/*
 * dcclass.c		Jim Piper		21-01-87
 *
 * perform box classification on dicentric candidate/feature data
 *
 * dcclass [-R method] [-C n] [-D dist] [-d dist] [-E dist ] [-p] [-m PC1 PC2] [-F n f1 .. fn] [file]
 *
 * -C n		selects whether classification on type 1 candidates (n=1),
 *		type 2 candidates (n=2), or some other candidate selection
 *		method (to be determined).  Default 1.
 * -D dist	If flag -D is set, then
 *		candidates of the "other" type are also included if their
 *		nearest candidate of the selected type is more than
 *		"dist" away (feature neardist).  Default 8, i.e. will
 *		reject "other" candidates within 1 micron of selected candidate.
 * -d dist	If two candidates of the SAME selected type are closer than
 *		"dist", reject one.  Default 8.
 * -E dist	reject any candidate less than "dist" to medial axis end.
 *		Default 8.
 * -p		turn on printing
 * -P		print feature vectors and classification for objects classified
 *		as dicentric (only the feature vectors selected by the method).
 * -R method	Incorporate a final review stage of the positives, to reduce the
 *		false positives.
 * -m PC1 PC2	setbox classifier percentages (see write-up).
 * -F n f1 ... fn select n features (numbered from one, as in dicen.h)
 * -X n		box classifier method (default 0)
 * -Y file	output FP/FN/TP identifiers to file
 *
 * MODIFICATIONS
 * -------------
 * 22-01-91	jimp	-R split to two methods, as on OS9 system
 * 21-09-88	jimp	Option -Y added
 * 12-04-88	jimp	Incorporate positives review (flag '-R').
 * 07-04-88	jimp	Flag '-P' for information about classified positives.
 * 26-02-88	jimp	classifier limits set by selected candidate type only
 * 25-02-88	jimp	Added flags -d, -E to reduce acceptable candidates.
 * 24-02-88	jimp	Do not permit dicentrics smaller than cell median area
 */

#include <stdio.h>
#include <math.h>
#include <wstruct.h>
#include <chromanal.h>
#include <dicen.h>

#define SCALE	24


static struct pframe f;

/* which features (numbering from one, as in dicen.h) */
int nfeat = 9;
int selfeat[MAXFEATURES] = {1,3,5,6,8,9,13,14,15};
int selllim[MAXFEATURES] = {1,1,1,0,0,0, 1, 1, 0};


main(argc,argv)
char **argv;
{
	struct chromcands *chcp,chc[MAXOBJS];
	struct cand *cndp,cnd[MAXCANDS];
	int i, j, number, numberused;
	int PC1, PC2;
	char *cell,s[256];
	FILE *infile, *pf, *idents;
	struct dcresults r;
	int DISPLAY = 0;
	int PRINT = 0;
	int POSPRINT = 0;
	int CANDSEL = 1;
	int OTHNEARDIST = 8;
	int SELNEARDIST = 8;
	int ENDDIST = 8;
	int BOXMETHOD = 0;
	int REVIEWP = 0;
	int IDENTS = 0;

	r.TP = r.FP = r.FN = r.UTP = r.UFN = 0;
	r.compoFP = r.twistedFP = r.acroFN = 0;
	r.onecandFN = r.nchrom = r.nwithcands = 0;
	r.areaFN = r.ovFP = r.ovFN = 0;
	/*
	 * defaults for PC1, PC2
	 */
	PC1 = 90;
	PC2 = 120;

	while (argc > 1 && argv[1][0] == '-') {
		switch (argv[1][1]) {
		case 'p':
			PRINT++;
			break;
		case 'P':
			POSPRINT++;
			break;
		case 'R':
			REVIEWP = atoi(argv[2]);
			argc--;
			argv++;
			break;
		case 'm':
			PC1 = atoi(argv[2]);
			PC2 = atoi(argv[3]);
			argc -= 2;
			argv += 2;
			break;
		case 'C':
			CANDSEL = atoi(argv[2]);
			argc--;
			argv++;
			if (CANDSEL != 1 && CANDSEL != 2) {
				fprintf(stderr,"Illegal -C value\n");
				exit(1);
			}
			break;
		case 'D':
			OTHNEARDIST = atoi(argv[2]);
			argc--;
			argv++;
			break;
		case 'E':
			ENDDIST = atoi(argv[2]);
			argc--;
			argv++;
			break;
		case 'd':
			SELNEARDIST = atoi(argv[2]);
			argc--;
			argv++;
			break;
		case 'F':
			nfeat = atoi(argv[2]);
			argc--;
			argv++;
			for (i=0; i<nfeat; i++) {
				selfeat[i] = atoi(argv[2]);
				argc--;
				argv++;
			}
			break;
		case 'X':
			BOXMETHOD = atoi(argv[2]);
			argc--;
			argv++;
			if (BOXMETHOD < 0 || BOXMETHOD > 7) {
				fprintf(stderr,"Unknown box method\n");
				exit(1);
			}
			break;
		case 'Y':
			IDENTS++;
			idents = fopen(argv[2],"w");
			if (idents == NULL) {
				fprintf(stderr,"Cannot open %s for identifiers\n",argv[2]);
				exit(1);
			}
			argc--;
			argv++;
			break;
		default:
			fprintf(stderr,"unrecognised switch -%c\n",argv[1][1]);
			break;
		}
		argc--;
		argv++;
	}
	if (argc > 1) {
		cell = argv[1];
		infile = fopen(cell,"r");
		if (infile == NULL) {
			fprintf(stderr,"Can't open %s\n",cell);
			exit(1);
		}
	} else {
		cell = "<stdin";
		infile = stdin;
	}
	pf = stdout;
	if (PRINT >= 1) {
		fprintf(pf,"DATA FILE %s PC1 %d PC2 %d \n",cell,PC1,PC2);
		fprintf(pf,"FEATURES USED BY BOX CLASSIFIER: ");
		for (i=0; i<nfeat; i++)
			fprintf(pf,"%2d ",selfeat[i]);
		fprintf(pf,"\n\n");
	}

	/*
	 * read data
	 */
	numberused = dcread(chc,cnd,infile,CANDSEL,OTHNEARDIST,SELNEARDIST,ENDDIST,&r);

	/*
	 * summary about candidates
	 */
	if (PRINT) {
		dccandsummary(chc,numberused,pf);
		chcp = chc;
		for (i=0; i<numberused; i++)
			dcprint(chcp++,pf);
	}

	/*
	 * normalise features
	 */
	dcnormalise(chc,numberused);

	/*
	 * do the classification
	 */
	dcboxclass(CANDSEL,BOXMETHOD,chc,numberused,nfeat,selfeat,selllim,PC1,PC2,PRINT,pf);

	/*
	 * review positives
	 */
	if (REVIEWP & 1)
		dcreview1(chc,numberused);
	if (REVIEWP & 2)
		dcreview2(chc,numberused);
	/*
	 * display the found true and false positives
	 * and the false negatives
	 */
	if (PRINT)
		dcresprint(chc,numberused,pf);
	dcresaccum(chc,numberused,pf,&r,POSPRINT);
	if (IDENTS)
		dcidentwrite(chc,numberused,cell,idents);
}