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  Teem: Tools to process and visualize scientific data and images              
  Copyright (C) 2008, 2007, 2006, 2005  Gordon Kindlmann
  Copyright (C) 2004, 2003, 2002, 2001, 2000, 1999, 1998  University of Utah

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public License
  (LGPL) as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
  The terms of redistributing and/or modifying this software also
  include exceptions to the LGPL that facilitate static linking.

  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public License
  along with this library; if not, write to Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA


#include <stdio.h>
#include <stdlib.h>
#include <limits.h>
#include <math.h>

#include <teem/air.h>
#include <teem/biff.h>
#include <teem/nrrd.h>
#include <teem/unrrdu.h>
#include <teem/gage.h>

#if defined(_WIN32) && !defined(__CYGWIN__) && !defined(TEEM_STATIC)
#  if defined(TEEM_BUILD) || defined(bane_EXPORTS) || defined(teem_EXPORTS)
#    define BANE_EXPORT extern __declspec(dllexport)
#  else
#    define BANE_EXPORT extern __declspec(dllimport)
#  endif
#else /* TEEM_STATIC || UNIX */
#  define BANE_EXPORT extern

#ifdef __cplusplus
extern "C" {

#define BANE baneBiffKey

******** #define BANE_PARM_NUM
** maximum number of parameters that may be needed by a baneInc, baneClip...
#define BANE_PARM_NUM 5

/* -------------------------- ranges -------------------------- */

******** baneRange... enum
** Range: nature of the values generated by a measure- are they
** strictly positive (such as gradient magnitude), should they be
** considered to be centered around zero (2nd directional
** derivative) or could they be anywhere (data
** value).
** The job of the answer() function in the range is not to exclude
** any data.  Indeed, if the range is set correctly for the type
** of data used, then range->ans() should always return a range
** that is as large or larger than the one which was passed.  
** Doing otherwise would make ranges too complicated (such as
** requiring a parm array), and besides, its the job of the
** inclusion methods to be smart about things like this.
enum {
  baneRangeUnknown,      /* 0: nobody knows */
  baneRangePositive,     /* 1: always positive: enforce that min == 0 */
  baneRangeNegative,     /* 2: always negative: enforce that max == 0 */
  baneRangeZeroCentered, /* 3: positive and negative, centered around
                            zero: enforce (conservative) centering of
                            interval around 0 */
  baneRangeAnywhere,     /* 4: anywhere: essentially a no-op */

******** baneRange struct
** things used to operate on ranges
typedef struct {
  char name[AIR_STRLEN_SMALL];
  int type;
  double center;  /* for baneRangeAnywhere: nominal center of value range
                     NOTE: there is currently no API for setting this,
                     it has to be set manually */
  int (*answer)(double *ominP, double *omaxP,
                double imin, double imax);
} baneRange;

/* -------------------------- inc -------------------------- */

******** baneInc... enum
** Inc: methods for determing what range of measured values deserves
** to be included along one axes of a histogram volume.  Each
** inclusion method has some parameters (at most BANE_PARM_NUM)
** which are (or can be harmlessly cast to) floats.  Some of them need
** a histogram (a Nrrd) in order to determine the new min and max,
** some just use a Nrrd as a place to store some information.
** To make matters confusing, the behavior of some of these varies with
** the baneRange they are associated with... 
** As version 1.7, the incParm[] is no longer used to communicate the
** center of a baneRangeAnywhere- that is now (as it should be) in
** the baneRange itself.
enum {
  baneIncUnknown,     /* 0: nobody knows */
  baneIncAbsolute,    /* 1: within explicitly specified bounds 
                         -- incParm[0]: new min
                         -- incParm[1]: new max */
  baneIncRangeRatio,  /* 2: some fraction of the total range
                         -- incParm[0]: scales the size of the range, after
                            it has been sent through the associated range
                            function. */
  baneIncPercentile,  /* 3: exclude some percentile
                         -- incParm[0]: resolution of histogram generated
                         -- incParm[1]: PERCENT of hits to throw away,
                            by nibbling away at lower and upper ends of
                            range, in a manner dependant on the range type */
  baneIncStdv,        /* 4: some multiple of the standard deviation
                         -- incParm[0]: range is standard deviation 
                            times this */

******** baneInc struct
** things used to calculate and describe inclusion ranges.  The return
** from histNew should be eventually passed to nrrdNuke.
typedef struct baneInc_t {
  char name[AIR_STRLEN_SMALL];
  int type;
  double S, SS; int num;  /* used for calculating standard dev */
  Nrrd *nhist;
  baneRange *range;
  double parm[BANE_PARM_NUM];
  void (*process[2])(struct baneInc_t *inc, double val);
  int (*answer)(double *minP, double *maxP,
                Nrrd *hist, double *parm, baneRange *range);
} baneInc;

/* -------------------------- clip -------------------------- */

******** baneClip... enum
** Clip: how to map values in the "raw" histogram volume to the more
** convenient 8-bit version.  The number of hits for the semi-constant
** background of a large volume can be huge, so some scheme for dealing
** with this is needed.
enum {
  baneClipUnknown,     /* 0: nobody knows */
  baneClipAbsolute,    /* 1: clip at explicitly specified bin count */
  baneClipPeakRatio,   /* 2: some fraction of maximum #hits in any bin */
  baneClipPercentile,  /* 3: percentile of values, sorted by hits */
  baneClipTopN,        /* 4: ignore the N bins with the highest counts */

******** baneClip struct
** things used to calculate and describe clipping
typedef struct {
  char name[AIR_STRLEN_SMALL];
  int type;
  double parm[BANE_PARM_NUM];
  int (*answer)(int *countP, Nrrd *hvol, double *clipParm);
} baneClip;

/* -------------------------- measr -------------------------- */

******** baneMeasr... enum
** Measr: one of the kind of measurement which determines location along
** one of the axes of the histogram volume.
** In this latest version of bane (1.4), I nixed the "gradient of magnitude
** of gradient" (GMG) based measure of the second directional
** derivative.  I felt that the benefits of using gage for value and
** derivative measurement (allowing arbitrary kernels), combined with
** the fact that doing GMG can't be done directly in gage (because its
** a derivative of pre-computed derivatives), outweighed the loss of
** GMG.  Besides, according to Appendix C of my Master's thesis the
** only thing its really good at avoiding is quantization noise in
** 8-bit data, but gage isn't limited to 8-bit data anyway.
** The reason for not simply using the pre-defined gageScl values is
** that eventually I'll want to do things which modify/combine those
** values in a parameter-controlled way, something which will never be
** in gage.  Hence the parm array, even though nothing currently
** uses them.
enum {
  baneMeasrUnknown,           /* 0: nobody knows */
  baneMeasrValuePositive,     /* 1: the data value, with positive range
                                 (gageSclValue) */
  baneMeasrValueZeroCentered, /* 2: the data value, with zero-centered range
                                 (gageSclValue) */
  baneMeasrValueAnywhere,     /* 3: the data value, with anywhere range
                                 (gageSclValue) */
  baneMeasrGradMag,           /* 4: gradient magnitude (gageSclGradMag) */
  baneMeasrLaplacian,         /* 5: Laplacian (gageSclLaplacian) */
  baneMeasr2ndDD,             /* 6: Hessian-based measure of 2nd DD along
                                 gradient (gageScl2ndDD) */
  baneMeasrTotalCurv,         /* 7: L2 norm of K1, K2 principal curvatures
                                 (gageSclTotalCurv) */
  baneMeasrFlowlineCurv,      /* 8: curvature of normal streamline
                                 (gageSclFlowlineCurv) */

******** baneMeasr struct
** things used to calculate and describe measurements
typedef struct baneMeasr_t {
  char name[AIR_STRLEN_SMALL];
  int type;
  double parm[BANE_PARM_NUM];
  gageQuery query;       /* the gageScl query needed for this measure,
                            but NOT its recursive prerequisite expansion). */
  baneRange *range;
  int offset0;
  double (*answer)(struct baneMeasr_t *, double *, double *parm);
} baneMeasr;

/* -------------------- histogram volumes, etc. ---------------------- */

******** baneAxis struct
** Information for how to do measurement and inclusion along each axis
** of the histogram volume.
typedef struct {
  unsigned int res;                     /* resolution = number of bins */
  baneMeasr *measr;
  baneInc *inc;
} baneAxis;

******** baneHVolParm struct
** Information for how to create a histogram volume.
typedef struct {
  /* -------------- input */
  int verbose,                         /* status messages to stderr */
    makeMeasrVol,                      /* create a 3 x X x Y x Z volume of
                                          measurements, so that they aren't
                                          measured (as many as) three times */
    renormalize,                       /* use gage's mask renormalization */
  const NrrdKernel *k[GAGE_KERNEL_MAX+1];
  baneClip *clip;
  double incLimit;                     /* lowest permissible fraction of the
                                          data remaining after new inclusion
                                          has been determined */
  baneAxis axis[3];
  /* -------------- internal */
  Nrrd *measrVol;
  int measrVolDone;                    /* values in measrVol are filled */
} baneHVolParm;

/* defaultsBane.c */
BANE_EXPORT const char *baneBiffKey;
BANE_EXPORT int baneDefVerbose;
BANE_EXPORT int baneDefMakeMeasrVol;
BANE_EXPORT double baneDefIncLimit;
BANE_EXPORT int baneDefRenormalize;
BANE_EXPORT int baneDefPercHistBins;
BANE_EXPORT int baneStateHistEqBins;
BANE_EXPORT int baneStateHistEqSmart;
BANE_EXPORT int baneHack;

/* rangeBane.c */
BANE_EXPORT baneRange *baneRangeNew(int type);
BANE_EXPORT baneRange *baneRangeCopy(baneRange *range);
BANE_EXPORT int baneRangeAnswer(baneRange *range,
                                double *ominP, double *omaxP,
                                double imin, double imax);
BANE_EXPORT baneRange *baneRangeNix(baneRange *range);

/* inc.c */
BANE_EXPORT baneInc *baneIncNew(int type, baneRange *range, double *parm);
BANE_EXPORT void baneIncProcess(baneInc *inc, int passIdx, double val);
BANE_EXPORT int baneIncAnswer(baneInc *inc, double *minP, double *maxP);
BANE_EXPORT baneInc *baneIncCopy(baneInc *inc);
BANE_EXPORT baneInc *baneIncNix(baneInc *inc);

/* clip.c */
BANE_EXPORT baneClip *baneClipNew(int type, double *parm);
BANE_EXPORT int baneClipAnswer(int *countP, baneClip *clip, Nrrd *hvol);
BANE_EXPORT baneClip *baneClipCopy(baneClip *clip);
BANE_EXPORT baneClip *baneClipNix(baneClip *clip);

/* measr.c */
BANE_EXPORT baneMeasr *baneMeasrNew(int type, double *parm);
BANE_EXPORT double baneMeasrAnswer(baneMeasr *measr, gageContext *gctx);
BANE_EXPORT baneMeasr *baneMeasrCopy(baneMeasr *measr);
BANE_EXPORT baneMeasr *baneMeasrNix(baneMeasr *measr);

/* methodsBane.c */
/* NOTE: this is NOT a complete API, like gage has.  Currently there
   is only API for things that have to be allocated internally */
BANE_EXPORT baneHVolParm *baneHVolParmNew();
BANE_EXPORT void baneHVolParmGKMSInit(baneHVolParm *hvp);
BANE_EXPORT void baneHVolParmAxisSet(baneHVolParm *hvp, unsigned int axisIdx,
                                     unsigned int res,
                                     baneMeasr *measr, baneInc *inc);
BANE_EXPORT void baneHVolParmClipSet(baneHVolParm *hvp, baneClip *clip);
BANE_EXPORT baneHVolParm *baneHVolParmNix(baneHVolParm *hvp);

/* valid.c */
BANE_EXPORT int baneInputCheck(Nrrd *nin, baneHVolParm *hvp);
BANE_EXPORT int baneHVolCheck(Nrrd *hvol);
BANE_EXPORT int baneInfoCheck(Nrrd *info2D, int wantDim);
BANE_EXPORT int banePosCheck(Nrrd *pos, int wantDim);
BANE_EXPORT int baneBcptsCheck(Nrrd *Bcpts);

/* hvol.c */
BANE_EXPORT void baneProbe(double val[3],
                           Nrrd *nin, baneHVolParm *hvp, gageContext *ctx,
                           unsigned int x, unsigned int y, unsigned int z);
BANE_EXPORT int baneFindInclusion(double min[3], double max[3], 
                                  Nrrd *nin, baneHVolParm *hvp,
                                  gageContext *ctx);
BANE_EXPORT int baneMakeHVol(Nrrd *hvol, Nrrd *nin, baneHVolParm *hvp);
BANE_EXPORT Nrrd *baneGKMSHVol(Nrrd *nin, float gradPerc, float hessPerc);

/* trnsf.c */
BANE_EXPORT int baneOpacInfo(Nrrd *info, Nrrd *hvol, int dim, int measr);
BANE_EXPORT int bane1DOpacInfoFrom2D(Nrrd *info1D, Nrrd *info2D);
BANE_EXPORT int baneSigmaCalc(float *sP, Nrrd *info);
BANE_EXPORT int banePosCalc(Nrrd *pos, float sigma, float gthresh, Nrrd *info);
BANE_EXPORT void _baneOpacCalcA(unsigned int lutLen, float *opacLut, 
                                unsigned int numCpts, float *xo,
                                float *pos);
BANE_EXPORT void _baneOpacCalcB(unsigned int lutLen, float *opacLut, 
                                unsigned int numCpts, float *x, float *o,
                                float *pos);
BANE_EXPORT int baneOpacCalc(Nrrd *opac, Nrrd *Bcpts, Nrrd *pos);

/* trex.c */
BANE_EXPORT float *_baneTRexRead(char *fname);
BANE_EXPORT void _baneTRexDone();

/* scat.c */
BANE_EXPORT int baneRawScatterplots(Nrrd *nvg, Nrrd *nvh, Nrrd *hvol,
                                    int histEq);

/* gkms{Flotsam,Hvol,Scat,Pvg,Opac,Mite}.c */
#define BANE_GKMS_DECLARE(C) BANE_EXPORT unrrduCmd baneGkms_##C##Cmd;
#define BANE_GKMS_LIST(C) &baneGkms_##C##Cmd,
#define BANE_GKMS_MAP(F) \
F(hvol) \
F(scat) \
F(info) \
F(pvg) \
F(opac) \
F(mite) \
BANE_EXPORT airEnum *baneGkmsMeasr;
BANE_EXPORT unrrduCmd *baneGkmsCmdList[]; 
BANE_EXPORT void baneGkmsUsage(char *me, hestParm *hparm);
BANE_EXPORT hestCB *baneGkmsHestIncStrategy;
BANE_EXPORT hestCB *baneGkmsHestBEF;
BANE_EXPORT hestCB *baneGkmsHestGthresh;

#ifdef __cplusplus


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