINT4         n,
                         RandomParams *randParam
                         );
 
 
/** Calculate shortest angular distance between a1 and a2 (modulo 2PI) */
REAL8 LALInferenceAngularDistance(REAL8 a1, REAL8 a2);
 
/** Calculate the variance of a distribution on an angle (modulo 2PI) */
REAL8 LALInferenceAngularVariance(LALInferenceVariables **list,const char *pname, int N);
 
/** Sanity check the structures in the given state. Will scan data for infinities and nans, and look for null pointers. */
INT4 LALInferenceSanityCheck(LALInferenceRunState *state);
 
/**
 * Dump all waveforms from the ifodata structure. (currently: timeData, freqData)
 * basefilename is optional text to append to file names
 */
void LALInferenceDumpWaveforms(LALInferenceModel *model, const char *basefilename);
 
/**
 * Write a LALInferenceVariables as binary to a given FILE pointer, returns the number
 * of items written (should be the dimension of the variables) or -1 on error
 */
int LALInferenceWriteVariablesBinary(FILE *file, LALInferenceVariables *vars);
 
/**
 * Read from the given FILE * a LALInferenceVariables, which was previously
 * written with LALInferenceWriteVariablesBinary() Returns a new LALInferenceVariables
 */
LALInferenceVariables *LALInferenceReadVariablesBinary(FILE *stream);
 
/**
 * Write an array N of LALInferenceVariables to the given FILE * using
 * LALInferenceWriteVariablesBinary(). Returns the number written (should be ==N)
 */
int LALInferenceWriteVariablesArrayBinary(FILE *file, LALInferenceVariables **vars, UINT4 N);
 
/**
 * Read N LALInferenceVariables from the binary FILE *file, previously written with
 * LALInferenceWriteVariablesArrayBinary() returns the number read
 */
int LALInferenceReadVariablesArrayBinary(FILE *file, LALInferenceVariables **vars, UINT4 N);
 
/**
 * Write the LALInferenceVariables contents of runState to a file in binary format
 */
int LALInferenceWriteRunStateBinary(FILE *file, LALInferenceRunState *state);
 
/**
 * Reads the file and populates LALInferenceVariables in the runState that
 * were saved with LALInferenceReadVariablesArrayBinary()
 */
int LALInferenceReadRunStateBinary(FILE *file, LALInferenceRunState *state);
 
 
void LALInferenceAddINT4Variable(LALInferenceVariables * vars, const char * name, INT4 value, LALInferenceParamVaryType vary);
 
INT4 LALInferenceGetINT4Variable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetINT4Variable(LALInferenceVariables* vars,const char* name,INT4 value);
 
void LALInferenceAddINT8Variable(LALInferenceVariables * vars, const char * name, INT8 value, LALInferenceParamVaryType vary);
 
INT8 LALInferenceGetINT8Variable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetINT8Variable(LALInferenceVariables* vars,const char* name,INT8 value);
 
void LALInferenceAddUINT4Variable(LALInferenceVariables * vars, const char * name, UINT4 value, LALInferenceParamVaryType vary);
 
UINT4 LALInferenceGetUINT4Variable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetUINT4Variable(LALInferenceVariables* vars,const char* name,UINT4 value);
 
void LALInferenceAddREAL4Variable(LALInferenceVariables * vars, const char * name, REAL4 value, LALInferenceParamVaryType vary);
 
REAL4 LALInferenceGetREAL4Variable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetREAL4Variable(LALInferenceVariables* vars,const char* name,REAL4 value);
 
void LALInferenceAddREAL8Variable(LALInferenceVariables * vars, const char * name, REAL8 value, LALInferenceParamVaryType vary);
 
REAL8 LALInferenceGetREAL8Variable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetREAL8Variable(LALInferenceVariables* vars,const char* name,REAL8 value);
 
void LALInferenceAddCOMPLEX8Variable(LALInferenceVariables * vars, const char * name, COMPLEX8 value, LALInferenceParamVaryType vary);
 
COMPLEX8 LALInferenceGetCOMPLEX8Variable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetCOMPLEX8Variable(LALInferenceVariables* vars,const char* name,COMPLEX8 value);
 
void LALInferenceAddCOMPLEX16Variable(LALInferenceVariables * vars, const char * name, COMPLEX16 value, LALInferenceParamVaryType vary);
 
COMPLEX16 LALInferenceGetCOMPLEX16Variable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetCOMPLEX16Variable(LALInferenceVariables* vars,const char* name,COMPLEX16 value);
 
void LALInferenceAddgslMatrixVariable(LALInferenceVariables * vars, const char * name, gsl_matrix* value, LALInferenceParamVaryType vary);
 
gsl_matrix* LALInferenceGetgslMatrixVariable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetgslMatrixVariable(LALInferenceVariables* vars,const char* name,gsl_matrix* value);
 
void LALInferenceAddREAL8VectorVariable(LALInferenceVariables * vars, const char * name, REAL8Vector* value, LALInferenceParamVaryType vary);
 
REAL8Vector* LALInferenceGetREAL8VectorVariable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetREAL8VectorVariable(LALInferenceVariables* vars,const char* name,REAL8Vector* value);
 
void LALInferenceAddCOMPLEX16VectorVariable(LALInferenceVariables * vars, const char * name, COMPLEX16Vector* value, LALInferenceParamVaryType vary);
 
COMPLEX16Vector* LALInferenceGetCOMPLEX16VectorVariable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetCOMPLEX16VectorVariable(LALInferenceVariables* vars,const char* name,COMPLEX16Vector* value);
 
void LALInferenceAddINT4VectorVariable(LALInferenceVariables * vars, const char * name, INT4Vector* value, LALInferenceParamVaryType vary);
 
void LALInferenceAddUINT4VectorVariable(LALInferenceVariables * vars, const char * name, UINT4Vector* value, LALInferenceParamVaryType vary);
 
INT4Vector* LALInferenceGetINT4VectorVariable(LALInferenceVariables * vars, const char * name);
 
UINT4Vector* LALInferenceGetUINT4VectorVariable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetINT4VectorVariable(LALInferenceVariables* vars, const char* name, INT4Vector* value);
 
void LALInferenceSetUINT4VectorVariable(LALInferenceVariables* vars, const char* name, UINT4Vector* value);
 
void LALInferenceAddMCMCrunphase_ptrVariable(LALInferenceVariables * vars, const char * name, LALInferenceMCMCRunPhase* value, LALInferenceParamVaryType vary);
 
LALInferenceMCMCRunPhase* LALInferenceGetMCMCrunphase_ptrVariable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetMCMCrunphase_ptrVariable(LALInferenceVariables* vars,const char* name,LALInferenceMCMCRunPhase* value);
 
#ifdef SWIG   /* SWIG interface directives */
SWIGLAL(OWNS_THIS_ARG(const CHAR*, value));
#endif
 
void LALInferenceAddstringVariable(LALInferenceVariables * vars, const char * name, const CHAR* value, LALInferenceParamVaryType vary);
 
const CHAR* LALInferenceGetstringVariable(LALInferenceVariables * vars, const char * name);
 
void LALInferenceSetstringVariable(LALInferenceVariables* vars,const char* name, const CHAR* value);
 
#ifdef SWIG   /* SWIG interface directives */
SWIGLAL_CLEAR(OWNS_THIS_ARG(const CHAR*, value));
#endif
 
/**
 * Print spline calibration parameter names as tab-separated ASCII
 */
void LALInferenceFprintSplineCalibrationHeader(FILE *output, LALInferenceThreadState *thread);
 
/**
 * Compute Tidal deformabilities following BinaryLove Universal relations
 */
void LALInferenceBinaryLove(LALInferenceVariables *vars, REAL8 *lambda1, REAL8 *lambda2);
 
 
/**
 * Conversion routines between Equatorial (RA,DEC) and detector-based coordinate systems, where
 * new "north pole" points along vector from det0 to det1.
 * theta - azimuth angle about vector joining det0 and det1
 * alpha - co-latitude (0,pi) relative to det0-det1 vector
 */
void LALInferenceDetFrameToEquatorial(LALDetector *det0, LALDetector *det1,
                                      REAL8 t0, REAL8 alpha, REAL8 theta,
                                      REAL8 *tg, REAL8 *ra, REAL8 *dec);
 
void LALInferenceEquatorialToDetFrame(LALDetector *det0, LALDetector *det1,
                                 REAL8 tg, REAL8 ra, REAL8 dec,
                                 REAL8 *t0, REAL8 *alpha, REAL8 *theta);
 
/** @} */
 
#endif