Preparation for handing precessed data

git-svn-id: svn://cook.msm.cam.ac.uk:745/diff-tomo/dtr@65 bf6ca9ba-c028-0410-8290-897cf20841d1

1 files changed, 4 insertions, 50 deletions

diff --git a/src/mrc.c b/src/mrc.c
index b9b6efc..26a31de 100644
--- a/src/mrc.c
+++ b/src/mrc.c
@@ -15,7 +15,7 @@
 
 #include <stdlib.h>
 #include <stdio.h>
-#include <stdint.h>
+#include <inttypes.h>
 #include <string.h>
 
 #include "mrc.h"
@@ -33,11 +33,6 @@ int mrc_read(ControlContext *ctx) {
 	unsigned int i;
 	unsigned int extsize;
 	double pixel_size;
-	int16_t *image_total;
-	unsigned int x, y;
-	int max_x, max_y;
-	int16_t max_val;
-	ImageDisplay *sum_id;
 	
 	fh = fopen(ctx->filename, "rb");
 
@@ -68,50 +63,16 @@ int mrc_read(ControlContext *ctx) {
 	
 	pixel_size = ext[0].pixel_size;
 	printf("pixel_size = %f m^-1\n", pixel_size);
-	ctx->reflectionctx = reflection_init();
 	ctx->fmode = FORMULATION_PIXELSIZE;
 	ctx->first_image = 1;
 	ctx->width = mrc.nx;
 	ctx->height = mrc.ny;
 	
-	printf("Judging centre...");
-	image_total = malloc(mrc.ny * mrc.nx * sizeof(int16_t));
-	for ( y=0; y<mrc.ny; y++ ) {
-		for ( x=0; x<mrc.nx; x++ ) {
-			image_total[x + mrc.nx*y] = 0;
-		}
-	}
-	for ( i=0; i<mrc.nz; i++ ) {
-		int16_t *image = malloc(mrc.ny * mrc.nx * sizeof(int16_t));
-		fseek(fh, mrc.next + sizeof(MRCHeader) + mrc.nx*mrc.ny*2*i, SEEK_SET);
-		fread(image, mrc.nx*mrc.ny*2, 1, fh);
-		for ( y=0; y<mrc.ny; y++ ) {
-			for ( x=0; x<mrc.nx; x++ ) {
-				image_total[x + mrc.nx*y] += image[x + mrc.nx*y]/mrc.nz;
-			}
-		}
-	}
-	sum_id = imagedisplay_open(image_total, mrc.nx, mrc.ny, "Sum of All Images");
-	/* Locate the highest point */
-	max_val = 0;	max_x = 0;	max_y = 0;
-	for ( y=0; y<ctx->height; y++ ) {
-		for ( x=0; x<ctx->width; x++ ) {
-			if ( image_total[x + ctx->width*y] > max_val ) {
-				max_val = image_total[x + ctx->width*y];
-				max_x = x;  max_y = y;
-			}
-		}
-	}
-	imagedisplay_mark_point(sum_id, max_x, max_y);
-	ctx->x_centre = max_x;
-	ctx->y_centre = max_y;
-	printf("done\n");
-	
 	for ( i=0; i<mrc.nz; i++ ) {
 	
 		int16_t *image = malloc(mrc.ny * mrc.nx * sizeof(int16_t));
 		
-		printf("Image #%3i: tilt=%f omega=%f L=%f\t", i, ext[i].a_tilt, ext[i].tilt_axis, ext[i].magnification);
+		printf("Image #%3i: tilt=%f omega=%f L=%f\n", i, ext[i].a_tilt, ext[i].tilt_axis, ext[i].magnification);
 		ctx->camera_length = ext[i].magnification;
 		if ( ext[i].voltage == 0 ) {
 			ctx->lambda = lambda(200000);
@@ -123,15 +84,8 @@ int mrc_read(ControlContext *ctx) {
 		
 		fseek(fh, mrc.next + sizeof(MRCHeader) + mrc.nx*mrc.ny*2*i, SEEK_SET);
 		fread(image, mrc.nx*mrc.ny*2, 1, fh);
-
-		for ( y=0; y<mrc.ny; y++ ) {
-			for ( x=0; x<mrc.nx; x++ ) {
-				image_total[x + mrc.nx*y] += image[x + mrc.nx*y]/mrc.nz;
-			}
-		}
-
-		itrans_process_image(image, ctx, ext[i].a_tilt);
-		free(image);
+		
+		control_add_image_ps(ctx, image, mrc.nx, mrc.ny, ext[i].a_tilt, ctx->omega, ctx->pixel_size);
 		
 	}