Give image centres in qdrp.rc if desired

git-svn-id: svn://cook.msm.cam.ac.uk:745/diff-tomo/dtr@90 bf6ca9ba-c028-0410-8290-897cf20841d1

6 files changed, 45 insertions, 22 deletions

diff --git a/src/control.c b/src/control.c
index c79ca17..ac3de0b 100644
--- a/src/control.c
+++ b/src/control.c
@@ -10,6 +10,7 @@
  */
 
 #include <inttypes.h>
+#include <stdlib.h>
 
 #include "control.h"
 
@@ -22,6 +23,8 @@ int control_add_image(ControlContext *ctx, uint16_t *image, int width, int heigh
 	ctx->images[ctx->n_images].height = height;
 	ctx->images[ctx->n_images].lambda = ctx->lambda;
 	ctx->images[ctx->n_images].fmode = ctx->fmode;
+	ctx->images[ctx->n_images].x_centre = ctx->x_centre;
+	ctx->images[ctx->n_images].y_centre = ctx->y_centre;
 	
 	if ( ctx->fmode == FORMULATION_PIXELSIZE ) {
 		ctx->images[ctx->n_images].pixel_size = ctx->pixel_size;
@@ -39,3 +42,17 @@ int control_add_image(ControlContext *ctx, uint16_t *image, int width, int heigh
 
 }
 
+ControlContext *control_ctx_new() {
+
+	ControlContext *ctx;
+	
+	ctx = malloc(sizeof(ControlContext));
+
+	ctx->x_centre = 0;
+	ctx->y_centre = 0;
+	ctx->have_centres = 0;
+	
+	return ctx;
+
+}
+
diff --git a/src/control.h b/src/control.h
index 5ab8efd..bae9f4b 100644
--- a/src/control.h
+++ b/src/control.h
@@ -81,6 +81,7 @@ typedef struct cctx_struct {
 	PeakSearchMode 		psmode;
 	unsigned int		prealign;
 	unsigned int		savecache;
+	unsigned int		have_centres;
 	
 	/* Input filename */
 	char 			*filename;
@@ -92,6 +93,8 @@ typedef struct cctx_struct {
 	double			resolution;
 	double			lambda;
 	double			pixel_size;
+	double			x_centre;
+	double			y_centre;
 	
 	/* QDRP Parser flags */
 	unsigned int		started;
@@ -116,6 +119,7 @@ typedef struct cctx_struct {
 } ControlContext;
 
 extern int control_add_image(ControlContext *ctx, uint16_t *image, int width, int height, double tilt);
+extern ControlContext *control_ctx_new(void);
 
 #endif	/* CONTROL_H */
 
diff --git a/src/ipr.c b/src/ipr.c
index 0043eec..6df83c3 100644
--- a/src/ipr.c
+++ b/src/ipr.c
@@ -205,9 +205,9 @@ static ReflectionContext *ipr_generate(ControlContext *ctx, Basis *basis) {
 	}
 	
 	ordered = reflection_init();
-	//basis->a.x = 5e9;  basis->a.y = 0.0;  basis->a.z = 0.0;
-	//basis->b.x = 0.0;  basis->b.y = 5e9;  basis->b.z = 0.0;
-	//basis->c.x = 0.0;  basis->c.y = 0.0;  basis->c.z = 3e9;
+	basis->a.x = 5e9;  basis->a.y = 0.0;  basis->a.z = 0.0;
+	basis->b.x = 0.0;  basis->b.y = 5e9;  basis->b.z = 0.0;
+	basis->c.x = 0.0;  basis->c.y = 0.0;  basis->c.z = 3e9;
 	for ( h=-30; h<=30; h++ ) {
 		for ( k=-30; k<=30; k++ ) {
 			for ( l=-30; l<=30; l++ ) {
@@ -263,6 +263,7 @@ int ipr_refine(ControlContext *ctx) {
 		
 		/* Select an image */
 		i = ipr_random_image(ctx);
+		i = 45; /* Temporary! */
 		cur = imagedisplay_open(ctx->images[i], "Current Image", IMAGEDISPLAY_SHOW_CENTRE | IMAGEDISPLAY_SHOW_TILT_AXIS);
 		
 		refl = reproject_get_reflections(ctx->images[i], &n, lat, ctx);
diff --git a/src/main.c b/src/main.c
index f957eb3..0750f14 100644
--- a/src/main.c
+++ b/src/main.c
@@ -32,6 +32,7 @@
 #include "cache.h"
 #include "mapping.h"
 #include "prealign.h"
+#include "control.h"
 
 void main_do_reconstruction(ControlContext *ctx) {
 
@@ -212,7 +213,7 @@ int main(int argc, char *argv[]) {
 	}
 	
 	filename = basename(argv[1]);
-	ctx = malloc(sizeof(ControlContext));
+	ctx = control_ctx_new();
 	type = INPUT_NONE;
 	
 	if ( qdrp_is_qdrprc(filename) ) {
@@ -229,22 +230,6 @@ int main(int argc, char *argv[]) {
 		return 1;
 	}
 	
-	#if 0
-	if ( strcmp(filename, "qdrp.rc") == 0 ) {
-		printf("QDRP input file detected.\n");
-		ctx->inputfiletype = INPUT_QDRP;
-	} else if ( strcmp(filename+(strlen(filename)-4), ".mrc") == 0 ) {
-		printf("MRC tomography file detected.\n");
-		ctx->inputfiletype = INPUT_MRC;
-	} else if ( strcmp(filename, "reflect.cache") == 0 ) {
-		printf("reflect.cache detected.\n");
-		ctx->inputfiletype = INPUT_CACHE;
-	} else {
-		fprintf(stderr, "Unrecognised input file type\n");
-		return 1;
-	}
-	#endif
-	
 	ctx->filename = strdup(argv[1]);
 	ctx->n_images = 0;
 	
diff --git a/src/prealign.c b/src/prealign.c
index a89b8de..b72943c 100644
--- a/src/prealign.c
+++ b/src/prealign.c
@@ -61,6 +61,7 @@ void prealign_do_series(ControlContext *ctx) {
 
 	PreAlignBlock *pb;
 
+	ctx->have_centres = 1;	/* Inhibit "centre-finding by stacking" */
 	pb = malloc(sizeof(PreAlignBlock));
 	pb->n = 0;
 	pb->ctx = ctx;
@@ -94,7 +95,7 @@ void prealign_sum_stack(ControlContext *ctx) {
 	memset(image_total, 0, twidth * theight * sizeof(uint16_t));
 	
 	/* Add the image stack together */
-	if ( !ctx->prealign ) {
+	if ( !ctx->have_centres ) {
 		
 		int max_x, max_y;
 		uint16_t max_val;
@@ -135,7 +136,7 @@ void prealign_sum_stack(ControlContext *ctx) {
 		total_record.y_centre = max_y;
 	
 	} else {
-
+		
 		for ( i=0; i<ctx->n_images; i++ ) {
 		
 			int xoffs, yoffs;
diff --git a/src/qdrp.c b/src/qdrp.c
index c46c1ae..86384bd 100644
--- a/src/qdrp.c
+++ b/src/qdrp.c
@@ -182,6 +182,21 @@ static int qdrp_parseline(ControlContext *ctx, const char *line) {
 				
 		}
 		
+		if ( strncasecmp(line+pos, "centre", 6) == 0 ) {
+			
+			float xc, yc;
+			
+			if ( sscanf(line+pos, "centre %f %f", &xc, &yc) != 2 ) {
+				fprintf(stderr, "Couldn't parse 'centre' line\n");
+				return 1;
+			}
+			ctx->x_centre = xc;
+			ctx->y_centre = yc;
+			ctx->have_centres = 1;
+			printf("QD: centre %.2f, %.2f px\n", ctx->x_centre, ctx->y_centre);
+
+		}
+		
 	}
 
 	return 0;