Revert "Tidyup up of MOSFLM"

This reverts commit bed93cd3c6fb285c66c9bbda53c24d34c975181b.

1 files changed, 54 insertions, 17 deletions

diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index 0f530244..886fbd56 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -150,13 +150,38 @@ static int read_newmat(const char *filename, struct image *image)
 }
 
 
+/* Need to sort mosflm peaks by intensity... */
+struct sptline {
+	double x; /* x coordinate of peak */
+	double y; /* y coordinate of peak */
+	double h; /* height of peak */
+	double s; /* sigma of peak */
+};
+
+
+static int compare_vals(const void *ap, const void *bp)
+{
+	const struct sptline a = *(struct sptline *)ap;
+	const struct sptline b = *(struct sptline *)bp;
+
+	if ( a.h < b.h ) return 1;
+	if ( a.h > b.h ) return -1;
+	return 0;
+}
+
+
 /* Write .spt file for mosflm */
 static void write_spt(struct image *image, const char *filename)
 {
 	FILE *fh;
-	int i, nPeaks;
-	const double fclen = 100.0e-3;  /* Fake camera length in m */
-	const double fpix = 7.5e-6;     /* Fake pixel size in m */
+	int i;
+	double fclen = 67.8;  /* fake camera length in mm */
+	double fpix = 0.075;  /* fake pixel size in mm */
+	double pix;
+	double height = 100.0;
+	double sigma = 1.0;
+	int nPeaks = image_feature_count(image->features);
+	struct sptline *sptlines;
 
 	fh = fopen(filename, "w");
 	if ( !fh ) {
@@ -164,17 +189,17 @@ static void write_spt(struct image *image, const char *filename)
 		return;
 	}
 
-	fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n",
-	            1, 1, fpix*1e3, 1.0, 0.0);
+	fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, fpix, 1.0, 0.0);
 	fprintf(fh, "%10d %10d\n", 1, 1);
 	fprintf(fh, "%10.5f %10.5f\n", 0.0, 0.0);
 
-	nPeaks = image_feature_count(image->features);
+	sptlines = malloc(sizeof(struct sptline)*nPeaks);
+
 	for ( i=0; i<nPeaks; i++ ) {
 
 		struct imagefeature *f;
 		struct panel *p;
-		double xs, ys, rx, ry, x, y;
+		double xs, ys, rx, ry;
 
 		f = image_get_feature(image->features, i);
 		if ( f == NULL ) continue;
@@ -182,21 +207,33 @@ static void write_spt(struct image *image, const char *filename)
 		p = find_panel(image->det, f->fs, f->ss);
 		if ( p == NULL ) continue;
 
-		xs = (f->fs-(double)p->min_fs)*p->fsx
-		   + (f->ss-(double)p->min_ss)*p->ssx;
-		ys = (f->fs-(double)p->min_fs)*p->fsy
-		   + (f->ss-(double)p->min_ss)*p->ssy;
-		rx = (xs + p->cnx) / p->res;
-		ry = (ys + p->cny) / p->res;
+		pix = 1000.0/p->res; /* pixel size in mm */
+		height = f->intensity;
+
+		xs = (f->fs-p->min_fs)*p->fsx + (f->ss-p->min_ss)*p->ssx;
+		ys = (f->fs-p->min_fs)*p->fsy + (f->ss-p->min_ss)*p->ssy;
+		rx = xs + p->cnx;
+		ry = ys + p->cny;
 
-		x = rx*fclen/(fpix*p->clen);
-		y = ry*fclen/(fpix*p->clen);
+		sptlines[i].x = ry*pix*fclen/p->clen/1000.0;
+		sptlines[i].y = -rx*pix*fclen/p->clen/1000.0;
+		sptlines[i].h = height;
+		sptlines[i].s = sigma/1000.0;
+
+	}
+
+	qsort(sptlines, nPeaks, sizeof(struct sptline), compare_vals);
+
+	for ( i=0; i<nPeaks; i++ ) {
 
 		fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
-		            x, y, 0.0, 0.0, 100.0, 1.0);
+		        sptlines[i].x, sptlines[i].y, 0.0, 0.0,
+		        sptlines[i].h, sptlines[i].s);
 
 	}
 
+	free(sptlines);
+
 	fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
 	           -999.0,-999.0,-999.0,-999.0,-999.0,-999.0);
 	fclose(fh);
@@ -306,7 +343,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
 		break;
 
 	case 4 :
-		mosflm_sendline("DISTANCE 100.0\n", mosflm);
+		mosflm_sendline("DISTANCE 67.8\n", mosflm);
 		break;
 
 	case 5 :