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-rw-r--r--src/hdf5-file.c23
-rw-r--r--src/image.h1
-rw-r--r--src/peaks.c63
3 files changed, 74 insertions, 13 deletions
diff --git a/src/hdf5-file.c b/src/hdf5-file.c
index 5573267b..d635923d 100644
--- a/src/hdf5-file.c
+++ b/src/hdf5-file.c
@@ -318,6 +318,11 @@ int hdf5_read(struct hdfile *f, struct image *image)
{
herr_t r;
float *buf;
+ uint8_t *flags;
+ hid_t mask_dh;
+
+ image->height = f->nx;
+ image->width = f->ny;
buf = malloc(sizeof(float)*f->nx*f->ny);
@@ -327,10 +332,22 @@ int hdf5_read(struct hdfile *f, struct image *image)
ERROR("Couldn't read data\n");
return 1;
}
-
image->data = buf;
- image->height = f->nx;
- image->width = f->ny;
+
+ mask_dh = H5Dopen(f->fh, "/processing/hitfinder/masks", H5P_DEFAULT);
+ if ( mask_dh <= 0 ) {
+ ERROR("Couldn't open flags\n");
+ } else {
+ flags = malloc(sizeof(uint8_t)*f->nx*f->ny);
+ r = H5Dread(mask_dh, H5T_NATIVE_B8, H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, flags);
+ if ( r < 0 ) {
+ ERROR("Couldn't read flags\n");
+ image->flags = NULL;
+ } else {
+ image->flags = flags;
+ }
+ }
/* Read wavelength from file */
image->lambda = get_wavelength(f);
diff --git a/src/image.h b/src/image.h
index db1b491e..e3a520ca 100644
--- a/src/image.h
+++ b/src/image.h
@@ -81,6 +81,7 @@ struct reflhit {
struct image {
float *data;
+ uint8_t *flags;
double *twotheta;
UnitCell *indexed_cell;
UnitCell *candidate_cells[MAX_CELL_CANDIDATES];
diff --git a/src/peaks.c b/src/peaks.c
index 22e12949..0d4292d3 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -133,7 +133,9 @@ static void cull_peaks(struct image *image)
}
-static void integrate_peak(struct image *image, int xp, int yp,
+/* Returns non-zero if peak has been vetoed.
+ * i.e. don't use result if return value is not zero. */
+static int integrate_peak(struct image *image, int xp, int yp,
float *xc, float *yc, float *intensity,
int do_polar)
{
@@ -150,6 +152,7 @@ static void integrate_peak(struct image *image, int xp, int yp,
double val, sa, pix_area, Lsq, dsq, proj_area;
float tt;
double phi, pa, pb, pol;
+ uint8_t flags;
/* Circular mask */
if ( x*x + y*y > lim ) continue;
@@ -157,6 +160,12 @@ static void integrate_peak(struct image *image, int xp, int yp,
if ( ((x+xp)>=image->width) || ((x+xp)<0) ) continue;
if ( ((y+yp)>=image->height) || ((y+yp)<0) ) continue;
+ /* Veto this peak if we tried to integrate in a bad region */
+ if ( image->flags != NULL ) {
+ flags = image->flags[(x+xp)+image->width*(y+yp)];
+ if ( flags & 0x03 ) return 1;
+ }
+
p = find_panel(&image->det, x+xp, y+yp);
/* Area of one pixel */
@@ -203,6 +212,8 @@ static void integrate_peak(struct image *image, int xp, int yp,
*yc = (float)yp;
*intensity = 0;
}
+
+ return 0;
}
@@ -219,6 +230,7 @@ void search_peaks(struct image *image)
int nrej_hot = 0;
int nrej_pro = 0;
int nrej_fra = 0;
+ int nrej_bad = 0;
int nacc = 0;
data = image->data;
@@ -240,6 +252,7 @@ void search_peaks(struct image *image)
int sx, sy;
double max;
unsigned int did_something;
+ int r;
/* Overall threshold */
if ( data[x+width*y] < 800 ) continue;
@@ -313,7 +326,13 @@ void search_peaks(struct image *image)
/* Centroid peak and get better coordinates.
* Don't bother doing polarisation correction, because the
* intensity of this peak is only an estimate at this stage. */
- integrate_peak(image, mask_x, mask_y, &fx, &fy, &intensity, 0);
+ r = integrate_peak(image, mask_x, mask_y,
+ &fx, &fy, &intensity, 0);
+ if ( r ) {
+ /* Bad region - don't detect peak */
+ nrej_bad++;
+ continue;
+ }
/* It is possible for the centroid to fall outside the image */
if ( (fx < 0.0) || (fx > image->width)
@@ -337,8 +356,9 @@ void search_peaks(struct image *image)
}
}
- STATUS("%i accepted, %i box, %i hot, %i proximity, %i outside frame\n",
- nacc, nrej_dis, nrej_hot, nrej_pro, nrej_fra);
+ STATUS("%i accepted, %i box, %i hot, %i proximity, %i outside frame,"
+ "%i in bad regions.\n",
+ nacc, nrej_dis, nrej_hot, nrej_pro, nrej_fra, nrej_bad);
cull_peaks(image);
}
@@ -492,6 +512,8 @@ void output_intensities(struct image *image, UnitCell *cell,
int n_found;
int n_indclose = 0;
int n_foundclose = 0;
+ int n_veto = 0;
+ int n_veto_second = 0;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
@@ -543,17 +565,35 @@ void output_intensities(struct image *image, UnitCell *cell,
&d, &idx);
if ( (f != NULL) && (d < PEAK_REALLY_CLOSE) ) {
+ int r;
+
/* f->intensity was measured on the filtered pattern,
* so instead re-integrate using old coordinates.
* This will produce further revised coordinates. */
- integrate_peak(image, f->x, f->y, &x, &y, &intensity,
- !unpolar);
+ r = integrate_peak(image, f->x, f->y, &x, &y,
+ &intensity, !unpolar);
+ if ( r ) {
+ /* The original peak (which also went through
+ * integrate_peak(), but with the mangled
+ * image data) would have been rejected if it
+ * was in a bad region. Integration of the same
+ * peak included a bad region this time. */
+ n_veto_second++;
+ continue;
+ }
intensity = f->intensity;
} else {
- integrate_peak(image, hits[i].x, hits[i].y,
- &x, &y, &intensity, !unpolar);
+ int r;
+
+ r = integrate_peak(image, hits[i].x, hits[i].y,
+ &x, &y, &intensity, !unpolar);
+ if ( r ) {
+ /* Plain old ordinary peak veto */
+ n_veto++;
+ continue;
+ }
}
@@ -592,9 +632,12 @@ void output_intensities(struct image *image, UnitCell *cell,
printf("Peak statistics: %i peaks found by the peak search out of "
"%i were close to indexed positions. "
- "%i indexed positions out of %i were close to detected peaks\n",
+ "%i indexed positions out of %i were close to detected peaks.\n",
n_foundclose, n_found, n_indclose, n_hits);
-
+ printf("%i integrations using indexed locations were aborted because "
+ "they hit one or more bad pixels.\n", n_veto);
+ printf("%i integrations using peak search locations were aborted "
+ "because they hit one or more bad pixels.\n", n_veto_second);
/* Blank line at end */
printf("\n");