/*
 * dicen.h
 *
 * structure and constant definitions for dicentric detection
 * by the candidate generation from density profile followed
 * by feature extraction and within-cell box classification method.
 *
 *******************************************************************************
 * MODIFICATION HISTORY
 * --------------------
 * 22-05-90	jimp	added kurtosis and crossing-profile curvature features.
 *			Needed to increase MAXFEATURES.
 *
 * ??-??-90	joanne	added various bits and bobs.
 *
 * 21-06-88	jimp	added ->obj,->cpol for display program
 * 08-04-88	jimp	added mom1ratio feature
 * 28-03-88	jimp	added ovFP, ovFN to struct dcresults
 * 23-03-88	jimp	Added porigin
 * 11-03-88	simon	Added curvsum
 * 02-03-88	jimp	Added profcurv
 * 25-02-88	jimp	Added axislen,neardistfeat
 * 02-02-88	jimp	Added struct dcresults.
 * 20-01-88	jimp	Added "neardist" for nearest other-type candidate.
 * 21-01-87	jimp	First atempt to expand to accomodate both Jim and Simon.
 * 10-02-87	jimp	Candtype comment
 */

#define MAXCANDS	300	/* max candidates in a cell */
#define CQUANTUM	20	/* for profile analysis */
#define MAXOBJECTS	100
#define MAXFEATURES	25
#define XSCALE		1.0	/* Objects were digitised on FIP, */
#define YSCALE		0.75	/* had 4:3 aspect ratio originally */
#define MAXVALUE        3000
#define COLNUMBER       10
#define Atype           'a'
#define Btype           'b'
#define screendist      100.0


struct chromcands {
	int number;	/* object number in some ordering */
	int ncands;	/* number of candidates on this object */
	int selected;	/* selected for inclusion in classification ? */
	int otype;	/* object type as in property list */
	int Cotype;	/* correct object type */
	int btype;	/* object "biological" type as in property list */
	int Cbtype;	/* correct object "biological" type */
	int porigin;	/* parental origin, as plist->history[0] (qv.) */
	int profmax;	/* profile maximum value */
	int quantum;	/* true quantum value used for candidate extraction */
	int axislen;	/* length of medial axis / profiles */
	int area;	/* object area */
	int density;	/* object relative density (mass/area) */
	struct object *obj;	/* image object */
	struct cand *cands;	/* the actual candidate centromeres */
};

struct cand {
	int candtype;	/* 1: derived from profile,
			   2: derived from boundary,
			   3: randomly positioned candidate,
			   4: acrocentric candidate,
			  -1: unusable */
	int candnum;	/* candidate serial number for this chromosome */
	int profpos;	/* location (index) on density profile */
	int lboundpos;	/* location (index) of left chord end point on boundary */
	int rboundpos;	/* location (index) of right chord end point on boundary */
	int boundmaxcurv;	/* which end point has maximum curvature:
			1: left, 2: right, 3: identical */
	int nearest;	/* serial of nearest candidate of other type (-1 if none) */
	int neardist;	/* distance (along medial axis) to nearest (1000000 if none) */
	int ctype;	/* computed candidate type e.g. centromere, artefact */
	int Cctype;	/* true candidate type (training data) */
        char abtype;    
	struct object *cpol;	/* centromere polygon */
	union {
 		int af[MAXFEATURES];	/* array features of candidate */
		struct {		/* symbolic names of features */
			int profval;	/* 1: profile value at candidate */
			int profdepth;	/* 2: depth below profile peak */
			int width;	/* 3: width */
			int cprofsum;	/* 4: crossing profile sum */
			int cprofpeak;	/* 5: crossing profile peak */
			int modality;	/* 6: of crossing profile */
			int skewness;	/* 7: of crossing profile */
			int cvhdeficiency; /* 8: between crossing profile and its semi-hull */
			int cvhhwdiff;	/* 9: c.h. deficiency weighted by chord
					cotangent to horizontal */
			int curvmax;	/* 10: maximum curvature of bounda
					at chord end point */
			int curvmin;	/* 11: minimum curvature of boundary
					at chord end point */
			int chordprofconfig;	/* 12: configuration of profile
					where chord crosses:
					1 = profile local minimum, 0 = other */
			int nprofval;	/* 13: normalised by profmax */
			int ncprofpeak;	/* 14: normalised by density */
			int ncvhdeficiency;	/* 15: normalised by cprofsum */
			int neardistfeat;	/* 16: as neardist but max 20 if none */
			int profcurv;	/* 17 profile 2nd derivative at candidate */
			int curvsum;	/* 18 sum of curvmax and curvmin */
			int mom1ratio;	/* 19 ratio 1st to 0th central moment of crossing profile */
			int cprofcurv;	/* 20 curvature at centroid of crossing profile */
			int kurtosis;	/* 21 of crossing profile */
		} sy;
	} u;
};

struct dcresults {
	int ncells;
	int TP;		/* true positive */
	int FP;		/* false positive */
	int FN;		/* false negative */
	int UTP;	/* unsure true positive */
	int UFN;	/* unsure false negative */
	int twistedFP;	/* false positive (twisted arms) */
	int compoFP;	/* false positive (undetected composite ) */
	int ovFP;	/* false positive (from overlap split) */
	int acroFN;	/* false negative (acrocentric) */
	int onecandFN;	/* false negative (only one candidate) */
	int areaFN;	/* false negative (too small) */
	int ovFN;	/* false negative (from overlap split) */
	int nchrom;	/* number of "chromosomes" analysed */
	int nwithcands;	/* number of "chromosomes" with >=1 candidates */
};


struct ftrvalueStruct {
        int min[MAXVALUE];
        int other[MAXVALUE];
       };

struct scaledftrvalueStruct {
        int min[2*COLNUMBER];
        int other[2*COLNUMBER];
        int value[2*COLNUMBER];
       };