Avoid very slow loop over pixels to create bad pixel map

Bad regions specified in terms of x/y still require an iteration over
all pixels of the detector, but I don't see an easy way around that.
Avoiding x/y bad regions will give best performance.

5 files changed, 169 insertions, 98 deletions

diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
index 4f767c45..d2257f9e 100644
--- a/libcrystfel/src/datatemplate.c
+++ b/libcrystfel/src/datatemplate.c
@@ -103,7 +103,8 @@ static struct dt_badregion *new_bad_region(DataTemplate *det, const char *name)
 	new->min_ss = 0;
 	new->max_ss = 0;
 	new->is_fsss = 99; /* Slightly nasty: means "unassigned" */
-	new->panel = NULL;
+	new->panel_name = NULL;
+	new->panel_number = 0;  /* Needs to be set after loading */
 	strcpy(new->name, name);
 
 	return new;
@@ -654,7 +655,7 @@ static int parse_field_bad(struct dt_badregion *badr, const char *key,
 		badr->max_ss = atof(val);
 		reject = check_badr_fsss(badr, 1);
 	} else if ( strcmp(key, "panel") == 0 ) {
-		badr->panel = strdup(val);
+		badr->panel_name = strdup(val);
 	} else {
 		ERROR("Unrecognised field '%s'\n", key);
 	}
@@ -915,6 +916,30 @@ signed int find_dim(signed int *dims, int which)
 }
 
 
+static int lookup_panel(const char *panel_name,
+                        const DataTemplate *dt,
+                        int *res)
+{
+	int i;
+
+	/* If there is exactly one panel, you can get away without
+	 * specifying the panel name */
+	if ( (panel_name == NULL) && (dt->n_panels == 1) ) {
+		*res = 0;
+		return 0;
+	}
+
+	for ( i=0; i<dt->n_panels; i++ ) {
+		if ( strcmp(dt->panels[i].name, panel_name) == 0 ) {
+			*res = i;
+			return 0;
+		}
+	}
+
+	return 1;
+}
+
+
 DataTemplate *data_template_new_from_string(const char *string_in)
 {
 	DataTemplate *dt;
@@ -1241,17 +1266,31 @@ DataTemplate *data_template_new_from_string(const char *string_in)
 	}
 
 	for ( i=0; i<dt->n_bad; i++ ) {
+
 		if ( dt->bad[i].is_fsss == 99 ) {
 			ERROR("Please specify the coordinate ranges for"
 			      " bad region %s\n", dt->bad[i].name);
 			reject = 1;
 		}
+
+		if ( dt->bad[i].is_fsss ) {
+			if ( lookup_panel(dt->bad[i].panel_name, dt,
+			                  &dt->bad[i].panel_number) )
+			{
+				ERROR("No such panel '%s' for bad "
+				      "region %s\n",
+				      dt->bad[i].panel_name,
+				      dt->bad[i].name);
+				reject = 1;
+			}
+		}
 	}
 
 	free(defaults.cnz_from);
 	free(defaults.data);
 	free(defaults.mask);
 
+
 	for ( rgi=0; rgi<n_rg_definitions; rgi++) {
 
 		int pi, n1;
@@ -1495,65 +1534,3 @@ int data_template_get_slab_extents(const DataTemplate *dt,
 	*ph = h + 1;
 	return 0;
 }
-
-
-/* Return non-zero if pixel fs,ss on panel p is in a bad region
- * as specified in the geometry file (regions only, not including
- * masks, NaN/inf, no_index etc */
-int data_template_in_bad_region(const DataTemplate *dtempl,
-                                int pn, double fs, double ss)
-{
-	double rx, ry;
-	double xs, ys;
-	int i;
-	struct panel_template *p;
-
-	if ( pn >= dtempl->n_panels ) {
-		ERROR("Panel index out of range\n");
-		return 0;
-	}
-	p = &dtempl->panels[pn];
-
-	/* Convert xs and ys, which are in fast scan/slow scan coordinates,
-	 * to x and y */
-	xs = fs*p->fsx + ss*p->ssx;
-	ys = fs*p->fsy + ss*p->ssy;
-
-	rx = xs + p->cnx;
-	ry = ys + p->cny;
-
-	for ( i=0; i<dtempl->n_bad; i++ ) {
-
-		struct dt_badregion *b = &dtempl->bad[i];
-
-		if ( (b->panel != NULL)
-		  && (strcmp(b->panel, p->name) != 0) ) continue;
-
-		if ( b->is_fsss ) {
-
-			int nfs, nss;
-
-			/* fs/ss bad regions are specified according
-			 * to the original coordinates */
-			nfs = fs + p->orig_min_fs;
-			nss = ss + p->orig_min_ss;
-
-			if ( nfs < b->min_fs ) continue;
-			if ( nfs > b->max_fs ) continue;
-			if ( nss < b->min_ss ) continue;
-			if ( nss > b->max_ss ) continue;
-
-		} else {
-
-			if ( rx < b->min_x ) continue;
-			if ( rx > b->max_x ) continue;
-			if ( ry < b->min_y ) continue;
-			if ( ry > b->max_y ) continue;
-
-		}
-
-		return 1;
-	}
-
-	return 0;
-}
diff --git a/libcrystfel/src/datatemplate.h b/libcrystfel/src/datatemplate.h
index 66545786..5975f90c 100644
--- a/libcrystfel/src/datatemplate.h
+++ b/libcrystfel/src/datatemplate.h
@@ -87,9 +87,6 @@ extern void data_template_add_copy_header(DataTemplate *dt,
 
 extern int data_template_get_slab_extents(const DataTemplate *dt, int *pw, int *ph);
 
-extern int data_template_in_bad_region(const DataTemplate *dtempl,
-                                       int pn, double fs, double ss);
-
 extern struct rg_collection *data_template_get_rigid_groups(const DataTemplate *dtempl,
                                                             const char *collection_name);
 
diff --git a/libcrystfel/src/datatemplate_priv.h b/libcrystfel/src/datatemplate_priv.h
index c980b53a..f88a6ad0 100644
--- a/libcrystfel/src/datatemplate_priv.h
+++ b/libcrystfel/src/datatemplate_priv.h
@@ -171,14 +171,15 @@ struct dt_badregion
 {
 	char name[1024];
 	int is_fsss;
-	char *panel;
 
 	double min_x;
 	double max_x;
 	double min_y;
 	double max_y;
 
-	/* Specified INCLUSIVELY */
+	/* Coordinates are specified INCLUSIVELY */
+	int      panel_number;
+	char    *panel_name;
 	int      min_fs;
 	int      max_fs;
 	int      min_ss;
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index e8504f23..6da4b435 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -630,9 +630,67 @@ static void set_image_parameters(struct image *image,
 }
 
 
-static int flag_value(float pixel, struct panel_template *p)
+static void mark_flagged_pixels_lessthan(float *dp, int *bad,
+                                         long int n, float val)
 {
+	long int i;
+	for ( i=0; i<n; i++ ) {
+		if ( dp[i] < val ) bad[i] = 1;
+	}
+}
+
+
+static void mark_flagged_pixels_morethan(float *dp, int *bad,
+                                         long int n, float val)
+{
+	long int i;
+	for ( i=0; i<n; i++ ) {
+		if ( dp[i] > val ) bad[i] = 1;
+	}
+}
+
+
+static void mark_flagged_pixels_equal(float *dp, int *bad,
+                                      long int n, float val)
+{
+	long int i;
+	fenv_t envp;
+
+	fegetenv(&envp);
+	fesetround(1);  /* Round to nearest (for flag_value) */
+
+	for ( i=0; i<n; i++ ) {
+		if ( rint(dp[i]) == val ) bad[i] = 1;
+	}
+
+	fesetenv(&envp);
+}
+
+
+static void mark_flagged_pixels_naninf(float *dp, int *bad,
+                                       long int n)
+{
+	long int i;
+	for ( i=0; i<n; i++ ) {
+		float val = dp[i];
+		if ( isnan(val) || isinf(val) ) bad[i] = 1;
+	}
+}
+
+
+static void mark_flagged_pixels(struct panel_template *p,
+                                float *dp, int *bad)
+{
+	int p_w, p_h;
+	long int n;
 	int i;
+
+	p_w = p->orig_max_fs - p->orig_min_fs + 1;
+	p_h = p->orig_max_ss - p->orig_min_ss + 1;
+	n = p_w * p_h;
+
+	mark_flagged_pixels_naninf(dp, bad, n);
+
 	for ( i=0; i<MAX_FLAG_VALUES; i++ ) {
 
 		float fv = p->flag_values[i];
@@ -643,53 +701,88 @@ static int flag_value(float pixel, struct panel_template *p)
 			break;
 
 			case FLAG_LESSTHAN:
-			if ( pixel < fv ) return 1;
+			mark_flagged_pixels_lessthan(dp, bad, n, fv);
 			break;
 
 			case FLAG_MORETHAN:
-			if ( pixel > fv ) return 1;
+			mark_flagged_pixels_morethan(dp, bad, n, fv);
 			break;
 
 			case FLAG_EQUAL:
-			if ( rint(pixel) == fv) return 1;
+			mark_flagged_pixels_equal(dp, bad, n, fv);
 			break;
 
 		}
 	}
-	return 0;
 }
 
 
-static void mark_bad_regions(struct panel_template *p,
-                             float *dp, int *bad,
-                             const DataTemplate *dtempl,
-                             int i)
+static void draw_bad_region_fsss(struct dt_badregion *region,
+                                 int **bad,
+                                 struct detgeom *detgeom)
 {
-	int p_w, p_h;
+	struct detgeom_panel *panel;
 	int fs, ss;
-	fenv_t envp;
 
-	fegetenv(&envp);
-	fesetround(1);  /* Round to nearest (for flag_value) */
+	panel = &detgeom->panels[region->panel_number];
 
-	p_w = p->orig_max_fs - p->orig_min_fs + 1;
-	p_h = p->orig_max_ss - p->orig_min_ss + 1;
+	for ( ss=region->min_ss; ss<=region->max_ss; ss++ ) {
+		for ( fs=region->min_fs; fs<=region->max_fs; fs++ ) {
+			bad[region->panel_number][fs+ss*panel->w] = 1;
+		}
+	}
+}
+
+
+static void draw_bad_region_xy(struct dt_badregion *region,
+                               int **bad,
+                               struct detgeom *detgeom)
+{
+	int i;
+
+	for ( i=0; i<detgeom->n_panels; i++ ) {
+
+		int fs, ss;
+
+		struct detgeom_panel *p = &detgeom->panels[i];
+		for ( ss=0; ss<p->h; ss++ ) {
+			for ( fs=0; fs<p->w; fs++ ) {
+
+				double x, y;
+
+				x = fs*p->fsx + ss*p->ssx + p->cnx;
+				y = fs*p->fsy + ss*p->ssy + p->cny;
+
+				if ( (x > region->min_x )
+				     && (x < region->max_x)
+				     && (y > region->min_y)
+				     && (y < region->max_y) )
+				{
+					bad[i][fs+ss*p->w] = 1;
+				}
 
-	for ( ss=0; ss<p_h; ss++ ) {
-		for ( fs=0; fs<p_w; fs++ ) {
-			float val = dp[fs+ss*p_w];
-			if ( data_template_in_bad_region(dtempl, i,
-			                                 fs, ss)
-			  || isnan(val)
-			  || isinf(val)
-			  || flag_value(val, p) )
-			{
-				bad[fs+ss*p_w] = 1;
 			}
 		}
 	}
+}
 
-	fesetenv(&envp);
+
+static void mark_bad_regions(struct image *image,
+                             const DataTemplate *dtempl)
+{
+	int i;
+
+	for ( i=0; i<dtempl->n_bad; i++ ) {
+		if ( dtempl->bad[i].is_fsss ) {
+			draw_bad_region_fsss(&dtempl->bad[i],
+			                     image->bad,
+			                     image->detgeom);
+		} else {
+			draw_bad_region_xy(&dtempl->bad[i],
+			                   image->bad,
+			                   image->detgeom);
+		}
+	}
 }
 
 
@@ -756,8 +849,8 @@ static int create_badmap(struct image *image,
 
 		/* Add bad regions (skip if panel is bad anyway) */
 		if ( !p->bad ) {
-			mark_bad_regions(p, image->dp[i], image->bad[i],
-			                 dtempl, i);
+			mark_flagged_pixels(p, image->dp[i],
+			                    image->bad[i]);
 		}
 
 		/* Load mask (skip if panel is bad anyway) */
@@ -775,6 +868,9 @@ static int create_badmap(struct image *image,
 			          dtempl->mask_good, dtempl->mask_bad);
 		}
 	}
+
+	mark_bad_regions(image, dtempl);
+
 	return 0;
 }
 
diff --git a/src/make_pixelmap.c b/src/make_pixelmap.c
index 099ba79f..577c1a1a 100644
--- a/src/make_pixelmap.c
+++ b/src/make_pixelmap.c
@@ -330,7 +330,7 @@ int main(int argc, char *argv[])
 		y[fs + w*ss] = ry;
 		z[fs + w*ss] = 0.0;  /* 2D part only */
 
-		if ( data_template_in_bad_region(dtempl, pn, cfs, css) ) {
+		if ( image->bad[pn][fs + w*ss] ) {
 			b[fs + w*ss] = bad_pixel_val;
 		} else {
 			b[fs + w*ss] = good_pixel_val;