Add skeleton prealignment procedure

git-svn-id: svn://cook.msm.cam.ac.uk:745/diff-tomo/dtr@79 bf6ca9ba-c028-0410-8290-897cf20841d1

1 files changed, 40 insertions, 35 deletions

diff --git a/src/mapping.c b/src/mapping.c
index a8d50b3..d9ca94d 100644
--- a/src/mapping.c
+++ b/src/mapping.c
@@ -31,52 +31,57 @@ ReflectionContext *mapping_create(ControlContext *ctx) {
 	/* Create reflection context */
 	rctx = reflection_init();
 	
-	/* Find centre of image stack
-	 * Determine maximum size of image to accommodate, and allocate memory */
-	twidth = 0;  theight = 0;
-	for ( i=0; i<ctx->n_images; i++ ) {
-		if ( ctx->images[i].width > twidth ) twidth = ctx->images[i].width;
-		if ( ctx->images[i].height > theight ) theight = ctx->images[i].height;
-	}
-	image_total = malloc(twidth * theight * sizeof(int16_t));
-	memset(image_total, 0, twidth * theight * sizeof(int16_t));
-	
-	/* Add the image stack together */
-	for ( i=0; i<ctx->n_images; i++ ) {
-		int xoffs, yoffs;
-		xoffs = (twidth - ctx->images[i].width)/2;
-		yoffs = (theight - ctx->images[i].height)/2;
+	if ( !ctx->prealign ) {
+		/* Find centre of image stack
+		 * Determine maximum size of image to accommodate, and allocate memory */
+		twidth = 0;  theight = 0;
+		for ( i=0; i<ctx->n_images; i++ ) {
+			if ( ctx->images[i].width > twidth ) twidth = ctx->images[i].width;
+			if ( ctx->images[i].height > theight ) theight = ctx->images[i].height;
+		}
+		image_total = malloc(twidth * theight * sizeof(int16_t));
+		memset(image_total, 0, twidth * theight * sizeof(int16_t));
+		
+		/* Add the image stack together */
+		for ( i=0; i<ctx->n_images; i++ ) {
+			int xoffs, yoffs;
+			xoffs = (twidth - ctx->images[i].width)/2;
+			yoffs = (theight - ctx->images[i].height)/2;
+			for ( y=0; y<theight; y++ ) {
+				for ( x=0; x<twidth; x++ ) {
+					image_total[x + twidth*y] += ctx->images[i].image[x + twidth*y]/ctx->n_images;
+				}
+			}
+		}
+		
+		/* Locate the highest point */
+		max_val = 0;	max_x = 0;	max_y = 0;
 		for ( y=0; y<theight; y++ ) {
 			for ( x=0; x<twidth; x++ ) {
-				image_total[x + twidth*y] += ctx->images[i].image[x + twidth*y]/ctx->n_images;
+				if ( image_total[x + twidth*y] > max_val ) {
+					max_val = image_total[x + twidth*y];
+					max_x = x;  max_y = y;
+				}
 			}
 		}
-	}
+		ctx->x_centre = max_x;
+		ctx->y_centre = max_y;
 	
-	/* Locate the highest point */
-	max_val = 0;	max_x = 0;	max_y = 0;
-	for ( y=0; y<theight; y++ ) {
-		for ( x=0; x<twidth; x++ ) {
-			if ( image_total[x + twidth*y] > max_val ) {
-				max_val = image_total[x + twidth*y];
-				max_x = x;  max_y = y;
-			}
-		}
+		/* Display */
+		sum_id = imagedisplay_open(image_total, twidth, theight, "Sum of All Images");
+		imagedisplay_mark_point(sum_id, ctx->x_centre, ctx->y_centre);
+		imagedisplay_add_tilt_axis(sum_id, ctx, ctx->omega);
+		
 	}
-	ctx->x_centre = max_x;
-	ctx->y_centre = max_y;
-	
-	/* Display */
-	sum_id = imagedisplay_open(image_total, twidth, theight, "Sum of All Images");
-	imagedisplay_mark_point(sum_id, ctx->x_centre, ctx->y_centre);
-	imagedisplay_add_tilt_axis(sum_id, ctx, ctx->omega);
 	
 	/* Pass all images through itrans
 	 *   (let itrans add the reflections to rctx for now) */
 	ctx->reflectionctx = rctx;
 	for ( i=0; i<ctx->n_images; i++ ) {
-		ctx->images[i].x_centre = ctx->x_centre;
-		ctx->images[i].y_centre = ctx->y_centre;
+		if ( !ctx->prealign ) {
+			ctx->images[i].x_centre = ctx->x_centre;
+			ctx->images[i].y_centre = ctx->y_centre;
+		}
 		itrans_process_image(ctx->images[i].image, ctx, ctx->images[i].tilt);
 	}