Improve bad pixel handling

8 files changed, 68 insertions, 19 deletions

diff --git a/doc/examples/lcls-dec.geom b/doc/examples/lcls-dec.geom
index 8db61144..349d2b16 100644
--- a/doc/examples/lcls-dec.geom
+++ b/doc/examples/lcls-dec.geom
@@ -1,3 +1,7 @@
+mask = /processing/hitfinder/masks
+mask_good = 0x07
+mask_bad = 0x00
+
 upper/min_fs = 0
 upper/max_fs = 1023
 upper/min_ss = 512
diff --git a/doc/examples/lcls-june-r0013-r0128.geom b/doc/examples/lcls-june-r0013-r0128.geom
index 0184f852..8a31ada6 100644
--- a/doc/examples/lcls-june-r0013-r0128.geom
+++ b/doc/examples/lcls-june-r0013-r0128.geom
@@ -1,4 +1,6 @@
-n_panels = 2
+mask = /processing/hitfinder/masks
+mask_good = 0x27
+mask_bad = 0x00
 
 ; Upper panel (nearest the beam)
 0/min_fs = 0
diff --git a/doc/examples/lcls-xpp-estimate.geom b/doc/examples/lcls-xpp-estimate.geom
index 7e53d3d9..c64c985a 100644
--- a/doc/examples/lcls-xpp-estimate.geom
+++ b/doc/examples/lcls-xpp-estimate.geom
@@ -1,5 +1,3 @@
-n_panels = 1
-
 0/min_fs = 0
 0/max_fs = 1455
 0/min_ss = 0
diff --git a/doc/examples/simple.geom b/doc/examples/simple.geom
index aa762b47..62ee53db 100644
--- a/doc/examples/simple.geom
+++ b/doc/examples/simple.geom
@@ -1,5 +1,3 @@
-n_panels = 2
-
 ; Upper panel
 0/min_fs = 0
 0/max_fs = 1023
diff --git a/src/detector.c b/src/detector.c
index 3a00607a..95cbc08a 100644
--- a/src/detector.c
+++ b/src/detector.c
@@ -464,6 +464,36 @@ static int parse_field_bad(struct badregion *panel, const char *key,
 }
 
 
+static void parse_toplevel(struct detector *det, const char *key,
+                           const char *val)
+{
+	if ( strcmp(key, "mask") == 0 ) {
+
+		det->mask = strdup(val);
+
+	} else if ( strcmp(key, "mask_bad") == 0 ) {
+
+		char *end;
+		double v = strtod(val, &end);
+
+		if ( end != val ) {
+			det->mask_bad = v;
+		}
+
+	} else if ( strcmp(key, "mask_good") == 0 ) {
+
+		char *end;
+		double v = strtod(val, &end);
+
+		if ( end != val ) {
+			det->mask_good = v;
+		}
+
+	} else {
+		ERROR("Unrecognised top level field '%s'\n", key);
+	}
+}
+
 struct detector *get_detector_geometry(const char *filename)
 {
 	FILE *fh;
@@ -516,6 +546,7 @@ struct detector *get_detector_geometry(const char *filename)
 		n2 = assplode(bits[0], "/\\.", &path, ASSPLODE_NONE);
 		if ( n2 < 2 ) {
 			/* This was a top-level option, but not handled above. */
+			parse_toplevel(det, bits[0], bits[2]);
 			for ( i=0; i<n1; i++ ) free(bits[i]);
 			free(bits);
 			for ( i=0; i<n2; i++ ) free(path[i]);
diff --git a/src/detector.h b/src/detector.h
index 67b10870..42651ebd 100644
--- a/src/detector.h
+++ b/src/detector.h
@@ -72,6 +72,10 @@ struct detector
 
 	struct badregion *bad;
 	int               n_bad;
+
+	char              *mask;
+	unsigned int       mask_bad;
+	unsigned int       mask_good;
 };
 
 
diff --git a/src/hdf5-file.c b/src/hdf5-file.c
index be0b5444..83850afe 100644
--- a/src/hdf5-file.c
+++ b/src/hdf5-file.c
@@ -412,22 +412,26 @@ int hdf5_read(struct hdfile *f, struct image *image, int satcorr)
 	}
 	image->data = buf;
 
-	mask_dh = H5Dopen2(f->fh, "/processing/hitfinder/masks", H5P_DEFAULT);
-	if ( mask_dh <= 0 ) {
-		ERROR("Couldn't open flags\n");
-		image->flags = NULL;
-	} else {
-		flags = malloc(sizeof(uint16_t)*f->nx*f->ny);
-		r = H5Dread(mask_dh, H5T_NATIVE_UINT16, H5S_ALL, H5S_ALL,
-		            H5P_DEFAULT, flags);
-		if ( r < 0 ) {
-			ERROR("Couldn't read flags\n");
-			free(flags);
+	if ( image->det->mask != NULL ) {
+
+		mask_dh = H5Dopen2(f->fh, image->det->mask, H5P_DEFAULT);
+		if ( mask_dh <= 0 ) {
+			ERROR("Couldn't open flags\n");
 			image->flags = NULL;
 		} else {
-			image->flags = flags;
+			flags = malloc(sizeof(uint16_t)*f->nx*f->ny);
+			r = H5Dread(mask_dh, H5T_NATIVE_UINT16, H5S_ALL, H5S_ALL,
+				    H5P_DEFAULT, flags);
+			if ( r < 0 ) {
+				ERROR("Couldn't read flags\n");
+				free(flags);
+				image->flags = NULL;
+			} else {
+				image->flags = flags;
+			}
+			H5Dclose(mask_dh);
 		}
-		H5Dclose(mask_dh);
+
 	}
 
 	/* Read wavelength from file */
diff --git a/src/peaks.c b/src/peaks.c
index e5ba5337..453f46e9 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -186,8 +186,16 @@ int integrate_peak(struct image *image, int cfs, int css,
 
 		/* Veto this peak if we tried to integrate in a bad region */
 		if ( image->flags != NULL ) {
+
 			flags = image->flags[idx];
-			if ( !(flags & 0x01) ) return 1;
+
+			/* It must have all the "good" bits to be valid */
+			if ( !((flags & image->det->mask_good)
+			                   == image->det->mask_good) ) return 1;
+
+			/* If it has any of the "bad" bits, reject */
+			if ( flags & image->det->mask_bad ) return 1;
+
 		}
 
 		val = image->data[idx];