Add "no peak search" option, tidy up code

2 files changed, 218 insertions, 150 deletions

diff --git a/src/itrans.c b/src/itrans.c
index 1018a66..fb5f649 100644
--- a/src/itrans.c
+++ b/src/itrans.c
@@ -3,8 +3,8 @@
  *
  * Parameterise features in an image for reconstruction
  *
- * (c) 2007 Thomas White <taw27@cam.ac.uk>
- *	    Gordon Ball <gfb21@cam.ac.uk>
+ * (c) 2007-2009 Thomas White <taw27@cam.ac.uk>
+ * (c) 2007      Gordon Ball <gfb21@cam.ac.uk>
  *
  *  dtr - Diffraction Tomography Reconstruction
  *
@@ -21,83 +21,107 @@
 #include "itrans-zaefferer.h"
 #include "itrans-stat.h"
 
+/* Return an empty feature list */
+ImageFeatureList *itrans_peaksearch_none(ImageRecord *imagerecord)
+{
+	return image_feature_list_new();
+}
+
 /* Return a feature list for the given image */
-ImageFeatureList *itrans_process_image(ImageRecord *image, PeakSearchMode psmode) {
-	
+ImageFeatureList *itrans_process_image(ImageRecord *image,
+						PeakSearchMode psmode)
+{
 	ImageFeatureList *list;
 
 	switch ( psmode ) {
-		case PEAKSEARCH_THRESHOLD :		{ list = itrans_peaksearch_threshold(image); break; }
-		case PEAKSEARCH_ADAPTIVE_THRESHOLD :	{ list = itrans_peaksearch_adaptive_threshold(image); break; }
-		case PEAKSEARCH_ZAEFFERER :		{ list = itrans_peaksearch_zaefferer(image); break; }
-		case PEAKSEARCH_STAT :			{ list = itrans_peaksearch_stat(image); break; }
+		case PEAKSEARCH_NONE : {
+			list = itrans_peaksearch_none(image);
+			break;
+		}
+		case PEAKSEARCH_THRESHOLD : {
+			list = itrans_peaksearch_threshold(image);
+			break;
+		}
+		case PEAKSEARCH_ADAPTIVE_THRESHOLD : {
+			list = itrans_peaksearch_adaptive_threshold(image);
+			break;
+		}
+		case PEAKSEARCH_ZAEFFERER : {
+			list = itrans_peaksearch_zaefferer(image);
+			break;
+		}
+		case PEAKSEARCH_STAT : {
+			list = itrans_peaksearch_stat(image);
+			break;
+		}
 		default: list = NULL;
 	}
-	
+
 	return list;
-	
 }
 
 /* Quantification radius */
 #define R 20
 
 /* Quantify each feature in the image's feature list */
-void itrans_quantify_features(ImageRecord *image) {
-
+void itrans_quantify_features(ImageRecord *image)
+{
 	int i;
-	
+
 	for ( i=0; i<image->features->n_features; i++ ) {
 
 		double theta;
 		double background, total;
 		int n;
 		int xi, yi;
-		
+
 		background = 0.0;
 		n = 0;
 		for ( theta=0; theta<2*M_PI; theta+=2*M_PI/10 ) {
-		
+
 			double x, y;
 			long int xd, yd;
-			
+
 			x = image->features->features[i].x + R*sin(theta);
 			y = image->features->features[i].y + R*cos(theta);
 			xd = rint(x);
 			yd = rint(y);
-			
-			if ( (xd>=0) && (yd>=0) && (xd<image->width) && (yd<image->height) ) {
-				background += image->image[xd + yd*image->width];
+
+			if ( (xd>=0) && (yd>=0)
+			  && (xd<image->width) && (yd<image->height) ) {
+				background += image->image[xd+yd*image->width];
 				n++;
 			}
 
 		}
 		background /= n;
-		
+
 		total = 0.0;
 		for ( xi=-20; xi<=20; xi++ ) {
 			for ( yi=-20; yi<=20; yi++ ) {
-			
+
 				double x, y;
 				long int xd, yd;
-				
+
 				if ( xi*xi + yi*yi > 20 ) continue;
-				
+
 				x = image->features->features[i].x + xi;
 				y = image->features->features[i].y + yi;
-				
+
 				xd = rint(x);
 				yd = rint(y);
-				
-				if ( (xd>=0) && (yd>=0) && (xd<image->width) && (yd<image->height) ) {
-					total += image->image[xd + yd*image->width] - background;
+
+				if ( (xd>=0) && (yd>=0)
+				  && (xd<image->width) && (yd<image->height) ) {
+					total +=
+						image->image[xd+yd*image->width]
+								- background;
 				}
-			
+
 			}
 		}
-		
+
 		image->features->features[i].intensity = total;
 
 	}
-
 }
-
diff --git a/src/main.c b/src/main.c
index 494dc46..a70afaf 100644
--- a/src/main.c
+++ b/src/main.c
@@ -3,7 +3,7 @@
  *
  * The Top Level Source File
  *
- * (c) 2007-2008 Thomas White <taw27@cam.ac.uk>
+ * (c) 2007-2009 Thomas White <taw27@cam.ac.uk>
  * (c) 2007      Gordon Ball <gfb21@cam.ac.uk>
  *
  *  dtr - Diffraction Tomography Reconstruction
@@ -36,108 +36,123 @@
 #include "dirax.h"
 #include "itrans.h"
 
-void main_do_reconstruction(ControlContext *ctx) {
-
+void main_do_reconstruction(ControlContext *ctx)
+{
 	if ( ctx->inputfiletype != INPUT_DRX ) {
-		
+
 		int val = 0;
-		
+
 		/* Initial centering */
-		prealign_sum_stack(ctx->images, ctx->have_centres, ctx->sum_stack);
+		prealign_sum_stack(ctx->images, ctx->have_centres,
+								ctx->sum_stack);
 		if ( ctx->finecentering ) {
 			prealign_fine_centering(ctx->images, ctx->sum_stack);
 		}
-		
+
 		if ( ctx->cache_filename == NULL ) {
-			
+
 			int i;
-		
+
 			/* Find all the features */
 			printf("MA: Analysing images..."); fflush(stdout);
 			for ( i=0; i<ctx->images->n_images; i++ ) {
-				ctx->images->images[i].features = itrans_process_image(&ctx->images->images[i],
-										       ctx->psmode);
-				itrans_quantify_features(&ctx->images->images[i]);
+				ctx->images->images[i].features =
+				   itrans_process_image(&ctx->images->images[i],
+				   ctx->psmode);
+				itrans_quantify_features(
+						       &ctx->images->images[i]);
 			}
 			printf("done.\n");
-		
+
 		} else {
-		
+
 			int i;
-			
-			printf("MA: Loading previous image analysis from '%s'\n", ctx->cache_filename);
-			if ( cache_load(ctx->images, ctx->cache_filename) ) val = 1;
-			
-			/* Quantify all the features (unnecessary if the file already contains intensities,
-			 *	but many of mine don't, and it doesn't hurt. */
+
+			printf("MA: Loading previous image analysis from %s\n",
+							ctx->cache_filename);
+			if ( cache_load(ctx->images, ctx->cache_filename) )
+									val = 1;
+
+			/* Quantify all the features (unnecessary if the file
+			 *  already contains intensities,
+			 *  but many of mine don't, and it doesn't hurt. */
 			printf("MA: Quantifying features..."); fflush(stdout);
 			for ( i=0; i<ctx->images->n_images; i++ ) {
-				itrans_quantify_features(&ctx->images->images[i]);
+				itrans_quantify_features(
+						       &ctx->images->images[i]);
 			}
 			printf("done.\n");
-		
+
 		}
-		
+
 		if ( ctx->finecentering ) {
 			prealign_feature_centering(ctx->images);
 		}
-		
+
 		if ( !val ) mapping_map_features(ctx);
-	
+
 	} /* else has already been created by dirax_load() */
-	
+
 	if ( ctx->reflectionlist ) {
 		ctx->dw = displaywindow_open(ctx);
 	} else {
 		fprintf(stderr, "Reconstruction failed.\n");
 		gtk_exit(0);
 	}
-	
 }
 
-static gint main_method_window_response(GtkWidget *method_window, gint response, ControlContext *ctx) {
-
+static gint main_method_window_response(GtkWidget *method_window, gint response,
+					ControlContext *ctx)
+{
 	if ( response == GTK_RESPONSE_OK ) {
-	
+
 		int val = 0;
-		
-		switch ( gtk_combo_box_get_active(GTK_COMBO_BOX(ctx->combo_peaksearch)) ) {
-			case 0 : ctx->psmode = PEAKSEARCH_THRESHOLD; break;
-			case 1 : ctx->psmode = PEAKSEARCH_ADAPTIVE_THRESHOLD; break;
-			case 2 : ctx->psmode = PEAKSEARCH_ZAEFFERER; break;
-			case 3 : ctx->psmode = PEAKSEARCH_STAT; break;
-			case 4 : ctx->psmode = PEAKSEARCH_CACHED; break;
-			default: ctx->psmode = PEAKSEARCH_NONE; break;	/* Happens when reading from a cache file */
+
+		switch ( gtk_combo_box_get_active(
+				GTK_COMBO_BOX(ctx->combo_peaksearch)) ) {
+			case 0 : ctx->psmode = PEAKSEARCH_NONE; break;
+			case 1 : ctx->psmode = PEAKSEARCH_THRESHOLD; break;
+			case 2 : ctx->psmode = PEAKSEARCH_ADAPTIVE_THRESHOLD;
+									break;
+			case 3 : ctx->psmode = PEAKSEARCH_ZAEFFERER; break;
+			case 4 : ctx->psmode = PEAKSEARCH_STAT; break;
+			case 5 : ctx->psmode = PEAKSEARCH_CACHED; break;
+			/* Happens when reading from a cache file */
+			default: ctx->psmode = PEAKSEARCH_NONE; break;
 		}
-		
-		if ( gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(ctx->checkbox_prealign)) ) {
+
+		if ( gtk_toggle_button_get_active(
+				GTK_TOGGLE_BUTTON(ctx->checkbox_prealign)) ) {
 			ctx->prealign = TRUE;
 		} else {
 			ctx->prealign = FALSE;
 		}
-		
-		if ( gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(ctx->checkbox_finecentering)) ) {
+
+		if ( gtk_toggle_button_get_active(
+			GTK_TOGGLE_BUTTON(ctx->checkbox_finecentering)) ) {
 			ctx->finecentering = TRUE;
 		} else {
 			ctx->finecentering = FALSE;
 		}
-		
-		if ( gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(ctx->checkbox_sumstack)) ) {
+
+		if ( gtk_toggle_button_get_active(
+				GTK_TOGGLE_BUTTON(ctx->checkbox_sumstack)) ) {
 			ctx->sum_stack = TRUE;
 		} else {
 			ctx->sum_stack = FALSE;
 		}
-		
+
 		if ( ctx->psmode == PEAKSEARCH_CACHED ) {
-			ctx->cache_filename = gtk_file_chooser_get_filename(GTK_FILE_CHOOSER(ctx->cache_file_selector));
+			ctx->cache_filename = gtk_file_chooser_get_filename(
+				GTK_FILE_CHOOSER(ctx->cache_file_selector));
 			if ( !ctx->cache_filename ) {
 				return 1;
 			}
 		}
-		
+
 		gtk_widget_destroy(method_window);
 		while ( gtk_events_pending() ) gtk_main_iteration();
-		
+
 		/* Load the input */
 		if ( ctx->inputfiletype == INPUT_QDRP ) {
 			val = qdrp_read(ctx);
@@ -147,139 +162,170 @@ static gint main_method_window_response(GtkWidget *method_window, gint response,
 			ctx->reflectionlist = dirax_load(ctx->filename);
 			if ( !ctx->reflectionlist ) val = 1;
 		}
-		
+
 		if ( val ) {
 			fprintf(stderr, "Reconstruction failed.\n");
 			gtk_exit(0);
 		}
-		
+
 		if ( ctx->prealign ) {
-			prealign_do_series(ctx);	/* this will eventually call main_do_reconstruction() */
+			/* this will eventually call main_do_reconstruction() */
+			prealign_do_series(ctx);
 		} else {
 			main_do_reconstruction(ctx);
 		}
-		
+
 	} else {
 		gtk_exit(0);
 	}
-	
-	return 0;
 
+	return 0;
 }
 
-static gint main_peaksearch_changed(GtkWidget *method_window, ControlContext *ctx) {
-
-	if ( gtk_combo_box_get_active(GTK_COMBO_BOX(ctx->combo_peaksearch)) == 4 ) {
-		gtk_widget_set_sensitive(GTK_WIDGET(ctx->cache_file_selector), TRUE);
+static gint main_peaksearch_changed(GtkWidget *method_window,
+					ControlContext *ctx)
+{
+	if ( gtk_combo_box_get_active(
+				GTK_COMBO_BOX(ctx->combo_peaksearch)) == 5 ) {
+		gtk_widget_set_sensitive(GTK_WIDGET(ctx->cache_file_selector),
+						TRUE);
 	} else {
-		gtk_widget_set_sensitive(GTK_WIDGET(ctx->cache_file_selector), FALSE);
+		gtk_widget_set_sensitive(GTK_WIDGET(ctx->cache_file_selector),
+						FALSE);
 	}
 
 	return 0;
-
 }
 
-void main_method_dialog_open(ControlContext *ctx) {
-
+void main_method_dialog_open(ControlContext *ctx)
+{
 	GtkWidget *method_window;
 	GtkWidget *vbox;
 	GtkWidget *hbox;
 	GtkWidget *table;
 	GtkWidget *peaksearch_label;
 	GtkWidget *cache_file_selector_label;
-	
-	method_window = gtk_dialog_new_with_buttons("Reconstruction Parameters", NULL,
-		GTK_DIALOG_DESTROY_WITH_PARENT,	GTK_STOCK_CANCEL, GTK_RESPONSE_CLOSE,
-						GTK_STOCK_OK, GTK_RESPONSE_OK, NULL);
+
+	method_window = gtk_dialog_new_with_buttons("Reconstruction Parameters",
+					NULL,
+					GTK_DIALOG_DESTROY_WITH_PARENT,
+					GTK_STOCK_CANCEL, GTK_RESPONSE_CLOSE,
+					GTK_STOCK_OK, GTK_RESPONSE_OK, NULL);
 	gtk_window_set_default_size(GTK_WINDOW(method_window), 400, -1);
-	
+
 	vbox = gtk_vbox_new(FALSE, 0);
 	hbox = gtk_hbox_new(TRUE, 0);
-	gtk_box_pack_start(GTK_BOX(GTK_DIALOG(method_window)->vbox), GTK_WIDGET(hbox), FALSE, FALSE, 7);
+	gtk_box_pack_start(GTK_BOX(GTK_DIALOG(method_window)->vbox),
+					GTK_WIDGET(hbox), FALSE, FALSE, 7);
 	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(vbox), FALSE, TRUE, 10);
-	
+
 	table = gtk_table_new(5, 2, FALSE);
 	gtk_table_set_row_spacings(GTK_TABLE(table), 5);
-	
+
 	peaksearch_label = gtk_label_new("Peak Search: ");
-	gtk_table_attach_defaults(GTK_TABLE(table), peaksearch_label, 1, 2, 1, 2);
+	gtk_table_attach_defaults(GTK_TABLE(table), peaksearch_label,
+								1, 2, 1, 2);
 	gtk_misc_set_alignment(GTK_MISC(peaksearch_label), 1, 0.5);
 	ctx->combo_peaksearch = gtk_combo_box_new_text();
-	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Simple Thresholding");
-	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Adaptive Thresholding");
-	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Zaefferer Gradient Search");
-	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Iterative Statistical Analysis");
-	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "Get From Cache File");
-	gtk_combo_box_set_active(GTK_COMBO_BOX(ctx->combo_peaksearch), 2);
-	gtk_table_attach_defaults(GTK_TABLE(table), ctx->combo_peaksearch, 2, 3, 1, 2);
-	g_signal_connect(G_OBJECT(ctx->combo_peaksearch), "changed", G_CALLBACK(main_peaksearch_changed), ctx);
-	
+	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch),
+					"None");
+	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch),
+					"Simple Thresholding");
+	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch),
+					"Adaptive Thresholding");
+	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch),
+					"Zaefferer Gradient Search");
+	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch),
+					"Iterative Statistical Analysis");
+	gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch),
+					"Get From Cache File");
+	gtk_combo_box_set_active(GTK_COMBO_BOX(ctx->combo_peaksearch), 3);
+	gtk_table_attach_defaults(GTK_TABLE(table), ctx->combo_peaksearch,
+								2, 3, 1, 2);
+	g_signal_connect(G_OBJECT(ctx->combo_peaksearch), "changed",
+				G_CALLBACK(main_peaksearch_changed), ctx);
+
 	cache_file_selector_label = gtk_label_new("Cache File to Load: ");
-	gtk_table_attach_defaults(GTK_TABLE(table), cache_file_selector_label, 1, 2, 2, 3);
+	gtk_table_attach_defaults(GTK_TABLE(table), cache_file_selector_label,
+								1, 2, 2, 3);
 	gtk_misc_set_alignment(GTK_MISC(cache_file_selector_label), 1, 0.5);
-	ctx->cache_file_selector = gtk_file_chooser_button_new("Select Cache File to Load",
-							       GTK_FILE_CHOOSER_ACTION_OPEN);
-	gtk_table_attach_defaults(GTK_TABLE(table), ctx->cache_file_selector, 2, 3, 2, 3);
+	ctx->cache_file_selector = gtk_file_chooser_button_new(
+						"Select Cache File to Load",
+						GTK_FILE_CHOOSER_ACTION_OPEN);
+	gtk_table_attach_defaults(GTK_TABLE(table), ctx->cache_file_selector,
+						2, 3, 2, 3);
 	gtk_widget_set_sensitive(GTK_WIDGET(ctx->cache_file_selector), FALSE);
-	
-	ctx->checkbox_prealign = gtk_check_button_new_with_label("Manually pre-align the image stack");
-	gtk_table_attach_defaults(GTK_TABLE(table), ctx->checkbox_prealign, 1, 3, 3, 4);
-	
-	ctx->checkbox_finecentering = gtk_check_button_new_with_label("Perform fine pattern centering");
-	gtk_table_attach_defaults(GTK_TABLE(table), ctx->checkbox_finecentering, 1, 3, 4, 5);
-	gtk_toggle_button_set_active(GTK_TOGGLE_BUTTON(ctx->checkbox_finecentering), TRUE);
-	
-	ctx->checkbox_sumstack = gtk_check_button_new_with_label("Show summed image stack");
-	gtk_table_attach_defaults(GTK_TABLE(table), ctx->checkbox_sumstack, 1, 3, 5, 6);
-	
+
+	ctx->checkbox_prealign = gtk_check_button_new_with_label(
+					"Manually pre-align the image stack");
+	gtk_table_attach_defaults(GTK_TABLE(table), ctx->checkbox_prealign,
+					1, 3, 3, 4);
+
+	ctx->checkbox_finecentering = gtk_check_button_new_with_label(
+					"Perform fine pattern centering");
+	gtk_table_attach_defaults(GTK_TABLE(table), ctx->checkbox_finecentering,
+					1, 3, 4, 5);
+	gtk_toggle_button_set_active(
+			GTK_TOGGLE_BUTTON(ctx->checkbox_finecentering), TRUE);
+
+	ctx->checkbox_sumstack = gtk_check_button_new_with_label(
+					"Show summed image stack");
+	gtk_table_attach_defaults(GTK_TABLE(table), ctx->checkbox_sumstack,
+					1, 3, 5, 6);
+
 	if ( ctx->inputfiletype == INPUT_DRX ) {
-		gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch), "3D coordinates from DirAx file");
-		gtk_widget_set_sensitive(GTK_WIDGET(ctx->combo_peaksearch), FALSE);
-		gtk_combo_box_set_active(GTK_COMBO_BOX(ctx->combo_peaksearch), 5);
+		gtk_combo_box_append_text(GTK_COMBO_BOX(ctx->combo_peaksearch),
+					"3D coordinates from DirAx file");
+		gtk_widget_set_sensitive(GTK_WIDGET(ctx->combo_peaksearch),
+						FALSE);
+		gtk_combo_box_set_active(GTK_COMBO_BOX(ctx->combo_peaksearch),
+									6);
 	}
-	
+
 	gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(table), TRUE, TRUE, 5);
-	
-	g_signal_connect(G_OBJECT(method_window), "response", G_CALLBACK(main_method_window_response), ctx);
-	
-	gtk_widget_show_all(method_window);
 
-}
+	g_signal_connect(G_OBJECT(method_window), "response",
+				G_CALLBACK(main_method_window_response), ctx);
 
+	gtk_widget_show_all(method_window);
+}
 
-int main(int argc, char *argv[]) {
 
+int main(int argc, char *argv[])
+{
 	ControlContext *ctx;
 	struct stat stat_buffer;
 	FILE *fh;
 
 	gtk_init(&argc, &argv);
-	
+
 	if ( gtk_gl_init_check(&argc, &argv) == FALSE ) {
 		fprintf(stderr, "Could not initialise gtkglext\n");
 		return 1;
 	}
-	
+
 	if ( gdk_gl_query_extension() == FALSE ) {
 		fprintf(stderr, "OpenGL not supported\n");
 		return 1;
 	}
-	
+
 	if ( argc != 2 ) {
-		fprintf(stderr, "Syntax: %s [<MRC file> | qdrp.rc | reflect.cache]\n", argv[0]);
+		fprintf(stderr,
+			"Syntax: %s [<MRC file> | qdrp.rc | reflect.cache]\n",
+			argv[0]);
 		return 1;
 	}
-	
+
 	ctx = control_ctx_new();
 	ctx->filename = strdup(argv[1]);
-	
+
 	fh = fopen(ctx->filename, "r");
 	if ( !fh ) {
 		printf("Couldn't open file '%s'\n", ctx->filename);
 		return 1;
 	}
 	fclose(fh);
-	
+
 	if ( qdrp_is_qdrprc(ctx->filename) ) {
 		printf("QDRP input file detected.\n");
 		ctx->inputfiletype = INPUT_QDRP;
@@ -293,20 +339,18 @@ int main(int argc, char *argv[]) {
 		fprintf(stderr, "Unrecognised input file type\n");
 		return 1;
 	}
-	
+
 	if ( stat(argv[1], &stat_buffer) == -1 ) {
 		fprintf(stderr, "File '%s' not found\n", argv[1]);
 		return 1;
 	}
-	
+
 	main_method_dialog_open(ctx);
-		
+
 	gtk_main();
-	
+
 	free(ctx->filename);
 	free(ctx);
-	
+
 	return 0;
-	
 }
-