Add "-e" options to power_plot and sum_stack

2 files changed, 86 insertions, 14 deletions

diff --git a/src/powder_plot.c b/src/powder_plot.c
index b75115b2..7d12f31b 100644
--- a/src/powder_plot.c
+++ b/src/powder_plot.c
@@ -597,7 +597,8 @@ static unsigned int process_stream_h5(FILE *fh, struct image *image,
                                       struct histogram_info *info,
                                       struct bin_stats *histdata,
                                       int config_satcorr, int only_indexed,
-                                      unsigned int *n_patterns)
+                                      unsigned int *n_patterns,
+                                      const char *element)
 {
 	int fs, ss, rval;
 	double intensity;
@@ -614,11 +615,29 @@ static unsigned int process_stream_h5(FILE *fh, struct image *image,
 		/* Get data from next chunk */
 		rval = read_chunk(fh, image);
 		if ( rval ) continue;
-		if ((only_indexed == 0) ||
-		   ((only_indexed == 1) &&
-		    ((*image).reflections != NULL))) {
-			hdfile = hdfile_open((*image).filename);
-			hdfile_set_image(hdfile, "/data/data");
+		if ( !only_indexed ||
+		   ( only_indexed && (image->reflections != NULL) ) )
+		{
+			hdfile = hdfile_open(image->filename);
+			if ( element != NULL ) {
+				int r;
+				r = hdfile_set_image(hdfile, element);
+				if ( r ) {
+					ERROR("Couldn't select path '%s'\n",
+					     element);
+					hdfile_close(hdfile);
+					return 0;
+				}
+			} else {
+				int r;
+				r = hdfile_set_first_image(hdfile, "/");
+				if ( r ) {
+					ERROR("Couldn't select first path\n");
+					hdfile_close(hdfile);
+					return 0;
+				}
+
+			}
 			hdf5_read(hdfile, image, config_satcorr);
 			hdfile_close(hdfile);
 			n_patterns++;
@@ -699,6 +718,10 @@ static void show_help(const char *s)
 "                            of measurements and not the number of symetrical\n"
 "                            equivelent reflections as the number of time a\n"
 "                            reflection occurs in the powder\n"
+" -e, --image=<element>    Use this image when reading an HDF5 file.\n"
+"                           Example: /data/data0.\n"
+"                           Default: The first one found.\n"
+
 "\n");
 }
 
@@ -720,6 +743,7 @@ int main(int argc, char *argv[])
 	image.lambda = -1.0;
 	image.beam = NULL;
 	image.det  = NULL;
+	char *element = NULL;
 
 	unsigned int n_patterns = 0;
 	unsigned int n_peaks    = 0;
@@ -763,6 +787,7 @@ int main(int argc, char *argv[])
 		{"ring-corr",          0, &ring_corr,          1 },
 		{"use-redundancy",     0, &use_redundancy,     1 },
 		{"data",               1, NULL,               'd'},
+		{"image",              1, NULL,               'e'},
 		{0, 0, NULL, 0}
 	};
 
@@ -805,6 +830,10 @@ int main(int argc, char *argv[])
 			hist_info.histsize = atoi(optarg);
 			break;
 
+		case 'e' :
+			element = strdup(optarg);
+			break;
+
 		case 1 :
 			hist_info.q_max = atof(optarg);
 			break;
@@ -864,7 +893,25 @@ int main(int argc, char *argv[])
 		file_type = FILE_H5;
 		need_geometry = 1;
 		hdfile = hdfile_open(filename);
-		hdfile_set_image(hdfile, "/data/data");
+		if ( element != NULL ) {
+			int r;
+			r = hdfile_set_image(hdfile, element);
+			if ( r ) {
+				ERROR("Couldn't select path '%s'\n",
+				     element);
+				hdfile_close(hdfile);
+				return 0;
+			}
+		} else {
+			int r;
+			r = hdfile_set_first_image(hdfile, "/");
+			if ( r ) {
+				ERROR("Couldn't select first path\n");
+				hdfile_close(hdfile);
+				return 0;
+			}
+
+		}
 		hdf5_read(hdfile, &image, config_satcorr);
 		hdfile_close(hdfile);
 
@@ -1066,7 +1113,7 @@ int main(int argc, char *argv[])
 		case PLOT_H5 :
 			n_peaks =  process_stream_h5(fh, &image, &hist_info,
 			             histdata, config_satcorr, only_indexed,
-			             &n_patterns);
+			             &n_patterns, element);
 			break;
 		default :
 			break;
diff --git a/src/sum_stack.c b/src/sum_stack.c
index 8d00a87f..2e5b138e 100644
--- a/src/sum_stack.c
+++ b/src/sum_stack.c
@@ -49,6 +49,7 @@ struct sum_args
 	SumMethod sum_method;
 	double threshold;
 	double min_gradient;
+	char *element;
 };
 
 
@@ -63,6 +64,7 @@ struct queue_args
 	SumMethod sum_method;
 	double threshold;
 	double min_gradient;
+	char *element;
 
 	char *use_this_one_instead;
 	char *prefix;
@@ -98,6 +100,9 @@ static void show_help(const char *s)
 "                           method.  Default: 400 adu\n"
 "      --min-gradient=<n>   Minimum gradient for Zaefferer peak search.\n"
 "                            Default: 100,000.\n"
+" -e, --image=<element>    Use this image from the HDF5 file.\n"
+"                           Example: /data/data0.\n"
+"                           Default: The first one found.\n"
 "\n"
 "      --filter-cm         Perform common-mode noise subtraction on images\n"
 "                           before proceeding.\n"
@@ -182,12 +187,25 @@ static void add_image(void *args, int cookie)
 	STATUS("%3i: Processing '%s'\n", cookie, pargs->filename);
 
 	hdfile = hdfile_open(pargs->filename);
-	if ( hdfile == NULL ) {
-		return;
-	} else if ( hdfile_set_first_image(hdfile, "/") ) {
-		ERROR("Couldn't select path\n");
-		hdfile_close(hdfile);
-		return;
+	if ( hdfile == NULL ) return;
+
+	if ( pargs->element != NULL ) {
+		int r;
+		r = hdfile_set_image(hdfile, pargs->element);
+		if ( r ) {
+			ERROR("Couldn't select path '%s'\n", pargs->element);
+			hdfile_close(hdfile);
+			return;
+		}
+	} else {
+		int r;
+		r = hdfile_set_first_image(hdfile, "/");
+		if ( r ) {
+			ERROR("Couldn't select first path\n");
+			hdfile_close(hdfile);
+			return;
+		}
+
 	}
 
 	hdf5_read(hdfile, &image, 1);
@@ -305,6 +323,7 @@ int main(int argc, char *argv[])
 	char prepare_filename[1024];
 	char *rval;
 	int config_basename = 0;
+	char *element = NULL;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -319,6 +338,7 @@ int main(int argc, char *argv[])
 		{"threshold",          1, NULL,               't'},
 		{"min-gradient",       1, NULL,                4},
 		{"basename",           0, &config_basename,    1},
+		{"image",              1, NULL,               'e'},
 		{0, 0, NULL, 0}
 	};
 
@@ -359,6 +379,10 @@ int main(int argc, char *argv[])
 			threshold = atof(optarg);
 			break;
 
+		case 'e' :
+			element = strdup(optarg);
+			break;
+
 		case 4 :
 			min_gradient = strtof(optarg, NULL);
 			break;
@@ -453,6 +477,7 @@ int main(int argc, char *argv[])
 	qargs.sum = calloc(qargs.w*qargs.h, sizeof(double));
 	qargs.prefix = prefix;
 	qargs.fh = fh;
+	qargs.element = element;
 
 	do {