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authorThomas White <taw@bitwiz.org.uk>2012-01-26 17:22:02 -0800
committerThomas White <taw@physics.org>2012-02-22 15:27:44 +0100
commit0805d18e588976f9a62f4f8ca71ef58b81df34bd (patch)
treee5eeaa328ad98d19359c92f592416e1030296e30
parent9e4764ea281a488dd014a4ef2ae2558cb592e3e7 (diff)
Revert "Tidyup up of MOSFLM"
This reverts commit bed93cd3c6fb285c66c9bbda53c24d34c975181b.
-rw-r--r--libcrystfel/src/mosflm.c71
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 :